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GIT Logs

This is a list of recent commits to git.bioconductor.org, the master(development) branch of the Bioconductor GIT repository.

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Package: igvR
Commit: e9384f0a3ed55d4c2a542ca0487aaf1ce6ce15ad
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2019-04-18 11:59:44 -0700
Commit message:

 removed obsolete bam file from example
 
Package: ENCODExplorer
Commit: ad5c7fdfc51c30a20acc16e7e1922463d6ceb885
Author: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Date: 2019-04-18 14:14:19 -0400
Commit message:

 Removed encode_df: replaced with ENCODExplorerData in AnnotationHub

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
 
Package: ENCODExplorer
Commit: f33aae81c1642f852dff9442483aa36159b951b2
Author: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Date: 2019-04-04 12:00:16 -0400
Commit message:

 Version bump

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
 
Package: ENCODExplorer
Commit: 05ba071dca48b8c281ae60ac9594733c8a2881d1
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-04-02 00:36:32 -0400
Commit message:

 R CMD CHECK fixes.
 
Package: ENCODExplorer
Commit: 815744b757f1f58ca41a2fd05279d09b7a13fb21
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-04-02 00:18:47 -0400
Commit message:

 Add unit test for downloadEncode.
 
Package: ENCODExplorer
Commit: 44a8d9a86e01a2e84d58c0b3adc02ab5879a2d45
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-04-01 14:27:48 -0400
Commit message:

 md5sum column needs to eb part of the main encode_df to validate downloaded files.
 
Package: ENCODExplorer
Commit: 21287d3a76d50c420c37084958088d34409cdfe7
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-03-27 23:10:32 -0400
Commit message:

 Fix warnings and errors for CHECK and BiocCheck.

Remove conflicting namespace imports
Add runnable examples
Change T/F to TRUE/FALSE
Change class== into is() calls.
 
Package: ENCODExplorer
Commit: 93e318f959ae87ad47ebdb615884ca2421700a92
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-03-26 14:14:17 -0400
Commit message:

 Add documentation for encode_df_ext objects.
 
Package: ENCODExplorer
Commit: 89d6ee3d3b7bf311bc02c90c21e4e5fc6eb7fa68
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-03-26 13:14:23 -0400
Commit message:

 Fix documentation.
 
Package: ENCODExplorer
Commit: 14d51eb353525115d24a79559d62c83d88247ea6
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-03-26 12:50:58 -0400
Commit message:

 Rename function to get full metadata data-frame.
 
Package: ENCODExplorer
Commit: 985db92b973de58534aecfa88735454f8e5969c3
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-03-26 12:27:26 -0400
Commit message:

 USe ENCODExplorer::encode_df directly as default df parameter.
 
Package: ENCODExplorer
Commit: 5e285fad27b18e9062740be6a2dafdbd7d0294cd
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-03-25 13:12:30 -0400
Commit message:

 Add cache to load_ENCODEdf_matrix_lite. Add it to exports.
 
Package: ENCODExplorer
Commit: b6e682aeeb8eccaf053af40f9f9f2a323a47558b
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-17 13:48:38 -0400
Commit message:

 Remove duplicate check.
 
Package: ENCODExplorer
Commit: 1117e04b857a7b4e2c2ebcff4a8ce8c8c7860a97
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-17 11:31:21 -0400
Commit message:

 Fix unit test.

Target file has been revoked. It is still in encode_df, but since file_status' default value is "released", it was not found anymore.
 
Package: ENCODExplorer
Commit: f4a7022ba671216edb9993dfec426ef537e89d0c
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-17 10:13:15 -0400
Commit message:

 Split encode_df into four objects to stay under 50MB limit imposed by Bioconductor.

Splitting in 4 makes the main object much smaller, improving load times for the default use case.
Using four files also makes sure each one has room to grow without busting the limit.
 
Package: ENCODExplorer
Commit: 5481e90bf15ca0d5b0c59b6b61b39370b64ea260
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-17 10:10:43 -0400
Commit message:

 Fix unit tests. Resolve issue when calling from a package.

Remove usage of data/encode_df within functions, using ENCODExplorer::encode_df directly. This prevents these functions from crashing when called from a package.
Unit test messages expectations did not account for localization. They now do.
 
Package: ENCODExplorer
Commit: 816a4ecf31488b3e94fe98eb0ee6403f6f465f15
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-16 00:05:21 -0400
Commit message:

 Fixes #46.
 
Package: ENCODExplorer
Commit: bd3f8603268331d2546e64d26bd495864949a0eb
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-15 22:34:33 -0400
Commit message:

 Missing argument in export_ENCODEdb_matrix
 
Package: ENCODExplorer
Commit: 8adb24b501dc94a0b5181ecb489ae87e3a205bd5
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-15 11:20:06 -0400
Commit message:

 Merge branch 'master' into df_lite
 
Package: ENCODExplorer
Commit: 0baf6439405d873fdb87cac4d6bf44ff9d2ef8fb
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-15 11:12:28 -0400
Commit message:

 Get biosample info from biosample_type columns. Fixes #45.
 
Package: ENCODExplorer
Commit: 91e43a2b14430fb290c86fe0d1aeedb61407a1f9
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2019-03-14 10:57:38 -0400
Commit message:

 Stop ENCODExplorer from crashing on empty tables. Related to Issue #44, but more testing is required before the issue can be closed.
 
Package: ENCODExplorer
Commit: 7cb8f7605b13d9d14ff7b8678e580f5105cb7241
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2019-03-01 11:40:53 -0500
Commit message:

 Split ENCODE df in two.
 
Package: ENCODExplorer
Commit: 8102c3abe560ccc3afbee30c676d9d32b58d0f9d
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-23 16:32:43 -0400
Commit message:

 Improve encode_df biosample mapping and add columns.

Associate biosample_ids to files using the dataset's replicate list when the file's replicate id is NA.
Add treatment temperature and note.
Add biosample and dataset summaries.
Improve organism mapping by inferring it from biosample rather than from target.
 
Package: ENCODExplorer
Commit: ec26a5bfd421ceb375b5b405667f2b2143635f74
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-05-17 12:11:18 -0400
Commit message:

 Update encode_df.
 
Package: ENCODExplorer
Commit: e9e27548b4c9c0fb7cae28977c5155edede47173
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-05-17 12:10:42 -0400
Commit message:

 Bugfix in treatment import.
 
Package: ENCODExplorer
Commit: 63e311a41c60f3a46f6f40608bb7d99579678161
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-05-17 11:35:45 -0400
Commit message:

 Remove outdated DBmodel vignette, and add references to ENCODE schema in the data update documentation.
 
Package: ENCODExplorer
Commit: 474c526d6a4247cff667c410a1e9d1171f896e1b
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-05-17 11:08:09 -0400
Commit message:

 Track biosample_id and drop artefactual biosample/library ids in treatment column.
 
Package: ENCODExplorer
Commit: 2fbc9036e29468510d7b1884ffe479ef18122969
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-05-17 10:36:30 -0400
Commit message:

 More comments, small bug fix.
 
Package: ENCODExplorer
Commit: 33eaaed1f4b3c26765d3a741c456ed48073093f6
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-17 02:21:51 -0400
Commit message:

 Improve readability.
 
Package: ENCODExplorer
Commit: 7263a8d44e6900e80764aa953c8a37a657b0314f
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-17 01:57:51 -0400
Commit message:

 Update documentation.
 
Package: ENCODExplorer
Commit: aecab1cdd4872582ad5bca479745ef19ac2b6da0
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-17 01:33:55 -0400
Commit message:

 Refactor prefix-removing functions.
 
Package: ENCODExplorer
Commit: 5445bb748536a5fb36fc27e465d8bec530634ac6
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-17 01:20:46 -0400
Commit message:

 Remove unnecessary "convert to character" pull_column functions.
 
Package: ENCODExplorer
Commit: d0f0117f402987e2c3b0b655a4d44142088773c8
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-17 01:14:01 -0400
Commit message:

 Remove unnecessary indirection.
 
Package: ENCODExplorer
Commit: 96a8f5c015b833ba1d44a93cae57a1f17bbda56a
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-17 01:04:37 -0400
Commit message:

 Add new treatment columns.
 
Package: ENCODExplorer
Commit: 795d3c2791ba3ad5d1cad00fb164cf8296e77e44
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-16 16:46:41 -0400
Commit message:

 Refactor prepare_data.R, but return the exact same data.table.
 
Package: ENCODExplorer
Commit: 23586dd8da4a54fce197a830fb9db9ea15cfdb4f
Author: ericfournier2 <ericfournier2@yahoo.ca>
Date: 2018-05-16 10:48:56 -0400
Commit message:

 Removed paragraph about updating encode_df, since it is not possible on most installs.

encode_df.rda is not directly accessible, and is wrapped up inside R's own peculiar way of storing data objects. Thu it is not possible to update it.
 
Package: ENCODExplorer
Commit: 94f1f8085fafc6c886063eedaf3b6968a5a531ea
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-05-15 16:23:28 -0400
Commit message:

 Remove tables.RDA since it is out-of-date.
 
Package: ENCODExplorer
Commit: 7bca5a30271a97f8cbca8b27520ad15796babac4
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-05-15 13:45:48 -0400
Commit message:

 Improve data update vignettes
Change default parameters for prepare_ENCODEdb
 
Package: ENCODExplorer
Commit: dc3ba6939df10f932977c6ede9d069aa71d75dc1
Author: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Date: 2018-03-28 16:16:58 -0400
Commit message:

 Merge pull request #41 from ericfournier2/master

Restore functionality lost in last Bioconductor merge 
Package: ENCODExplorer
Commit: 1e8ab49bc9c65ba7b342f83319c40cb713dd4b9c
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-03-28 11:46:41 -0400
Commit message:

 Fix input validation that didn't work as expected.
 
Package: ENCODExplorer
Commit: 521eb8dec7147d45a7f6d25e5f7a3b21afcdf888
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-03-28 10:44:21 -0400
Commit message:

 Fix unit test where the ENCODE metadata changed.
 
Package: ENCODExplorer
Commit: 7a37a87757fd468b930d3ff3407ebfa1700821aa
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-03-27 15:16:25 -0400
Commit message:

 Restore queryEncodeGeneric function.
Restore "fuzzy" argument to queryEncode.Rd
Restore unit tests for new functionality.
Restore improved vignette.
 
Package: ENCODExplorer
Commit: 889cd39dfe73f230b3988d23b9f2108366391d5c
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-03-27 14:30:30 -0400
Commit message:

 Restore bug fixes.
Restore queryEncodeGeneric to list of exported functions.
Restore Eric Fournier to author list.
 
Package: ENCODExplorer
Commit: 00052e4a1a3d0341e75d86c8aa869646a744daee
Author: Eric Fournier <eric.fournier@fsaa.ulaval.ca>
Date: 2018-03-27 12:00:26 -0400
Commit message:

 Restore queryEncodeGeneric documentation.
 
Package: ENCODExplorer
Commit: 9ac4dbe29f7e1bc1a7202f19bc6b529717aabcc2
Author: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Date: 2018-01-15 15:27:52 -0500
Commit message:

 Updated encode_df

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
 
Package: DelayedDataFrame
Commit: 62af5d739059e4b460f6cc9959d4fe4c1f1d9bb8
Author: qian <qliu7@buffalo.edu>
Date: 2019-04-18 13:07:13 -0400
Commit message:

 added extractCOLS to be consistent with updates in S4Vectors
 
Package: DelayedDataFrame
Commit: 24f4966a027f4bb25dcb16f0601782228f7b34d7
Author: qian <qliu7@buffalo.edu>
Date: 2019-04-18 13:06:07 -0400
Commit message:

 some minor updates for e.g., documentation
 
Package: crossmeta
Commit: b6c53894621f6414d5991a896a87a02bff78f4d3
Author: alexvpickering <alexvpickering@gmail.com>
Date: 2019-04-18 10:23:51 -0700
Commit message:

 version bump
 
Package: crossmeta
Commit: 04b09981d2edfae89b7c590176576a68f247da7f
Author: alexvpickering <alexvpickering@gmail.com>
Date: 2019-04-18 10:23:29 -0700
Commit message:

 fix fdrtool call
 
Package: bcSeq
Commit: 6a4b49d6faf09616281090c5c3335eb63e7689e5
Author: Your Name <jiaxing.lin@duke.edu>
Date: 2019-04-18 13:17:24 -0400
Commit message:

 edits on test_bcSeq.R to speed up installation
 
Package: bcSeq
Commit: 1144bfad83238b64aab965022b3523add65ec4f2
Author: Your Name <jiaxing.lin@duke.edu>
Date: 2019-04-18 13:15:52 -0400
Commit message:

 fix bugs
 
Package: Biobase
Commit: c4e463a85ea7245c9a6865a16a472fb13c5a7a62
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-04-18 10:00:51 -0700
Commit message:

 Add README.md file
 
Package: biocViews
Commit: 6add3abb5b7a7820ddae658a6b20248d04d112a8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-04-18 09:53:51 -0700
Commit message:

 Add README.md file
 
Package: biocViews
Commit: eafcdeecea7ff57e4f51cb762d4420ceafa2fff1
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-04-18 09:48:42 -0700
Commit message:

 Depends on R >= 3.6.0
 
Package: biocViews
Commit: 02cf45245b1ecd8da6205ca7b90faaf2edee411b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-04-18 09:47:09 -0700
Commit message:

 No longer use deprecated 'compressed' arg when calling utils::untar()
 
Package: adductomicsR
Commit: 6cedbb753bad9624d98d6d82b8c02d1c986423e5
Author: josielhayes <jlhayes1982@gmail.com>
Date: 2019-04-18 07:32:55 -0700
Commit message:

 change access to ExperimentHub
 
Package: BEclear
Commit: 51f04ab61e98862faf2af4a3c4022d2ac26d418b
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-04-18 16:20:36 +0200
Commit message:

 closes #4
 
Package: TCGAbiolinks
Commit: c29f188dc8e533ff268cdd14859129b96b384e3b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-18 11:09:39 -0300
Commit message:

 fix merge
 
Package: TCGAbiolinks
Commit: 4182098fe99a89b2a06a74a1399878475ad5c637
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-18 11:02:58 -0300
Commit message:

 Removing warning
 
Package: TCGAbiolinks
Commit: f97abd5275158e50f42f8c4635d9b4fe7e8a88e1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-08 13:00:05 -0300
Commit message:

 typo fix


Former-commit-id: 1ec48012aefde9dc8a918b27e0bb9244cf1d3c0f 
Package: TCGAbiolinks
Commit: b93a5db7c8f44cb09021c5fa7260bdfab92aaaeb
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-08 12:37:36 -0300
Commit message:

 improving ensembl access


Former-commit-id: 0780d3941a2e3861c04010c3f317ae3f79899835 
Package: TCGAbiolinks
Commit: 24048e64a6f3cc435e186daed82d32b5c60f7f9e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:09:58 -0300
Commit message:

 version bump


Former-commit-id: b99acace01817512d73fea983739a21f8eab0fba 
Package: TCGAbiolinks
Commit: 695759e0cc1eb6d9392239f87df58c91d7e5a603
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:08:18 -0300
Commit message:

 Preparing multiple GISTIC files #304


Former-commit-id: 9cc27d9d86e9241838b1ef22e57ada516fa6306b 
Package: TCGAbiolinks
Commit: 5c6985a317c50ec87a9c1831a28b32f05ea543bc
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 10:56:15 -0300
Commit message:

 Changing from patinet ID to  sample ID #304


Former-commit-id: 965e9b171511d5402e1d0efbc192b82b6dbfd0db 
Package: TCGAbiolinks
Commit: 6a9c373232f57aedd29457982b6eb3052146bd26
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:16:50 -0300
Commit message:

 Improving error handling


Former-commit-id: 1745f7266f25f174264bfd93ac424d1f9bca6962 
Package: TCGAbiolinks
Commit: d9c7dc60eee670357cf1f363608f04b3dc593b32
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:12:37 -0300
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 5da7070caa40170e904d0e3cc6f2e377ea21a36b 
Package: TCGAbiolinks
Commit: dc3d6c6f6fbfa0f9353cc1ac72175c7a625182a5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:12:16 -0300
Commit message:

 Improving output


Former-commit-id: 1f854c2f5ff4d82c1f52419b8c90b5f2733d2388 
Package: TCGAbiolinks
Commit: f643293e18dbf19416e78b0a919d9edc99a5bf4f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 13:25:44 -0300
Commit message:

 Merge pull request #300 from reese3928/master

typos

Former-commit-id: 7aba66796f0bca48f13ee23948ecd67ed0410510 
Package: TCGAbiolinks
Commit: 588909befecc13ac9fb34b4a5d29b7c5e79c6ed5
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2019-03-15 12:39:12 -0400
Commit message:

 typos


Former-commit-id: 56b2ec946fd18455793b50e3795821201ebd43c8 
Package: TCGAbiolinks
Commit: 0ff1e4f7e2290a1083a29b8728ed73b6d66617d8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-05 13:48:37 -0300
Commit message:

 Fix second query if first is not able to access GDC


Former-commit-id: 6dbf5bdbb814457abc08b02248a92be36426446e 
Package: TCGAbiolinks
Commit: 8183a3e12454177351253b41a87eb6415a53f0a2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-04 11:56:49 -0300
Commit message:

 Bug fix, if legacy is used data type is not provided by user


Former-commit-id: 6d2b78e257f1a107b80d703a70630797ac72cc7a 
Package: TCGAbiolinks
Commit: 80b5f90ae6cec4bb3790022a993468a549b4352e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-28 10:36:29 -0600
Commit message:

 Add miRNA example


Former-commit-id: 4d0100aad323e21088d73c12aafa7733ebe111a8 
Package: TCGAbiolinks
Commit: 7cc4cf642d23c736b22c0efab054ef225f1fb509
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:45:08 -0600
Commit message:

 Removing masking from matrix DNA methylation to SE


Former-commit-id: 0cd9d4321c927b6386333ade82b2ce3f7ab76cbd 
Package: TCGAbiolinks
Commit: 32503253a0d663b7f9333d33eb504c8a9a8f96a8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:18:57 -0600
Commit message:

 Adding IDAT prepare to vignette


Former-commit-id: b98e37b1729971e11349a9e6fb907f34e60049a2 
Package: TCGAbiolinks
Commit: dc66a68de8d093f28ba6af416b85cf728bd29987
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:08:19 -0600
Commit message:

 Removing note


Former-commit-id: b5df31c3b5df9b1fef795528acc10082ba27050a 
Package: TCGAbiolinks
Commit: fc14d3c4e6184a23de542f6523cc3a582383264d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:36:45 -0600
Commit message:

 fixing appveyor


Former-commit-id: 23f215204caa187b1bcb521efe14cb4e872eed5f 
Package: TCGAbiolinks
Commit: 02df3e15805c715fe8531a37b78c1ca02c8a23eb
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:34:16 -0600
Commit message:

 bug fix


Former-commit-id: 1b1dd10ed90bba567b05ddb6266a2f251e395dec 
Package: TCGAbiolinks
Commit: 3fc753e1e9c03912e836864fec90cc100607ea6d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:16:29 -0600
Commit message:

 Fix Description


Former-commit-id: 5f09911d2dbe4113735bf2decb688a0927cf6f9e 
Package: TCGAbiolinks
Commit: d6ad88008458df53310e00793e966ca2f5868005
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:13:50 -0600
Commit message:

 updating aapveyor and namespace


Former-commit-id: f82a2f1dd260507e4bc7127598dc696775da012b 
Package: TCGAbiolinks
Commit: c2cb0dd38bcc17630de2a26511aaa2221929c111
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:36 -0600
Commit message:

 Version bump


Former-commit-id: 0fa8abf6b45a27e9906f4ad56cf2a82bee42a9cb 
Package: TCGAbiolinks
Commit: 8c8d5e37a2466d259a9e1cad6ac0e542a3f542fe
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:08 -0600
Commit message:

 Update internal function for idat function


Former-commit-id: 87e1384b529f652c647846882b60e90a36554e89 
Package: TCGAbiolinks
Commit: 642caa9ad6953edeab8fe59a3e2ca48974f6eef0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:06:35 -0600
Commit message:

 Adding IDAT pprepare using sesame


Former-commit-id: 76e1110adb46f67f58e287c28f6caf924f03cbb5 
Package: TCGAbiolinks
Commit: 038cbf8a723dda70a0a51b82588edcbcd4eb911e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 12:15:40 -0600
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 177572292a8d0425b7d710c83e8d6f4aedb71633 
Package: TCGAbiolinks
Commit: 773bfe3f7b3b387e6ecb77c315846b0d7465351c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 12:15:13 -0600
Commit message:

 Improving hg19 access


Former-commit-id: 8d684ae93c7377a966b7f328e2346931ca331041 
Package: TCGAbiolinks
Commit: 8c4fb98f4d782e1163ab65e8fa3eace9ca8e4423
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-02-04 12:53:00 -0500
Commit message:

 fix in TCGAanalyze_Preprocessing

fix in TCGAanalyze_Preprocessing


Former-commit-id: 85c3f3e63dcc4ac542958f84d61074443dca0f99 
Package: TCGAbiolinks
Commit: a1833495e55c04766458fc349ca3a4f03a733e7d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 11:02:27 -0600
Commit message:

 Change host for hg19 fix #292


Former-commit-id: 834122d9ca1e1e38b014529da5a0f07fa06644ee 
Package: TCGAbiolinks
Commit: 1edcade4a53ad8297dd9c46a83fe097bd254b11d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-24 17:16:03 -0600
Commit message:

 Bug fix in gistic preparing


Former-commit-id: 8c5449958ad2e1cd300daa033d57d1267e7c9d6d 
Package: TCGAbiolinks
Commit: adee31b050f5014279c8f58ff2d2329f78a23677
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-21 11:50:10 -0600
Commit message:

 Reduce query size by adding experimental strategy as a URL filter


Former-commit-id: ddd63c9b2a68eb2eb308a6c7528cb6bfa0119a07 
Package: TCGAbiolinks
Commit: e9895f6c07443718461c26cf47e69017e71742a7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 21:09:22 -0600
Commit message:

 Fix description


Former-commit-id: 57e7b0d0383ec4453878c578e4f621ae2f205abe 
Package: TCGAbiolinks
Commit: 6e6a8aaa05d5e028af3f462b48fdecccc77c2476
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 20:56:48 -0600
Commit message:

 improving man


Former-commit-id: 85d4e78b58ea56a8b94a24142fce0bf518f6a3ba 
Package: TCGAbiolinks
Commit: 6ab7a5abfd7f4283f1262f6cbb3e695a324b1f58
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 19:16:16 -0600
Commit message:

 remmoving warning


Former-commit-id: e7e085c07afec2bace12dbe290bef993e179348f 
Package: TCGAbiolinks
Commit: 7776da13471fef414757e267c3b6374108bddf9b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 18:49:15 -0600
Commit message:

 Exporting functions used in ELMER


Former-commit-id: ab28a07fb99bde5a25e952ab05ed0d032f7164ba 
Package: TCGAbiolinks
Commit: 741b733c7507f4e708052b317b358ff9d4e4f0a6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 12:21:29 -0600
Commit message:

 Add gistic example


Former-commit-id: 2806f566c9fd0c3ee5c1815babdfdf5b72f03bf1 
Package: TCGAbiolinks
Commit: 7a3a3641072e46a35cb915a45d7ce47b1ac00ed2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-07 10:37:18 -0600
Commit message:

 fix data category for the raw sequencing data in the harmonized database


Former-commit-id: 085fd97a99061a81c6971a9cdcd06fba435b5d2c 
Package: TCGAbiolinks
Commit: d906a4b57bc971848f08d346ca55aaf437a39e5b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-30 09:40:46 -0200
Commit message:

 Changes from complexheatmap 2.0


Former-commit-id: 0d79079c55cbd2bcec23cfcd54d662e8c236c2fd 
Package: TCGAbiolinks
Commit: 548ebd3f0dd2cce7df765c029f32c4bfe8460e04
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-27 09:44:38 -0200
Commit message:

 Adding option to filter by access


Former-commit-id: 4336e3848a5123891592000c92d565def817297b 
Package: TCGAbiolinks
Commit: c6516e3ecd344d391aadd4e05e38bbefb5f65f76
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-27 09:34:58 -0200
Commit message:

 Update function to retrive summary of files.


Former-commit-id: 2fcb1528263cdab1d9a866d4df29c8fbd30947d8 
Package: TCGAbiolinks
Commit: 935eec2e695c6e60b9fc6d656702106c56e2b197
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-27 09:28:57 -0200
Commit message:

 Fix dependencies


Former-commit-id: 2e65f0f59ed5e0aff4c2e0a7a5d01e40f061c4ef 
Package: TCGAbiolinks
Commit: a2c891102ee174b383c23a13c607749f21a65ec0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-27 08:59:41 -0200
Commit message:

 Add doc for new function


Former-commit-id: ed6c9c5092b4ea9ff511e5ce72e998e7c6f6fcb8 
Package: TCGAbiolinks
Commit: f448e7f1ecca8764aa466e0928f075bf57951db7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-27 08:58:03 -0200
Commit message:

 Fix documentation


Former-commit-id: 31281579cfbb62521dbe30e90a58e497d48b6512 
Package: TCGAbiolinks
Commit: 1f5f4b55c45dff1a671c5879c2fa8c9f23e1b275
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-26 22:31:33 -0200
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 05c95a13367f9bf169a43e8a032f897b0d542b92 
Package: TCGAbiolinks
Commit: 8bc8b9be95eb2ad0399a8c35e1325933c557e6ba
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-26 22:31:19 -0200
Commit message:

 Fix namespace


Former-commit-id: 4e533a19330c453e4e1dfe9cf63e1a4861e835c8 
Package: TCGAbiolinks
Commit: cccdde6cd17f89c969cd87664474605d25a1f1a4
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-26 16:06:50 -0200
Commit message:

 version bump


Former-commit-id: 6c562761251f720486c9ae8e12cc049379304369 
Package: TCGAbiolinks
Commit: 71f5fcd9b47dc3f51b873df6695a6b8626ad618a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-26 16:03:05 -0200
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 2039b10eac4da264f188cfa2973171a22e0897bd 
Package: TCGAbiolinks
Commit: 8c5d04df3eeb1364795d44ec189532a82739d0b2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-26 16:02:38 -0200
Commit message:

 Update vignette for query


Former-commit-id: ba84269cfce25dc81d6ea97efa25302b8afa0f03 
Package: TCGAbiolinks
Commit: ae0886912a6f8f66c9bf6dfbfe289014af6ec53b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-25 20:33:42 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: a2fc133b0678bae2ce6fdcbcf746ea9e6c859390 
Package: TCGAbiolinks
Commit: 2f30b1dfa001cb124badf578f2afcde530278314
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-25 20:33:18 -0200
Commit message:

 maftools is broken. we will not use its function until it is fixed


Former-commit-id: 69ddb328217b5045db7e438731994a3502faa102 
Package: TCGAbiolinks
Commit: 05ad1284fc92297f28efba6aaf7d434be2c953e8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-21 16:25:06 -0200
Commit message:

 Consider that data type might not be specified. In case it is open it will always be the masked one. #198


Former-commit-id: 4f2c935a61999404230ab2b37510e12a10db3862 
Package: TCGAbiolinks
Commit: bba939591637cd55d42dcb8b1ee791590e922cb4
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-21 12:30:35 -0200
Commit message:

 Include atac-seq function to download data


Former-commit-id: 96f5e1e7b2a3556a5b98b0e697bda89cd8f59640 
Package: TCGAbiolinks
Commit: d32ba3b86014d11a57713bf69b7a51c8aa2f7a2f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-20 20:36:17 -0200
Commit message:

 Start ATAC_seq function


Former-commit-id: 405c0dbedd1ecbf5be2742c79cf828c2ad00eaf5 
Package: TCGAbiolinks
Commit: c2c2e0f0cafeb5bbce174a56bc3f147e32a08795
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-12 09:25:13 -0200
Commit message:

 Adding WGBS example


Former-commit-id: 79626930df46b57d8dd74c8e3da6e1bf0a4a856a 
Package: TCGAbiolinks
Commit: 9944d4c5b48e5b78d391696ccedf5b0d6b4158dd
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-09 23:38:38 -0200
Commit message:

 Removing print


Former-commit-id: 7ecde6b7474cf9eb81fa062d200edfa030a76b08 
Package: TCGAbiolinks
Commit: 14822d78d7e2a07cd484627fabe4847aa98f125d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-09 18:40:26 -0200
Commit message:

 Removing part that was not working


Former-commit-id: 7ad98ff975bd586fad5ccc83a6bc448a166ac820 
Package: TCGAbiolinks
Commit: 1b5ac2f38f3ba4775058a50be8f9d22eb95fdb42
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-11-08 16:53:31 -0200
Commit message:

 Adding dplyr package


Former-commit-id: 88751050cbff575a490ad5a8b8af446da5a98f99 
Package: TCGAbiolinks
Commit: 71e1dc5c23ce8ff55fdac85d7f3aae87991dddf1
Author: vobencha <vobencha@gmail.com>
Date: 2018-10-30 11:54:34 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch


Former-commit-id: 39a4c1bd48fdc556aa8ffe9f2cf02261642295fc 
Package: TCGAbiolinks
Commit: 9a4127fc64706ed871627621fd1f91e646ff8e40
Author: vobencha <vobencha@gmail.com>
Date: 2018-10-30 11:41:58 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch


Former-commit-id: 7efd1840c05ee0005c1f6caf229bfaafc11bdeb7 
Package: TCGAbiolinks
Commit: 533358ee7812b8985e8e500edb02feed08b3de55
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-10-25 12:08:46 -0300
Commit message:

 Update table


Former-commit-id: 3ed11ca96e95656ab9f9c841c69ae74b1cf2e093 
Package: TCGAbiolinks
Commit: 1e31f27070c7a0f291c63136584de7ca79337d54
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-10-25 12:01:20 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 1a7c093c5180fdd03a2580e4560426424329cb94 
Package: TCGAbiolinks
Commit: 6eba3c1c49f22f6ec68a4b7afeb52dd589541d8a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-10-25 12:01:10 -0300
Commit message:

 Fixing PAN-GI


Former-commit-id: fed0d0999f0653ac4443687e04ed665992592a5f 
Package: TCGAbiolinks
Commit: 1dbb938db74e76ffc44950407eca0923f0593a4e
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-10-08 20:28:55 -0400
Commit message:

 Update of TCGAanalyze_DEA

Update of TCGAanalyze_DEA


Former-commit-id: 73dbdfd29706b4e163a04277c3ea4ff845cd8ba8 
Package: TCGAbiolinks
Commit: 5f8bf6ff264f424bca8adda50722c08755c66001
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-10-08 20:26:51 -0400
Commit message:

 Update of TCGA_MolecularSubtype

Update of TCGA_MolecularSubtype


Former-commit-id: cf21de4fbbd871896386113f86c45b4547bd8e1f 
Package: TCGAbiolinks
Commit: d0bf9fc7afa4d75611def9eaa567e609867ce320
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-09-26 16:35:32 -0400
Commit message:

 TCGAbatch_correction with unpublished datasets vignette example

TCGAbatch_correction with unpublished datasets vignette example


Former-commit-id: bc5facf089586b44b36dedf045a080b035d72de2 
Package: TCGAbiolinks
Commit: 85ef461fd1f6fbab49ec08415dd8d66de804628c
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-09-26 16:28:34 -0400
Commit message:

 Update TCGAbatch_Correction with UnpublishedData

Update TCGAbatch_Correction with UnpublishedData


Former-commit-id: f242b8b047ba62b9708b71c5c823361a585b0e31 
Package: TCGAbiolinks
Commit: d7e3fca8df54bc9e08c99d9990187c3206a31755
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-09-25 14:28:08 -0400
Commit message:

 Update TCGA_MolecularSubtype with 24 cancer types

Update TCGA_MolecularSubtype with 24 cancer types


Former-commit-id: e1ef0083497f533830b1092263ed2a31d68249eb 
Package: TCGAbiolinks
Commit: 51a709d020134863cf242e783bac59123d1b4740
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-21 14:52:46 -0700
Commit message:

 TCGA-AML does not have XML clinical information for radiation. #266


Former-commit-id: adc0d9e62eed61569fd1aed372f4e8f31b3fac25 
Package: TCGAbiolinks
Commit: 567254fca5912925cc583c50ee43b852cfbc0946
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-10 13:46:47 -0300
Commit message:

 Fixing check if no results is available


Former-commit-id: 7d3ee85da264e2b1d9b19ce3a6171b9a42e19a0e 
Package: TCGAbiolinks
Commit: 33f4e7f54582837c0582addeb3855e62aba69293
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-10 13:41:35 -0300
Commit message:

 Bug fix


Former-commit-id: 325550836afe7ae6157d222124d406fd1e402d1a 
Package: TCGAbiolinks
Commit: 56038c64fcbfa1274968b8bc037929ca27cdc64b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-10 13:39:22 -0300
Commit message:

 Fixing getGDCquery for recurrent Tumor


Former-commit-id: 7133ef40f528b3d8c5e00952b505e2a34e17e8a0 
Package: TCGAbiolinks
Commit: 7b7c544764ff598374b37e3428d1ae50e0eabedd
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-09-03 18:32:49 -0300
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/TCGAbiolinks


Former-commit-id: 9383cf1dafc67fc5635dd5a13d9c5d486e446f07 
Package: TCGAbiolinks
Commit: abf8d1abc6503f5e09f6b8c7f4b9daa447a9dde7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-03 18:30:25 -0300
Commit message:

 Remove print


Former-commit-id: 23dadacb17dcd0af3656154fbfc0fff83bb4856e 
Package: TCGAbiolinks
Commit: af4624f4516c9d55942d459749a28752a9391123
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-03 18:28:03 -0300
Commit message:

 Reducing query size


Former-commit-id: e1ff8b50d00e7947353862452673d9e6847f077c 
Package: TCGAbiolinks
Commit: a27df24c8972ab41f2d96fcf8335b73d8e45fea5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-03 16:48:54 -0300
Commit message:

 Adding more option to decrese query size


Former-commit-id: d023b82ff6c4b3be5cfee62c2bda64c89bd55f03 
Package: TCGAbiolinks
Commit: 0eba183ec9b0f74b0adeee7d372be3ed58bb0f87
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-03 15:12:17 -0300
Commit message:

 Adding filter based on file tag. This should reduce the request size. #256


Former-commit-id: b4df0d4cb7335e8398105b29fd24a614e2a5a7c2 
Package: TCGAbiolinks
Commit: df568f3ecdf5407d307c7cd7419641c9e660f67a
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-08-30 13:57:30 -0400
Commit message:

 replace BiocInstaller biocLite mentions with BiocManager


Former-commit-id: cb1fa3a2f4d5afd92702dc41ba7f9372479f6854 
Package: TCGAbiolinks
Commit: 769700da4ee11332d9cd58d637089d92f10c7db5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-23 13:28:15 -0300
Commit message:

 fix travis


Former-commit-id: c6e644ab10fb594fafdbadcea55641e868f6fc94 
Package: TCGAbiolinks
Commit: 6669147ee264d78c11a63b659c7f871cbe568453
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-23 11:40:29 -0300
Commit message:

 Fixing aapveyor


Former-commit-id: f156bed674e367b7aa1801cba8b7bdb1ab00029f 
Package: TCGAbiolinks
Commit: dfbc6a83dbfaa84885477f3902f80f438b78159c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-23 10:57:34 -0300
Commit message:

 Fix travis


Former-commit-id: a229113e9c9856c8a41e1a7435eb7f23ce295a13 
Package: TCGAbiolinks
Commit: 63c4145795d55def19ff80991066826ce4cdb609
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-23 10:38:37 -0300
Commit message:

 installing r-recommended


Former-commit-id: 753f6d4e77d5318714ebe7078dd4c750b4591831 
Package: TCGAbiolinks
Commit: 309a7272a6858590a419f1e3364641cb946ea371
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-23 10:31:30 -0300
Commit message:

 Trying to fix appvyeor


Former-commit-id: da811c88fa343021e6210213da2f240af2f43bbb 
Package: TCGAbiolinks
Commit: 5316b9c52567da7512cb06fbd8bab51f0db2a2df
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-23 10:20:09 -0300
Commit message:

 Update appveyor


Former-commit-id: 1531a4caaef08ebbba1aa31c80b1f911b3395275 
Package: TCGAbiolinks
Commit: 2b6233a5fcc49a01b84f5fa929a97783a1020409
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-23 10:09:01 -0300
Commit message:

 Adding missing package


Former-commit-id: 181e193818378cf7b04e2a7528bed0e5b503e35c 
Package: TCGAbiolinks
Commit: a71db18d06903f40492664302a65132993b7fba8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-23 10:02:45 -0300
Commit message:

 GDCprepare_clinic can now handle several projects.
Closes #252


Former-commit-id: 50230eed64927a1cdae5250a76517e257746c8e5 
Package: TCGAbiolinks
Commit: b6132049551ca1b87be51fbe2271bf8854871b9c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-22 17:36:50 -0300
Commit message:

 Adding option to read exon quantification #253


Former-commit-id: d547c1f223ebc3d33d9a32ea4c9de215a676f6e0 
Package: TCGAbiolinks
Commit: de9c02aa6e4507be0e41add1d90c08008896c717
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-19 23:57:13 -0300
Commit message:

 GDCpreapre_clinic accepts multiple projects


Former-commit-id: cbf27b80820bdfb8e6ae183c21d20139a6a548a3 
Package: TCGAbiolinks
Commit: 2522477da6d34a75d12ef6679cd57ad124efac17
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-06 19:05:57 -0300
Commit message:

 Update BRCA molecular subtypes


Former-commit-id: 06b8133bd042f50e333f54bfc71b8f31031f3ea1 
Package: TCGAbiolinks
Commit: eb5c9f61fcad6f68403f5dbd68bb67298a9968e1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-03 11:00:41 -0300
Commit message:

 Improving tests run time.


Former-commit-id: 8134124586b0ad8a58bca2b4bcdea04db94de42b 
Package: TCGAbiolinks
Commit: 425fce0bf6835d13a44473053bd1e89007117eb7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-03 10:44:03 -0300
Commit message:

 Reducing examples runtime


Former-commit-id: 5c9387c70074618401512bc5dbadfe6e143b60a5 
Package: TCGAbiolinks
Commit: dca178bf6272a62856a16a383f91b8361d831f53
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-03 10:40:38 -0300
Commit message:

 Reducing examples run time #240.
Tests and vignette still need to be evaluated.


Former-commit-id: 8a9f5a71d4357291826459a3727aab92c62cb3d3 
Package: TCGAbiolinks
Commit: 78f8e9b983f46dd1891d366dcdb5190e68017d7b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-08-03 09:06:38 -0300
Commit message:

 Fix LIHC subtypes retrieval. Closes #249


Former-commit-id: 53d083f0311927c9a29544cb5f67441f984f621c 
Package: TCGAbiolinks
Commit: 96ce600b532eccf35fbfacc19fb0d8cbd78f99a1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-07-18 09:58:53 -0300
Commit message:

 JSON for demographic returned several empty rows. They should be removed, otherwise final data frame will have also NA rows. Closes #247


Former-commit-id: a4cd1bdc885e0549043487319eadc398e75fc8ed 
Package: TCGAbiolinks
Commit: 5b5350bb8faa288d8d5bcc5df574a3666bdfa82f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-07-18 09:44:24 -0300
Commit message:

 Merge pull request #244 from Melkaz/patch-1

Minor typos & rewording

Former-commit-id: 38082b01c7a5a8c05594bca76d42127a3dd57376 
Package: TCGAbiolinks
Commit: c0f2ad696372fb81a48e26ec5ee51e522d9b11e8
Author: Yohann <yohann.nedelec@gmail.com>
Date: 2018-07-02 23:21:46 +0200
Commit message:

 Minor typos & rewording

Former-commit-id: 4fd27cb47095adcefed35d0f6961fb4e1fa7ef90 
Package: TCGAbiolinks
Commit: 99150c63fa471b73669a5a1d102d27bee3786654
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-06-25 19:59:12 -0300
Commit message:

 typo fix. Closes #238


Former-commit-id: 5cdf7fe81eb3c18a3fa9698d4fdd168637f4c6ee 
Package: TCGAbiolinks
Commit: 39343f81f77caf148a2dfcdc9f97f355f580f6ed
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-22 12:47:39 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: c6c2fc5ebf1764e2edaf8af0a275ae1c9c66d305 
Package: TCGAbiolinks
Commit: 2b8d046e67ea2f6c3642818b52e1494bae37136a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-22 12:34:11 -0300
Commit message:

 Fix man


Former-commit-id: 8b8ab3b1114e8c9a9af516eba78acb5211a22bd4 
Package: TCGAbiolinks
Commit: 1c140b83691be5cce44af559f45c51504eb8cd3a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-22 12:34:11 -0300
Commit message:

 update man


Former-commit-id: 3b3da94a2b0616047731de37a925eb9f812a2763 
Package: TCGAbiolinks
Commit: 04bac51e345b7a7b8cde37842749b804a1bf58f3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-22 12:32:39 -0300
Commit message:

 fix example


Former-commit-id: 068f2820dc46333e55013431ca2aadd503307f31 
Package: TCGAbiolinks
Commit: 4ff0fe7329c4084ed8b73c5891729e7bc947f364
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-06-20 08:24:04 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: df5fe17ac3db19fda094ea1673bfa79c8828c082 
Package: TCGAbiolinks
Commit: 056dc23fd9011fa49d501ebaabad4edf98039235
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-20 08:19:38 -0300
Commit message:

 Fix GDC client install #231


Former-commit-id: a79e3779270b3aa0dd9beb5507d3dc515ad5331a 
Package: TCGAbiolinks
Commit: d72d42359cca4acb74c87e7a4746d81b903fca46
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-06-18 16:28:19 -0300
Commit message:

 update


Former-commit-id: 5bdcab47dfa88576cef98d7d3e4c78b95a9fa0a5 
Package: TCGAbiolinks
Commit: 1ff080e6b9feb4025a81b74c8c2165f5cad5652d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-18 16:22:05 -0300
Commit message:

 fixing api url


Former-commit-id: 97848f50069b1448f7c430f669af9e737c9a6dc8 
Package: TCGAbiolinks
Commit: 000a974e5470e1a5d51eb6d38f7282a93471b93f
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-06-15 16:25:57 -0400
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 447712fac71f480cfe319e37aa5d376bd4f57dc7 
Package: TCGAbiolinks
Commit: aab4247ae7b88511d4a808565443c94d64101e43
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-06-15 16:25:55 -0400
Commit message:

 TCGAanalyze_DEA

TCGAanalyze_DEA new functionalities


Former-commit-id: d162077307ccbd9b4a49447659ad0b494d1995dd 
Package: TCGAbiolinks
Commit: 64a49810e609477bf4f7d30696499c45bd3a7866
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-15 13:36:38 -0300
Commit message:

 Fixing tests


Former-commit-id: f2b290c29546e68baf430bc03beeba6a2d57b3e8 
Package: TCGAbiolinks
Commit: 4315b6ea71b7ea77dd3e47928fc355d0d244aec5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-14 16:44:03 -0300
Commit message:

 Fix xml parsing


Former-commit-id: 0a3da185054d7ff66fd7561290953a5809507c1a 
Package: TCGAbiolinks
Commit: 8ecaaeb3d9b529dee193de592b3ae8753a01c0f9
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-14 16:32:11 -0300
Commit message:

 fixing example


Former-commit-id: 1cfaa67a1a74bdf5874c39faf770cd148b2383bd 
Package: TCGAbiolinks
Commit: bb96c52a9ffa5b122ea40424d57b20b1a93a4ba3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-14 16:27:30 -0300
Commit message:

 Fixing example


Former-commit-id: 35ea9b43844337c2a0c8db19c6d11e6fc68a1c7e 
Package: TCGAbiolinks
Commit: 555d1d94b47933e98661015edd26db38da98d87b
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-06-14 15:06:38 -0400
Commit message:

 fix get_IDs

fix get_IDs


Former-commit-id: c0e6d68ab94c4d7c428f3271f4c8183036214478 
Package: TCGAbiolinks
Commit: 9a18b0a9a8fba36cf51631a8c7dd5109487678c5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-14 14:36:52 -0300
Commit message:

 Fixing example


Former-commit-id: bb2469ff971aef836539e3a5b27f089816ecdd83 
Package: TCGAbiolinks
Commit: e19e928f88a901fb1b7e2ee6521999cafd581622
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-14 14:34:36 -0300
Commit message:

 Finish adding file.type = "xml"


Former-commit-id: 81b05aba336dc189f1ac15e73cd13997f72d3b05 
Package: TCGAbiolinks
Commit: 1e1b55169c74cadd4b939b50aa5ec1033e8e155b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-14 14:31:53 -0300
Commit message:

 Update clinical.Rmd

 Add file.type = "xml". Now BCR Biotab exists.

Former-commit-id: c061679be04c839aa9dd034e72b03f1ba5fc26d4 
Package: TCGAbiolinks
Commit: 1aa12893a0c3a2295849ece3cf5da8b3aedefce2
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-06-14 12:22:45 -0400
Commit message:

 doc for getID ad batch correction

doc for getID ad batch correction


Former-commit-id: d10ac4a8c0f52547cc27a7fdf67fa5233f71fda2 
Package: TCGAbiolinks
Commit: 1c25205a820c29046d905eb9fbc69c738ea67fcf
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-06-14 12:08:12 -0400
Commit message:

 TCGAbatch_Correction

TCGAbatch_Correction update


Former-commit-id: bcf8494be259bbc8128fc4a02b1ae9e045bc4d17 
Package: TCGAbiolinks
Commit: 331d1fe367200ed6fb6ba4d8782ff0bfc11624e7
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2018-06-14 10:58:15 -0400
Commit message:

 TCGAanalyze_DEA and get_IDs

TCGAanalyze_DEA with limma,
get_IDs (information from TCGA barcodes.)


Former-commit-id: 3c7b03e2f0d560843c93453aee40ee5ff0951d37 
Package: TCGAbiolinks
Commit: 3537bd908bae0208077d08eb9e20b612ae79c0fc
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-06-12 09:46:17 -0300
Commit message:

 fix merge


Former-commit-id: 52536d7bc4b6496ad1f8ccfdd37cf4f48024b808 
Package: TCGAbiolinks
Commit: 156c70f8e281fa58af0c11e32c8da496e1f3e4af
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2018-06-12 10:13:51 +0200
Commit message:

 -added “Patients” as an option for batch correction
-Voom transformation is removed completely from TCGAbatch_correction() because data might be already transformed beforehand ==> two voom transformations lead to faulty data
-updated documentation and the tcgabiolinks2 Rmarkdown file


Former-commit-id: 48a50506887c195193a79e91f7ea2756d824489e 
Package: TCGAbiolinks
Commit: 804e3afa893b96a56c512840cd5409e342422c38
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-07 19:49:34 -0300
Commit message:

 Fixing vignette


Former-commit-id: e32a24e5b195168660da4f9461324faafcabdcce 
Package: TCGAbiolinks
Commit: 91a705996027eec6ab99b14f63ba9a297f54863f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-07 19:37:49 -0300
Commit message:

 Fixes #217


Former-commit-id: b090c55c378a35b258487413adc557af27fb5acf 
Package: TCGAbiolinks
Commit: 123b28a044ba10d78cc72cd3b70c9ea1db744b89
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-06 22:51:57 -0300
Commit message:

 revert code style


Former-commit-id: 678465350470679294ee19f90a8ab7d903cac72e 
Package: TCGAbiolinks
Commit: 2b7ac01370bb544ecab9f50f68d08fb47f61bd89
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-06 22:43:26 -0300
Commit message:

 bug fix and code style fix


Former-commit-id: a1b1ff35251eed30b272ead20ba7d42cb4b7db09 
Package: TCGAbiolinks
Commit: aeb78bb2eaa91d4467fcf83e049e77695cff1ac2
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-06-06 14:42:47 -0300
Commit message:

 version bump


Former-commit-id: df8e977fdf2587281fa819edb732a6b51a969d92 
Package: TCGAbiolinks
Commit: 770e16cc45016b85bf8eb5421364ea82e6cdd5e0
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-06-06 14:41:26 -0300
Commit message:

 git push origin masterMerge branch 'ELELAB-master'


Former-commit-id: 162f98e97f21fab0cdb981d300fba346a460a20f 
Package: TCGAbiolinks
Commit: e2196b45b165ba7caa5e659efe312f530bedea9a
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-06-06 14:40:31 -0300
Commit message:

 fix merge


Former-commit-id: bf8bf9a8b81485a5d8e92488fefc42ff159853d1 
Package: TCGAbiolinks
Commit: 5025a26d03dfe2da9ba9fdadd88531b26894d0e3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-04 14:14:21 -0300
Commit message:

 revert


Former-commit-id: 53a64014f38bd03e4a15145aa88c810bbd12a63a 
Package: TCGAbiolinks
Commit: 77d4bfeb8924173f49ee97cfbd0f982aabdcb67c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-04 13:38:43 -0300
Commit message:

 Trying to fix travis for mac


Former-commit-id: 0b8f5e680e1e45132ad890431d91518f69d411a8 
Package: TCGAbiolinks
Commit: ec27400b539b03105e4c137d2f862e647b7e6561
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-04 13:02:33 -0300
Commit message:

 Travis typo fix


Former-commit-id: 2b1659499182a5997b89e65e0c52e4d79333c096 
Package: TCGAbiolinks
Commit: ac22d8047874a9d5c8574214ad6b661312bd4fc1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-04 12:45:49 -0300
Commit message:

 Fix API link


Former-commit-id: d78c3927b4708023ac5fd85522d8e57d1dc292b0 
Package: TCGAbiolinks
Commit: d67acb04a4abbf16f280ed03f4b1d03f716f0f86
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-04 12:13:36 -0300
Commit message:

 Fixing examples. Slide image was added to harmonized database


Former-commit-id: 39094524a414d7580d1cc3f590a282f94700ceb1 
Package: TCGAbiolinks
Commit: c213f869ceca88976473aa215f81d431649f17cc
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-06-04 10:05:10 -0300
Commit message:

 API moved permentaly. This might fix the accessing problems. #221 #220 #219 #217 #216


Former-commit-id: 7c346a75d7a4cca95456a15fe20200dc5715ba9f 
Package: TCGAbiolinks
Commit: ca32c9687c73a73f9025f058d5f0e418c934e347
Author: tiago chedraoui silva <tiagochst@gmail.com>
Date: 2018-06-04 09:39:59 -0300
Commit message:

 Query_clinic workaround

GET method not working in WIndows. Still need to debug the cause.
But Download method is working. We will add this workaround for the moment.


Former-commit-id: d86ec3d834221cd4cb864dd3d325ff23b939de9a 
Package: TCGAbiolinks
Commit: 4252ecea484458dbfcf7bf3af84c2558dd907538
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-30 23:01:50 -0300
Commit message:

 Assing missing packages to travis


Former-commit-id: 39235bd37d5a8591168e7fc168e28eab88b6af76 
Package: TCGAbiolinks
Commit: db571c63f2a4884c7aad0deca0b6b63e4c55ff35
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-30 15:43:25 -0300
Commit message:

 Does legacy API still exists? or was it moved?


Former-commit-id: 166a98c73c369e99d349db690b4756d5de261e14 
Package: TCGAbiolinks
Commit: 4b82d0ccc37f3215792101c2549eb4744f42e9d9
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-30 14:40:03 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: ad0d20a4362b3ab01e168e56107d095971220617 
Package: TCGAbiolinks
Commit: 68007fe79dfe263342fcd7492fdc070a9cee382f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-30 14:39:52 -0300
Commit message:

 Remove warning


Former-commit-id: 4a7e1cfb0168d2a2584fc336ca582f373e209ef8 
Package: TCGAbiolinks
Commit: b9a7f212c969ec7e1240cc398a425e1ce9f22b5c
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2018-05-29 11:56:57 +0200
Commit message:

 Edited TCGAbatch_Correction to handle batch correction only and not voom. Voom transformation is handled by the DEA function


Former-commit-id: e3af48b97128025a6a5492ab5a839d262eaee621 
Package: TCGAbiolinks
Commit: c3942968583f2f54f2453feccf1c574eb33d6ad1
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-05-18 09:45:42 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 5b0e23257589377d172a6c96646ffe8c8a94b861 
Package: TCGAbiolinks
Commit: 509cfabbcc5c64fe986043e16849f986700362e6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-18 09:24:27 -0300
Commit message:

 bug fix


Former-commit-id: c995d07f9ae7240af597042175b9097798dac5bc 
Package: TCGAbiolinks
Commit: 15357546a3b5e7ccae0d0a44fab8c8fd69a509e6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-16 10:07:36 -0300
Commit message:

 Fix vignette


Former-commit-id: 7afbe3a314a8d6c5197c94cfdd363bd71f727aa3 
Package: TCGAbiolinks
Commit: c7a9f13baa36fd72cff41abcca3dc7f6466a4ab6
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-05-11 17:09:49 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: b5e04065a303761c38e44bbd5113fc3de0a4b284 
Package: TCGAbiolinks
Commit: 268c88ae81105bb0b2e36ecf9f5620b7a8d0fe24
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-11 17:05:49 -0300
Commit message:

 update table style


Former-commit-id: cb98531daf1ed0409cbf3386cf673041c7eec794 
Package: TCGAbiolinks
Commit: 31fdb5ea0ce4b6765d3050c022c9ff97eebd6eb9
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2018-04-30 10:41:41 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch


Former-commit-id: b975642d2e8babde2a7a3252e7e7b8f7dd0ac66f 
Package: TCGAbiolinks
Commit: c0a90167f0e32ef4c7e6d66e4f1bdc2512063541
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2018-04-30 10:35:37 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch


Former-commit-id: 59e91628231e6d062ffd3ab2c4bff3abf3d3d496 
Package: TCGAbiolinks
Commit: 2ec199d3abbed057b360705af9ab1a1a8c0278bb
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-03-23 10:58:37 -0300
Commit message:

 Update list of tumors with subtype for colDataprepare function


Former-commit-id: 541e842335456e026d1eeffcf4bca0e18a750223 
Package: TCGAbiolinks
Commit: 33069bba810d26b95781f1d7b254ebf820d7941a
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-03-07 16:34:14 -0300
Commit message:

 Small vignette fixes


Former-commit-id: ef65032d8b16ede6bd75628d774d32f5916bc0b3 
Package: TCGAbiolinks
Commit: e8c741790975291e16412fb610550546e8ca95a8
Author: Mohamed Mounir <simomounir@Mohameds-MacBook-Pro.local>
Date: 2018-03-07 10:13:04 +0100
Commit message:

 Better organization of TCGanalyze_DEA() code.


Former-commit-id: 0901e5df95b25b06233f7b15082bc8683d252677 
Package: TCGAbiolinks
Commit: fb80b1dd16e190f3d9ce1b6a0996640f71e67e6d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-21 20:44:57 -0300
Commit message:

 Merge pull request #197 from ELELAB/master

logCPM variable didnt was getting voom transformed but not used downs…

Former-commit-id: c4144de70315331b69aafd8637277175d2e72415 
Package: TCGAbiolinks
Commit: be7495f46f15b1222cc0ed5120f5aa3742008536
Author: Mohamed Mounir <simomounir@Mohameds-MacBook-Pro.local>
Date: 2018-02-20 15:49:07 +0100
Commit message:

 logCPM variable didnt was getting voom transformed but not used downstream. It changed to TOC so it goes in all the downstream analysis.


Former-commit-id: 6e507361a4d370a88ee85ac77876ea7d9b1ef7e2 
Package: TCGAbiolinks
Commit: e2091ce12472f373357fa5a4fff0fe43fdeceb13
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-16 11:58:55 -0200
Commit message:

 Correcting get_IDs and file indentation. Fixes #195


Former-commit-id: c838a678a5fdcb03334db6c5f7d9872c6572dc40 
Package: TCGAbiolinks
Commit: b2039a64835468872cc96e10fdab16eeff2984b6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-02 13:39:08 -0200
Commit message:

 Version bump


Former-commit-id: 32df036da5d0430668fb7508a891c39527a42f3c 
Package: TCGAbiolinks
Commit: 73255110727c3acdc0f05de35be4ec65e913d921
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-02 13:37:08 -0200
Commit message:

 Bug fix


Former-commit-id: ce30f90a0852fce8925dda6a49698e21fe5ab562 
Package: TCGAbiolinks
Commit: ecca1d0461ae81e19aed493164cdcc5c8b824fdc
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-02 13:32:28 -0200
Commit message:

 Check there is only one data type


Former-commit-id: dff234f213359781aea86707c413472f28d0d71d 
Package: TCGAbiolinks
Commit: ecf26c79aaf815172d92198f8b59755e03f3be15
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-02 12:59:01 -0200
Commit message:

 Add support to centos


Former-commit-id: 4c87d9070cf09ae338ed229efa3a60f6e5b6a66c 
Package: TCGAbiolinks
Commit: ca0042d1a20978b5ce5de98c0b6b81b72b98a7c8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-02 11:41:29 -0200
Commit message:

 If patient is selected has_new_tumor_events should consider follow up.
Closes  #188


Former-commit-id: 5e0f23cb514ea6dd9353cbb2d02e0ac67aca297d 
Package: TCGAbiolinks
Commit: 9227296feabfa07bd559d531a379371d22846dde
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-02 11:30:41 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: e80493590274c4111a068ae45b0b8d937092b2e5 
Package: TCGAbiolinks
Commit: 55b868edefad4937694833665ec5650173c16fd6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-02-02 11:30:35 -0200
Commit message:

 Bug fix #188


Former-commit-id: bb98eb39866828a46f181343cd3fbd46014ea0e4 
Package: TCGAbiolinks
Commit: f0e48767ad6bdf6184a26101e68c90371846fecb
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-01-24 15:54:31 -0200
Commit message:

 version bump


Former-commit-id: 00aeada25248988b29fdc87ce2c0a7bc83955eaa 
Package: TCGAbiolinks
Commit: b098dff8eaa4d55fda8aa9eef18ec0e9007eca0a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-24 15:52:03 -0200
Commit message:

 Fixing subtype information for chol and SARC. Closes #185


Former-commit-id: d4c76d1595a8ed8807802f4813a7b17d13510f4c 
Package: TCGAbiolinks
Commit: 5d888a8516f729422eed10a7707854ad8ab81775
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-14 12:35:22 -0200
Commit message:

 Fix enconding


Former-commit-id: 17d45de7deea7bb1a8920fa3b931bc605931bbf3 
Package: TCGAbiolinks
Commit: 405666776e7edafc03b65550fd5e63bc5b3bb8ff
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-13 00:33:22 -0200
Commit message:

 fix travis


Former-commit-id: d06acab14ea85464ea120b8b3c41633b2aa37f5b 
Package: TCGAbiolinks
Commit: a8323e1903ea2c8a10d2b1dfa748a6380ab5b40a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 19:40:00 -0200
Commit message:

 Fix numbering


Former-commit-id: 269b0747af4dcf8ef69906f666a973b09c7c3916 
Package: TCGAbiolinks
Commit: 7d5e3b981391ecbca9629f5edaa9601a7abbcea4
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 16:10:50 -0200
Commit message:

 fix download for windows


Former-commit-id: 3a0fed47ae5be5cba5d6e08e5ef9aaeb684e9f1a 
Package: TCGAbiolinks
Commit: be541304e3541a0049b2ffce3867c4cdf41b322e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 15:27:22 -0200
Commit message:

 Travis improvement speed


Former-commit-id: 905263f4f95663cb0c9d3f9cc580ee658803338f 
Package: TCGAbiolinks
Commit: d8f56d5f8af1342c35e795ea3a2ae4805f4d7200
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 15:16:21 -0200
Commit message:

 Using binary package travis


Former-commit-id: 097c3f7699a27be6c8ae8caafcbd276205dcf2ba 
Package: TCGAbiolinks
Commit: a1a6d198988c81b1cf1727f537a5abb6b872d95d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 15:06:56 -0200
Commit message:

 Improve travis speed


Former-commit-id: 55f667b1763bc43c2bdbd3bb817f3a1e9478b3c3 
Package: TCGAbiolinks
Commit: 89218a3645d445f4e48d58daf51272879b1ed356
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 14:54:51 -0200
Commit message:

 Fix travis


Former-commit-id: 97ed4eb39e1c40bc23219352acf18a06818dc74a 
Package: TCGAbiolinks
Commit: 8a27eb5f78cf1a2e88780bdf82d463078936b11f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 14:50:56 -0200
Commit message:

 fix binary


Former-commit-id: 942daffd7d26f0d456be3f583061ee27dc2d95e2 
Package: TCGAbiolinks
Commit: 67babddff0c3afd4b58db24ddb69cbbbb2ca371c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 14:37:41 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 5e26548d77673172f99404ab97c20c99c0f2a456 
Package: TCGAbiolinks
Commit: b7e2a8e4a9b4e2aa9487656b8f7781956c11ba82
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 14:37:31 -0200
Commit message:

 trying to reduce time to install in linux


Former-commit-id: 3f157b62156f1a2a634e1e2dbce9536301b5f47c 
Package: TCGAbiolinks
Commit: 1acd2d4e7d2e57510419b4e6a9a1393949c011aa
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-01-12 11:27:56 -0200
Commit message:

 update


Former-commit-id: 5fa4c21162d5b1cbbeb22554a23d191cab2fb3bc 
Package: TCGAbiolinks
Commit: 93727e3fa88b8c618a16c1d12dbb98b8c5d4a4f7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 11:25:23 -0200
Commit message:

 Bug fix in subtype all


Former-commit-id: 4ce79ef06941570d63373cc1c45ce8b8603bcae1 
Package: TCGAbiolinks
Commit: ffd9b37626391f72d9fa9110b50d441914689da9
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-11 21:32:53 -0200
Commit message:

 bug fix for TCARGET closes  #108


Former-commit-id: 0070be0cc013805993c7fc0efd76a76c20aec9e2 
Package: TCGAbiolinks
Commit: 02597a89b4c8259498983b978dd419592d7a680f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-11 17:15:54 -0200
Commit message:

 bug fix


Former-commit-id: a92f89a645d9c13be1f170bd44ab2add754c20d3 
Package: TCGAbiolinks
Commit: 920f7d8893d3c7e81d32edc7abce8593dbb5d655
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-11 16:26:36 -0200
Commit message:

 version bump


Former-commit-id: ef47274edc770c2d4af80f4872186e87e430e8c1 
Package: TCGAbiolinks
Commit: e85fe8e92c2daf22703ac47580aa034316dee8c2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-11 16:25:10 -0200
Commit message:

 Update subtypes


Former-commit-id: d7d4614439158ac414a03f4d261fa3ef877f0206 
Package: TCGAbiolinks
Commit: af984b356394ed2de20fd6b9410c9993430b2763
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-10 10:38:56 -0200
Commit message:

 bug fix


Former-commit-id: 0a377b97a27431e76c8520260034f74d56c649bf 
Package: TCGAbiolinks
Commit: 647d98a39d5dca61758ec32e1885b094fc2bdd5e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-10 10:34:16 -0200
Commit message:

 Add subtypes back


Former-commit-id: f4b9846559176b2aa168b604b66e74898c29ab29 
Package: TCGAbiolinks
Commit: 06c831f3a152138aeb6df1490a36b76c02851821
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-10 10:30:12 -0200
Commit message:

 version bump


Former-commit-id: c35d2eb24212df3549af57e059eada5d03c1bc0c 
Package: TCGAbiolinks
Commit: 7fea5f80f1d2121dc0e0ffdec983dcf45e90d14a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-10 10:26:54 -0200
Commit message:

 Add new data


Former-commit-id: 4978c0aa0f8a1dfeba8afa6f88458dc0c4571f2d 
Package: TCGAbiolinks
Commit: 72d91c61e026a830255d6dbfa63501f83b270595
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-06 12:30:57 -0200
Commit message:

 Remove wrong vignette


Former-commit-id: f09c7ddaa2ddfef3e75fd08e76c1d2f143097f2f 
Package: TCGAbiolinks
Commit: 41785578e4fcf6414ef2dde69d91c282528731a3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-06 12:29:06 -0200
Commit message:

 Version bump


Former-commit-id: 49918b0f0ed94d3e3363d39bb47b92dbf1942f12 
Package: TCGAbiolinks
Commit: f66b6fb3fa8eb17253f8f3d66c7abe062c25ccac
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-06 12:28:39 -0200
Commit message:

 Update numbers


Former-commit-id: 066e7c8c7466706ca609b5d85cbe54f331c108a1 
Package: TCGAbiolinks
Commit: 6b50550f5447dfaacacf177f61d8fca318e67d97
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-06 09:09:22 -0200
Commit message:

 Remove libs


Former-commit-id: bdf8206e6a3d245eb44589be85bfa707623b5220 
Package: TCGAbiolinks
Commit: bf9c824aab5c36f15e9777214f5a0aea945bfdbe
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-06 08:57:38 -0200
Commit message:

 Remove subtype part


Former-commit-id: 9feb29c9b604f25684dbdac138af7b719ed1ee22 
Package: TCGAbiolinks
Commit: 1aff06ad47adf756569f99ea73ccddc7fae5de58
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 19:37:44 -0200
Commit message:

 Add one more level in toc


Former-commit-id: edb37e023837f45be14e6295371fa22d25d53b92 
Package: TCGAbiolinks
Commit: 3fdab06887206696a7f6d80b781108268b5d10be
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 19:33:10 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: deb5f8a39eeec793cb611cf3ad16a566b5716351 
Package: TCGAbiolinks
Commit: b2f6a30d5b45bb89a2450b1ad6303cd83d0ebb6c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 19:33:04 -0200
Commit message:

 Remove libs


Former-commit-id: 1c90eb648d9c9c8095376bc99aba414404308529 
Package: TCGAbiolinks
Commit: 33af2d4ef4f516f15fb8e9e6d3027cbde59ac064
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-01-05 19:32:55 -0200
Commit message:

 version bump


Former-commit-id: 229da549079d0eaa934785a5ab7f87aede8914e5 
Package: TCGAbiolinks
Commit: eb963d4a21159057724913cfbb59d7495ea0fde5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 19:31:30 -0200
Commit message:

 Set eval to FALSE


Former-commit-id: b4573764edd9545d2a842d85201c0c4c7be8b676 
Package: TCGAbiolinks
Commit: 10aa18735be6f7f76cd7ef4350cc4c5a28f90393
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 19:21:19 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 45e3843aca00d8b9bb0d075298c27809d1d6af9a 
Package: TCGAbiolinks
Commit: bd4802e6ee02b984ad011c0917c0e1ac53350f90
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 19:21:07 -0200
Commit message:

 update vignette


Former-commit-id: c570e1fd8caa4bf3497ada0f5e73a02de5df2899 
Package: TCGAbiolinks
Commit: 7343312cf6f4f26a676b033dc7e3c26d7e0b612b
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-01-05 18:22:54 -0200
Commit message:

 Version bump


Former-commit-id: fdba3c9c899a5e9846e929c167e1826402536616 
Package: TCGAbiolinks
Commit: 0893e5858434d89f9dfd6a27c367a7ec3eaff0cd
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 18:19:25 -0200
Commit message:

 tbl fix


Former-commit-id: 0729bf9a53a253ca58c23da345c67a150143c5e3 
Package: TCGAbiolinks
Commit: a2ac88d07066af57383a6797ddee791b8d870916
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 18:11:38 -0200
Commit message:

 Update name


Former-commit-id: 791c1b10f1ea593c373c988316f0a6f699ab5311 
Package: TCGAbiolinks
Commit: 001c384dd316c014c9d5051a12b4a4e0e0aaf6c5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 16:12:04 -0200
Commit message:

 fix test


Former-commit-id: 74696b177f420e72a975522322cc5c73726cf59f 
Package: TCGAbiolinks
Commit: ba4a94332fb2c958223f9ce78ad12d0118465607
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 16:09:12 -0200
Commit message:

 fix test


Former-commit-id: 407c29631f27a766c5aab28933e65597e88e6450 
Package: TCGAbiolinks
Commit: 65c14d4b57f0d4f43519360614d0b5edfa7a3a5d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 15:46:06 -0200
Commit message:

 test fix


Former-commit-id: 5dcce27e72409f0792f7a9dab51cefc85e916e15 
Package: TCGAbiolinks
Commit: 75ecf0c8f45748f7c52d17c6bf9b48122bc45b99
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 15:33:13 -0200
Commit message:

 Change name


Former-commit-id: 918a91b904c1953905b8b2d75da644ae59099f9d 
Package: TCGAbiolinks
Commit: b01dbb9dfc6218d3701ae385dd7a3bfd3453b6c0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 15:32:56 -0200
Commit message:

 Change function name


Former-commit-id: 41389c26ade01d3d412374f02612852cd52607c9 
Package: TCGAbiolinks
Commit: 13dffdf5df31a840d4d10665bf29d870c783bb70
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 14:39:12 -0200
Commit message:

 Adding BLCA reference


Former-commit-id: 22a86662e3d91e322fe842de90bf9ae56d26d738 
Package: TCGAbiolinks
Commit: 0818317dee265ad47492687dc53a174b3f698daa
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 13:41:13 -0200
Commit message:

 Fix function


Former-commit-id: 18e873efe8b69542fdf82be2b90a32a7e24d4ff2 
Package: TCGAbiolinks
Commit: 94a9f05fcdaed70ea77650c7402c2ce68b4588b3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 13:30:59 -0200
Commit message:

 Update vignettes


Former-commit-id: c3ae7c4dc3fda22cad6357ab238d61045ccf2c0d 
Package: TCGAbiolinks
Commit: b552fb8735a31d0e7b3fe43a9bd04fca8176ed1f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 12:34:59 -0200
Commit message:

 Improving vignette


Former-commit-id: 987d6c2fd3fdd9d9a98d38d7fa29a752f3dead19 
Package: TCGAbiolinks
Commit: c188c9164c1bbfe1e44850db9d144a6c3e980cad
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 12:16:56 -0200
Commit message:

 Fix menu indentation


Former-commit-id: 63b7da2398d9951e4a62f1035f79197ecdcd1ee7 
Package: TCGAbiolinks
Commit: 4939c144fa4d5ea1b5136224f4e9f2b551178c13
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 12:09:29 -0200
Commit message:

 Improving vignette


Former-commit-id: d5f27acc3f0a3f390ce80233298af6ace0f22d2d 
Package: TCGAbiolinks
Commit: 932a24703195d81a16c8430054603fe33d562aa6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-05 12:08:24 -0200
Commit message:

 Start updating vigentte


Former-commit-id: a704dfa0428fe87f6e1accc65653798dfdd28aa2 
Package: TCGAbiolinks
Commit: 19ff5df0b4d0f9c1ae810d6d92d160d1716f287f
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-01-04 18:37:39 -0200
Commit message:

 version bump


Former-commit-id: 3b6321ce8575211ff4df3a6657b077acdad03708 
Package: TCGAbiolinks
Commit: 365f0858cbcf9871964b78dc4c847d76a142375b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-04 18:36:18 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 747a60cd0317d60860395a6d9e693b6e699614ef 
Package: TCGAbiolinks
Commit: a359c2a61d1f4b8fcdfca20c7bae87874426bf9b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-04 18:36:12 -0200
Commit message:

 Update vignette


Former-commit-id: 8c2f0b110e4dcf59afbc414ecc6f647f146c30cf 
Package: TCGAbiolinks
Commit: 1c7bfc9cce9d14905865553623594d00c916ccad
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-01-04 08:37:11 -0200
Commit message:

 version bump


Former-commit-id: 67ec42bfe5d4491ec78539e8104e9c2e4417a180 
Package: TCGAbiolinks
Commit: a804d514a18466458206503a929887f83ed90d92
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-04 08:32:39 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 39b8cc24ff9672b0849db70ce44c5dcac42f10a1 
Package: TCGAbiolinks
Commit: 5645c00bed03149dc22a0eba4bd26b61f74e8ed5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-04 08:32:16 -0200
Commit message:

 If use add repeated barcode it should not return the same result.


Former-commit-id: d528594db3c6261af4c4a5f52b133cb6ffccfa87 
Package: TCGAbiolinks
Commit: c18656359f142d87dc12ae22a8fbb067dd9e4988
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-03 08:58:27 -0200
Commit message:

 Merge pull request #183 from ELELAB/master

Bug in TCGAquery_recount2

Former-commit-id: e8ca38fb9a6e2b2ab6d3790c3de6c6bc736745cb 
Package: TCGAbiolinks
Commit: f8310bf79af9cdd11d6d8a43208700792412a07a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-03 08:58:12 -0200
Commit message:

 Merge branch 'master' into master

Former-commit-id: 769c03cf249dc22631b9b3e897662776b7b5d90c 
Package: TCGAbiolinks
Commit: 2d1c0046feaa4fef0715327c97d9377b8ccdfd17
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-03 08:56:53 -0200
Commit message:

 Merge branch 'master' into master

Former-commit-id: 240cf932dcd358b97c4a0a66fa0aee87047a33cb 
Package: TCGAbiolinks
Commit: 1876b23e5502da62bb8d3665ef5e7f1f3af2a5d0
Author: Mohamed Mounir <mounir.mohamed92@gmail.com>
Date: 2018-01-03 11:31:45 +0100
Commit message:

 Bug in TCGAquery_recount2

downloading from URL was not working for TCGA projects. It is fixed now

Former-commit-id: 481fedbb4906ab86515a459c7b95220382f34ee4 
Package: TCGAbiolinks
Commit: 53d76e527e03389c263a37ad25087c227a6f91ec
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-12-30 16:00:04 -0200
Commit message:

 adding missing man


Former-commit-id: 001c290bd2bce4eaa1061df59718b0846669945f 
Package: TCGAbiolinks
Commit: 277d2d8e3392cd21bf4201fa01cd34cafb3b522a
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-12-28 17:11:59 -0200
Commit message:

 test


Former-commit-id: 8d7bc3739140e03673be44d452cad3d45280f515 
Package: TCGAbiolinks
Commit: f609148a41ce1367f77aebd474bd71066706c46e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-28 17:09:49 -0200
Commit message:

 If sample column does not exists do not check. closes #182


Former-commit-id: 369cae81133dc3f980785ec176f8d72a111f4a3d 
Package: TCGAbiolinks
Commit: 485e28b68846eeee1af923288f45696008694cc0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-27 10:11:11 -0200
Commit message:

 Add getManifest function


Former-commit-id: 24662aac43136a7f02ece47a2df4e12b4dc113df 
Package: TCGAbiolinks
Commit: a789dd01a067bf9a9bb4b5cc5607e61f59564ba1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-27 09:42:23 -0200
Commit message:

 Fix


Former-commit-id: 78c455dcbfade149935e5e8944d17998d9067566 
Package: TCGAbiolinks
Commit: 8f90baa61515f98b70dc1211a987b5f704ee9112
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-27 09:41:08 -0200
Commit message:

 Fix. GDCinstall after update


Former-commit-id: 36a64fa24df17925663d6f34fd1b68850f7cac5e 
Package: TCGAbiolinks
Commit: f731a970190c2c048f7274ec55c40b9456935c06
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-12-18 16:42:07 -0200
Commit message:

 version bump


Former-commit-id: 0daae077cab5829ee2b3b781f04db2c61492cbd2 
Package: TCGAbiolinks
Commit: 79f877cf3bfddbcfba46335e63a62c4acc179dbe
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-12-18 16:40:42 -0200
Commit message:

 Remove X column


Former-commit-id: 3afb20d508d38ac47009933594b664ef97f3361b 
Package: TCGAbiolinks
Commit: 5c5af6da85167ab835050d64041a3d1ad443f67a
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-12-13 11:41:01 -0200
Commit message:

 update


Former-commit-id: 31eb838c451f7b2f48ad0ccf78cadb38945a00b2 
Package: TCGAbiolinks
Commit: 7afc08b5e945fd4d6034c412510e5c50e8eaf235
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-12-12 12:54:32 -0200
Commit message:

 Set to server to default location


Former-commit-id: e27ba8a6dfeb47db5310ba2f7333dab4021b60d9 
Package: TCGAbiolinks
Commit: d8c49218623655f10505f96d6aa630ca4957056f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-10 21:39:42 -0200
Commit message:

 Fix example


Former-commit-id: 46d4d632f804b967c551e55689ef5b4c67532aae 
Package: TCGAbiolinks
Commit: 84a587fa58722882c5f47a66108cd3a8ff98d716
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-10 21:27:26 -0200
Commit message:

 rm docs


Former-commit-id: bea848e90a02b68e322a61a36f124b2c0663383e 
Package: TCGAbiolinks
Commit: 1e2d1a8e955cd2af4457f342d9c2bf5ab534c1c4
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-10 21:22:52 -0200
Commit message:

 Improcing vigette to remove error.


Former-commit-id: 75c29515d13ca1f8729c18b261d99543e5e1df06 
Package: TCGAbiolinks
Commit: dd5d7ec5f9322e019fac62bad223204d9f710a1c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-07 15:18:54 -0200
Commit message:

 Remove NOTE


Former-commit-id: 33d6224dce12bc8768c4555b2c27dba6e37971e0 
Package: TCGAbiolinks
Commit: 3e9c40b682b555d8443ca5c87fcddf44daa6c55e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-07 15:08:48 -0200
Commit message:

 Fix doc


Former-commit-id: 572c820461c859d0783f3b077acde36c230f7ec9 
Package: TCGAbiolinks
Commit: 340c1b3c6b0cf268a2d24525f0e7fb0065916d9e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-07 14:50:22 -0200
Commit message:

 Fixing description


Former-commit-id: 2bbfa091ef8c2d80e27db0792bc9aa2b5ddbc2a0 
Package: TCGAbiolinks
Commit: 1ce0fad98c4145d32bbee7b11149a12d8c43e6d9
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-07 14:22:33 -0200
Commit message:

 Removing files not required in the repository


Former-commit-id: 678bb7fbba559c386030e4ccae455770a2f69849 
Package: TCGAbiolinks
Commit: 9f298535d2dfd5f0d9e7a5acf90f2bd2ec5ec848
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2017-12-07 10:34:19 -0500
Commit message:

 Merge pull request #177 from ELELAB/master

TCGAbiolinks 2.0 suggestions by ELELAB

Former-commit-id: 3a2ea02ed0173049bf027f109d60ad9befdb4755 
Package: TCGAbiolinks
Commit: a54cc55945fe1b7b525e74e576baf6971d4e5ac6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-06 14:52:58 -0200
Commit message:

 update case 2


Former-commit-id: bfae4a02df279de8de5a50e98f98d20981ab3e0c 
Package: TCGAbiolinks
Commit: 8552d4f71a1f48f37ca1cf5112f40c25f4daba26
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-12-06 14:49:12 -0200
Commit message:

 update case 2


Former-commit-id: b60432ad3651f3bcc0c9589902f60a51d7c75d1a 
Package: TCGAbiolinks
Commit: 4ed5e11b4e19e550235886ad09e29cd15578bc44
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2017-11-28 17:17:38 +0100
Commit message:

 Merge remote-tracking branch 'TCGAbiolinks_fork/master'

# Conflicts:
#	NAMESPACE
#	man/colDataPrepare.Rd


Former-commit-id: b48c6c97e6dcf22925fbdd20f489c58d19852f46 
Package: TCGAbiolinks
Commit: 91139ec66c451dd9a84761e6404d1ba655125a5e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-27 15:16:32 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: d972f292345c15d1608e6fb72d54ac8150e57aba 
Package: TCGAbiolinks
Commit: 67f68c076b7f3c1f656f8fe1e9ecde57a962532a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-27 15:16:25 -0200
Commit message:

 If all gene expression is 0 is gives a row with all 0, this should be removed. Related to #171


Former-commit-id: be5bdd1f72266abdc76bde0819fe1d59513435c5 
Package: TCGAbiolinks
Commit: dd42448bf9fcf75088628aaa2cc6d4ba197b314a
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-11-27 12:19:49 -0200
Commit message:

 version bump


Former-commit-id: 9bd07f7dcabebcd38bfd50db0ce8bfaf4dbe1ba5 
Package: TCGAbiolinks
Commit: 2fb3e81e77dd4cff1b0630e7d51394c518adc83e
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-11-27 12:19:04 -0200
Commit message:

 version bump


Former-commit-id: f630700de3cc00b44c193132501b8fe52150b888 
Package: TCGAbiolinks
Commit: ab261e2b885fd13772903abe065d82bada92b994
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-11-27 12:15:55 -0200
Commit message:

 version bump


Former-commit-id: cdeed3767c1c6da5ff2ba8298649d7913a93d393 
Package: TCGAbiolinks
Commit: 146158990f59eb6ec41ca03edd11548cce1d6705
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-27 12:11:38 -0200
Commit message:

 Fix 1 - Accepts only one gene.
Fix 2 - Considering length of vector instead of working with matrix.
Fix 3 - Also, if there is a singularity in the survival time, we will ignore that gene.
Closes #171


Former-commit-id: b7580335fbf71d5fb4c4ff9ce2d77f27f5c21422 
Package: TCGAbiolinks
Commit: eeee8bde238d4642fbb6164dea5c971f4886b47a
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-11-25 12:59:28 -0200
Commit message:

 Fix starburst test. There is no need to have the gene in the DNA methylation object


Former-commit-id: a33b6f750018f8f0962c4200baedc32ae5f16207 
Package: TCGAbiolinks
Commit: 023d1d8cb4783a80b76ac983a4888a31b0a086af
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-11-25 12:26:53 -0200
Commit message:

 Instead of transforming a named vector to a mtrix just use the names of the vector. Closes #170


Former-commit-id: 4aa3d75e80eebbd55459be042a82b35b449ef50a 
Package: TCGAbiolinks
Commit: c8694195f8ae3dac75fc12e8d89d9f1b588e972b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-21 17:30:57 -0200
Commit message:

 If Survresult is set to TRUE in TCGAanalyze_SurvivalKM a KM plot should be draw. Closes #165.


Former-commit-id: 22d73699555b87119bb69f87a951adfffb787d4a 
Package: TCGAbiolinks
Commit: 3f19ee5b41499aa44792c5bc61b97591aa7407bf
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-21 14:16:29 -0200
Commit message:

 Add missing import


Former-commit-id: 695fc7a38439710666d06367a972ff9f12a534c7 
Package: TCGAbiolinks
Commit: a2b3f6e02ca0269f143498b869d9ad0aa30255e3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-20 15:22:19 -0200
Commit message:

 Fix tests


Former-commit-id: 958af83c1a117b716ff9eb669d5029a6c05f90e7 
Package: TCGAbiolinks
Commit: ec163ce58f194ab3e97cf79ab71fdedc952b27d3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-20 14:11:53 -0200
Commit message:

 Fixing starburst plot


Former-commit-id: dfeb6bc32b661325815c4039c6f52336a1b05d09 
Package: TCGAbiolinks
Commit: a12b8feb8846744df5d76c40cbfc8f63023a329f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-09 08:56:12 -0200
Commit message:

 Version bump


Former-commit-id: 83dbdb84474ee51166a2c3cc07ed751691ab5db4 
Package: TCGAbiolinks
Commit: 97fec514b603afcdee4efb50fd04afe9a508c03d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-09 08:55:42 -0200
Commit message:

 Test to fix maf function in windows.


Former-commit-id: dc9f0d4c12af72f500a80256ef432ef2746aa879 
Package: TCGAbiolinks
Commit: b4f8b768b01e27faf3bb9db57ee3c082d15f0a3a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-06 15:01:27 -0200
Commit message:

 Version bump


Former-commit-id: 21e7e758d72a33fc97f236a14c62417951ee78b0 
Package: TCGAbiolinks
Commit: 6d74ad2a3d79c5e5819ba3d0bcd73f32e0222ffe
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-06 15:00:59 -0200
Commit message:

 Sort data frame for easier view.


Former-commit-id: 4b6fb2342390d6515ec445cc42dafcb07b71d5fc 
Package: TCGAbiolinks
Commit: 31a2a294d00c5df783a564a51f89d076040ea10d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-06 14:55:02 -0200
Commit message:

 Data frame for duplicated barcode was not being handled correctly for the warning # 161


Former-commit-id: 3eb736b4c23f08ab73f1dcd10bae4f17a0645e0b 
Package: TCGAbiolinks
Commit: 0bc240dba365f837a6d6d35811971734b7ac46ed
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-06 14:21:04 -0200
Commit message:

 Adding message if there are replicates in the object. Improving code for question #163.


Former-commit-id: e2cb1641c7d729c8fd23f9ca45b52f5c16212413 
Package: TCGAbiolinks
Commit: 72c5b08758a28de093bb615dea522089d8e69f23
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-06 14:08:42 -0200
Commit message:

 Update namespace


Former-commit-id: 636c444137232cabbfc77690153463329461a381 
Package: TCGAbiolinks
Commit: b5b9215439085efb390d4535a9b091cdb3429d37
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-06 14:06:10 -0200
Commit message:

 Add ffpe information


Former-commit-id: 6bd7822f1b6766e2ebea671fb3109c787e79e5d3 
Package: TCGAbiolinks
Commit: d81320db4f492c519df91586b32ca979640de508
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-03 13:51:15 -0200
Commit message:

 Reducing test problems.


Former-commit-id: 76190eba3a9824aa23b671673278155b7c1c9ca1 
Package: TCGAbiolinks
Commit: 4ae8d126c1d3aa2cd2efde9d861a188fb8d24455
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-02 07:18:55 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 7c3d626bde6675f943cfc7d82e6a226aaff7f202 
Package: TCGAbiolinks
Commit: 8d7e484ee9deb242c30b268bec4c1d851e030ecb
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-02 07:18:48 -0200
Commit message:

 Remove warning


Former-commit-id: 3af2e0ee8b7bb1dcaa131b20675f11eea1848fc8 
Package: TCGAbiolinks
Commit: c95f4152970ea34277e277a78663e177be9aea48
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-11-01 20:46:47 -0200
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 82793868e43463794dbe66ea9c4c4145cd8611f8 
Package: TCGAbiolinks
Commit: 2362d9900bb0db4d428962448c661e4a5503455a
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-11-01 20:46:34 -0200
Commit message:

 version bump


Former-commit-id: f0c4f9a5f2ba6cd5063fa0c93d4b887de0c473e0 
Package: TCGAbiolinks
Commit: 0ceee6d18e489381059208a59e55fb2a469e6920
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-01 20:45:50 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: ea735062b149108e2433192a272c1e1c6d5cc563 
Package: TCGAbiolinks
Commit: e9c18fb8e0e665cb1cdcbcdb193a26a120cbf397
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-01 20:45:44 -0200
Commit message:

 Adding missing packages to travis and appveyor


Former-commit-id: 4824bad01a1856b2f895fd5345f73c6e89786332 
Package: TCGAbiolinks
Commit: f41a6929b0077dfaa8c61dba3ecc52b681bd72c7
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-11-01 20:04:49 -0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/TCGAbiolinks


Former-commit-id: 733985663bf67f61f725c43bee82db6132fbe7ea 
Package: TCGAbiolinks
Commit: f365d9b6bb2bec352373954c708f332c57b8f58c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-01 20:03:18 -0200
Commit message:

 Improving vignette


Former-commit-id: fb48d49fb1e938f19451681c80b5e2f44fe3d4cc 
Package: TCGAbiolinks
Commit: 680aeea76233d6fd36ea6b27919737a9b662a6f8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-11-01 20:00:47 -0200
Commit message:

 Fixing object in vignette


Former-commit-id: c14e125ee535c7542a3750e571673d6130c61a90 
Package: TCGAbiolinks
Commit: b1fe76c150323df46ceac6d217f3f61fc13b6b50
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-10-30 12:54:11 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch


Former-commit-id: a523772defc51b9b15294f92b358a13b0e7b0865 
Package: TCGAbiolinks
Commit: 230b4b6591d63cf1ea026ffc75991530e3c9480f
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-10-30 12:40:53 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch


Former-commit-id: fba222764d37bc901d3fab8eb92ed1e96e04c459 
Package: TCGAbiolinks
Commit: e430fc2251f43f376c8995bd5bb95543844a661c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 21:25:33 -0200
Commit message:

 Adding maftools


Former-commit-id: 119e601e7b2e8490930bdfdec10c5c25ecfe377d 
Package: TCGAbiolinks
Commit: 1501841d8ee4dd4564fa303098ba370cfe22511c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 21:21:34 -0200
Commit message:

 Reducing data sizes


Former-commit-id: e8b2a9f55a71e28b165aebdc798f692d0da0779d 
Package: TCGAbiolinks
Commit: 26eaedd54e50091f23d70e6f57f919554de26fb0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 21:17:49 -0200
Commit message:

 Update doc to remove warnings


Former-commit-id: deca2a8234bcfd77d4ea6619026399331a799323 
Package: TCGAbiolinks
Commit: 85410355ec9924463ab41da6638f6320421a0dc3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 21:16:52 -0200
Commit message:

 Removing warnings


Former-commit-id: d4f55f5c4799bf85e8fa267c17b9776a008805a8 
Package: TCGAbiolinks
Commit: 277d7c6277467146516ad7c08de49da69e6bbfb3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 21:12:00 -0200
Commit message:

 Bug fix if all values are 0


Former-commit-id: af6ae834ea3bbf535eacbbb1078f8ac197ced1d0 
Package: TCGAbiolinks
Commit: 1d49cf4f9aeb40f6505743919f2281f14a06e73c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 20:29:59 -0200
Commit message:

 version bump trying to remove errors from vignette


Former-commit-id: 194d5b2035a48a87520fe39ea23a827fdd37feeb 
Package: TCGAbiolinks
Commit: d58b6186b7790ce4300751a5b03c7bde699492ae
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 15:33:42 -0200
Commit message:

 bug fix


Former-commit-id: f1927b4008dee52fd802e91780b9635fb660a2ef 
Package: TCGAbiolinks
Commit: 641d75890f3415af2f22a0203509b77daa28a86d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 15:26:58 -0200
Commit message:

 UPdate data info


Former-commit-id: 6da30e8076f4513969025d9b26d4919397c8f2a2 
Package: TCGAbiolinks
Commit: b07bb18adfbac1698d1a3a3b8e7227a2b805dcbe
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 15:23:43 -0200
Commit message:

 Add man to objects


Former-commit-id: 56a57b520616798f520ae40ead3b89dcae64cf9d 
Package: TCGAbiolinks
Commit: b8096079178c6fcbdc5c356af511944d3cbf1ec5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-29 15:18:53 -0200
Commit message:

 Reducing maf download


Former-commit-id: 1add5506c1904bc0093e31855489a81097b0e53a 
Package: TCGAbiolinks
Commit: 81ea667a1e2906c6d8bae607e7ccb4e4730c4404
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-26 18:00:13 -0200
Commit message:

 Adding data to reduce download errors in vignette build


Former-commit-id: 6c6eb633c03b3ee902ebfccd01604c5fcb4002d0 
Package: TCGAbiolinks
Commit: 2b7441df89657c55a7697255a5254a2433f8c779
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2017-10-26 21:52:20 +0200
Commit message:

 Last edits
-edit function name: TCGA_MolecularSubtype
-correct for “Patients” as batch factor
-vignettes added


Former-commit-id: 853143878a8e0be4588965a0132f1902074b3657 
Package: TCGAbiolinks
Commit: c888aae48054a41908bbf3d1f808bfade857189c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-26 10:27:21 -0200
Commit message:

 Version bump


Former-commit-id: ad8ed6d96ec905dbf770f66127821ac33344eaae 
Package: TCGAbiolinks
Commit: 1bf11c8c13429f4aab1c202c87ab7ece036054d8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-26 10:26:49 -0200
Commit message:

 Improving vignettes to prevent download failures in bioc.


Former-commit-id: bcd09fe37d0d35229ef9529e1e8a438ced1bb74a 
Package: TCGAbiolinks
Commit: fa7a0c33a8db9b480b0cd68414f5eb33d0f9c0a3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-26 10:09:30 -0200
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 71bda72f15a7db3976768355323e02ab0c54739e 
Package: TCGAbiolinks
Commit: 31f5dd385d5dc19a1ad55f18ef8b07421f3cb9dd
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-26 10:09:23 -0200
Commit message:

 Fixes #146


Former-commit-id: 2fbef30fec8b43f06024b8e1a7c4f2b468c3a451 
Package: TCGAbiolinks
Commit: 23b4038db5d23b8cb75b1a088f32e1e2112891c5
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-10-26 09:09:20 -0200
Commit message:

 version bump


Former-commit-id: ceaafcb356a83d6314808f6e0e4772d006a756bb 
Package: TCGAbiolinks
Commit: 5229fb9241c4b277124874c55b631800a960e4e6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-24 20:06:04 -0200
Commit message:

 Data from API for projects was changed. TSV model does not work anymore.
Closes #157


Former-commit-id: 2ab9ea63b0c423d1a2c895d8e7e42c896fdb51f1 
Package: TCGAbiolinks
Commit: af4add15c55dbb631702d3f8180fb8e2159d020b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-20 10:50:04 -0200
Commit message:

 Adding esca to coldata prepare


Former-commit-id: 50f010d2ef81e90f253c83e1dd24e0ba1c00443e 
Package: TCGAbiolinks
Commit: 1d1fa2d95accc779e66d7d28a183670897a35cdf
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-10-20 10:41:19 -0200
Commit message:

 Add esca subtype table


Former-commit-id: 9fb307a4ce99ebfa8b34060e239279d5b0af45a6 
Package: TCGAbiolinks
Commit: f88ab11df69c22cc712bc0ab408fbab700e606e8
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-09-22 10:36:42 -0300
Commit message:

 update vignette


Former-commit-id: 08f685e4809ec4e62f3a10d789eeacb6013606a3 
Package: TCGAbiolinks
Commit: d0cc6f84fcfea655cb5e5b659ba979ca3881087f
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-09-17 15:55:11 -0300
Commit message:

 removing unused data


Former-commit-id: a25f4064fd2cb55c37e2e16e2d708165bd629164 
Package: TCGAbiolinks
Commit: f6c9e5b304b9a71996a5245935b263bb6b1c27ac
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-09-14 21:07:50 -0300
Commit message:

 bugfix


Former-commit-id: 95ace942b5ae7bec681734e2f5ba452297aab6d6 
Package: TCGAbiolinks
Commit: 9babb9dad39251cce49c65956a61f837df4ed517
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2017-09-14 16:34:59 +0200
Commit message:

 -Update Tumor Purity function to ignore NaNs in filtering condition.


Former-commit-id: e02869fddec1c02132ffc324dde83282b2e12194 
Package: TCGAbiolinks
Commit: b3dfa07e4b80b33974d19c556c8958a6609b036a
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2017-09-14 11:58:48 +0200
Commit message:

 -corrected design matrix for edgeR
-added roxygen2 documentation for two datasets (Tumor.purity & Pam50 classification)
-documentation example for TCGAPam50


Former-commit-id: 50a4741ccc0939cfe92dd89e86bdc35ad1cdcdaf 
Package: TCGAbiolinks
Commit: 1ff69f9477bc4eaaafb47e3f342bb88d209d0a06
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-09-13 15:09:31 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: e977ac2a42628c5ffe8ea5f49b36bb23808bf98b 
Package: TCGAbiolinks
Commit: 24dd4053eda3bf33753fc4b14139d583590bf731
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-09-13 11:00:29 -0700
Commit message:

 Bug fix. Closes #145


Former-commit-id: 1ce47d36bb1ae9d95656b4454a3e9b54ce2a54bf 
Package: TCGAbiolinks
Commit: 2b24c23378308f118a570575ec10c34b58e677f7
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-09-12 19:25:09 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 3d31d6b74b25432502f031732f429521b23aeaa2 
Package: TCGAbiolinks
Commit: b809997f3b324118f6958717a45b8d9604704a0d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-09-12 15:15:47 -0700
Commit message:

 Fixing add mutation and gistic information
Closes #143


Former-commit-id: bff9ce41a0f7e0ea0a6355f9fb1c561137de936f 
Package: TCGAbiolinks
Commit: 2ff32fdf92c71ea5c3355d0820ea9d440fe699fd
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-09-12 09:39:35 -0700
Commit message:

 Removing alignment information when creating SE for raw counts data. Closes #142


Former-commit-id: bf51f006857b12dfd4409c3a2cf7ee32ba326af7 
Package: TCGAbiolinks
Commit: 318fffe1fbfeef4d18e524e3affe115061294c1a
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2017-09-12 17:08:33 +0200
Commit message:

 -Namespace gridExtra rbind.gtable updated to “gtable_rbind”
-fixed vignettes


Former-commit-id: e9d674fa3b0c9cd11a46375cb89a7a4a4e9bbc0b 
Package: TCGAbiolinks
Commit: 05be9990f28153f1043e743dcdbb16ac97a3c367
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-09-11 19:28:32 -0300
Commit message:

 version bump


Former-commit-id: 3a9d1c2a3e65a174cd20a7526d447ac5dd628f25 
Package: TCGAbiolinks
Commit: ab6c0830f640993a4b9986c931c4673278620490
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-09-11 15:19:49 -0700
Commit message:

 Correcting function name


Former-commit-id: 7136506d40765ee68c6a9b1657de04a100060568 
Package: TCGAbiolinks
Commit: f9aa9126b7c061b229627ca09b02f23cced3ad6e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-09-07 21:29:43 -0700
Commit message:

 Removing wrong comments


Former-commit-id: f3af27be6b42f5b2403dcb72eb036bd63e83305e 
Package: TCGAbiolinks
Commit: 9604f5b039a6629a4f832b2dd646f027d0741ba3
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-09-07 15:28:13 -0700
Commit message:

 Removing warning


Former-commit-id: fa604c4b9cfff84d2b9cb6e709d07427adefe1bd 
Package: TCGAbiolinks
Commit: b940e3374d7f535b662bf01f69140b9b7324ae20
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-09-07 09:01:19 -0700
Commit message:

 changing chunks.per.download to files.per.chunk. Clsoes #139


Former-commit-id: 63b6d11c881e15b265cfdff5ce5326297406fb52 
Package: TCGAbiolinks
Commit: 21f29dc747fe88ec50d919c22b21fc710bdbd744
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2017-09-07 01:57:23 +0200
Commit message:

 stable version


Former-commit-id: 3fc84506d66037bef15f25995afec423251cd639 
Package: TCGAbiolinks
Commit: 6122c74d76e2ebf8a685d4927d5af68dcdf100af
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2017-09-07 01:47:03 +0200
Commit message:

 Revert "Version ready to be tested:"

This reverts commit 94b665c1e7ebc280597848bb6e876209d37e3121 [formerly cd97f939439526945a7824341490e3822ba611c4].


Former-commit-id: 7f191e2df9014d68720dadf2c5ca941360dba876 
Package: TCGAbiolinks
Commit: 94b665c1e7ebc280597848bb6e876209d37e3121
Author: Simo Mounir <mounir.mohamed92@gmail.com>
Date: 2017-09-06 00:11:23 +0200
Commit message:

 Version ready to be tested:
-new design of TCGAanalyze_DEA
-TCGAbatch_correction: voom transformation and exploratory analysis using ComBat
-TCGAtumor_purity to filter TCGA samples according to tumor purity estimates
-TCGAPam50: returns dataframe with subtype for each TCGA barcodes
-UseRaw_afterFilter: recovers raw counts after gene filtering and normalization steps
-TCGAquery_recount2: Querying data from recount2 project

Former-commit-id: cd97f939439526945a7824341490e3822ba611c4 
Package: TCGAbiolinks
Commit: 35f1c666198c6d8c79193c2cb243d30b962df00d
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-09-01 09:43:14 -0700
Commit message:

 Update tests


Former-commit-id: 75d4904fb863ec7e8a6990f7698dfea58452a8b6 
Package: TCGAbiolinks
Commit: 44d5a25265c35eb42ab2741781153b7d7146d9c1
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-21 14:16:22 -0700
Commit message:

 Removing data not used.


Former-commit-id: 0ac17ab91992f307abbc3799ea6efe980a4fabb6 
Package: TCGAbiolinks
Commit: c98620df8cc444a483c53dd4135e3fef06846409
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-21 14:15:18 -0700
Commit message:

 Removing warning in man


Former-commit-id: e548b333034a2ffe16018f4f60953cbfcb502b72 
Package: TCGAbiolinks
Commit: c6290b957a152bcf6b7a85c690f6c2218bcf64a0
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-21 13:01:00 -0700
Commit message:

 Test bug fix


Former-commit-id: 43459d58e52223690ff8e227825a43a01dfc8b8c 
Package: TCGAbiolinks
Commit: 9f579f63025c3334e0c990b8ac2cb0d19401dbb6
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-08-21 15:25:31 -0300
Commit message:

 version bump


Former-commit-id: 30ba47f36535d57f349777cbe07dd7510c764579 
Package: TCGAbiolinks
Commit: da2e82f6a093f3bf12ec97f5b4e0beb96f4b2da2
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-21 11:16:25 -0700
Commit message:

 Improving doc


Former-commit-id: e06ca2179784ae0668879d6679d23d1f9b69b33b 
Package: TCGAbiolinks
Commit: 060619f80d7f4cb6620876edf59f70fad4336731
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-08-21 09:21:59 -0700
Commit message:

 Removing get TSS from export


Former-commit-id: fc15d75708dc2e4ca3901fdea0ace7a807622f27 
Package: TCGAbiolinks
Commit: 12fb4c471a75b724b54ee229a3fc0c00ddf12ddb
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-08-21 09:14:18 -0700
Commit message:

 Bug fix


Former-commit-id: 01be20513743a241d9012f7f6b28b51a6840ed3f 
Package: TCGAbiolinks
Commit: f46f97b7a9f3e92da37e2c91c900a67901b661f5
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-18 11:27:17 -0700
Commit message:

 doc fix


Former-commit-id: 9518c81ba0b7c62fa6bfa0d42e0abe5fee7b2114 
Package: TCGAbiolinks
Commit: 4eac2b97bd53d62004e4e22147acd62a15fc4314
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-18 10:26:32 -0700
Commit message:

 bug fix


Former-commit-id: 3b8ef31a0633b094f55970ec318c1082da6c1879 
Package: TCGAbiolinks
Commit: c5c53bb7cf070f4b18364c5207cf011b5f464630
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-18 09:51:58 -0700
Commit message:

 Bug fix starburst


Former-commit-id: 31b9627e5771a1d63db157971fd92cc7eb44df83 
Package: TCGAbiolinks
Commit: 3c7a2742f5fd348f11d2d1120f7e8d666ca8503f
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-18 09:03:23 -0700
Commit message:

 Fix doc


Former-commit-id: c66e26a66b2ce424281e11a148e6793c69f96e2c 
Package: TCGAbiolinks
Commit: dee80b809523ffea73d9df0a67244302463e4a05
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 17:50:45 -0700
Commit message:

 Undo wrong commit


Former-commit-id: 45d72cf5207a9169cb9d45cd84f9b30b014bf8d4 
Package: TCGAbiolinks
Commit: 2761a86eed701e770e5e4beb25b0f97d82dc1395
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 17:47:52 -0700
Commit message:

 Bug fix


Former-commit-id: 754740e83177623d6f0b6e03edb12aee1d04cbc8 
Package: TCGAbiolinks
Commit: cdc3dc2ab388225ffb8276573ddc54ebc491c042
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 17:47:23 -0700
Commit message:

 Bug fix


Former-commit-id: b0e8ad51ae29294889a26a412b2c4adb2f9d9586 
Package: TCGAbiolinks
Commit: 3682d6572d7ab262bbf939f88628e4e114eab0ad
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 15:21:06 -0700
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 83edc8d26f7b00227479e49d24f1d681e2542b99 
Package: TCGAbiolinks
Commit: 1ba0532663c5e112fa8b861ca3bf7352f12db601
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 15:21:02 -0700
Commit message:

 Fixing internal function


Former-commit-id: f2ae923076824ee7c62a09cbf9ba082c9cf0ac0a 
Package: TCGAbiolinks
Commit: cf326b1232fb33cafea1c3bc61a31bd6b0d25d90
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-08-17 13:13:45 -0700
Commit message:

 Fixing DESCRIPTION


Former-commit-id: e12f7e29ff87c8e30af970e13b3c4314ae75992d 
Package: TCGAbiolinks
Commit: de74b837637864c86190b9d5ad73876ee2e94804
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 12:43:53 -0700
Commit message:

 If already downloaded, and one chunk has been downloaded it should not redownload it.


Former-commit-id: f765f3eefdba9485de1862714f65eab86ffd8617 
Package: TCGAbiolinks
Commit: a127f9dca84254ae51c2893bad4bc1f063ef8c3c
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 12:38:06 -0700
Commit message:

 Remove old man


Former-commit-id: 904edcbf096ed6593aa15dd8be42eb872c0a27e2 
Package: TCGAbiolinks
Commit: b0541605c14b48780c78d66915077f319031b8b2
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 12:37:20 -0700
Commit message:

 Fixing download if several projects


Former-commit-id: 48e99750865e363a0cac8a8b80783829d7953206 
Package: TCGAbiolinks
Commit: 246c704c57eaf520e7af9078bce8ef4e6d3d6ac1
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 11:15:14 -0700
Commit message:

 Fixing starburst plot to map for each probe the nearest TSS (distance is now the distance to TSS instead of gene). Level of expression are in terms of genes (ENSG).


Former-commit-id: d70132af2314a1f3aebd1eb923f3d4012d6a1bf8 
Package: TCGAbiolinks
Commit: 62b901304a4f1ced68ddf873a96ced1335c79d8c
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-17 10:38:39 -0700
Commit message:

 Fixes #129


Former-commit-id: f27968f2f10e772f338996e9cbee0d626e5c82e7 
Package: TCGAbiolinks
Commit: 9fc2b3f07ad96d9e26beeab7bae9389a27c3b2e5
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-08-17 02:04:15 -0300
Commit message:

 removing docs


Former-commit-id: b3b6870e0a9d5743748919df7f95a0ecb201e15c 
Package: TCGAbiolinks
Commit: 859f349fc4056d17ca513bd15a9d938fe96aff34
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-08-17 02:03:51 -0300
Commit message:

 Merge remote-tracking branch 'upstream/master'


Former-commit-id: d3d206f6787b87115ec248d7dad6cf00f665782d 
Package: TCGAbiolinks
Commit: 6701c15de792ea436f3e376aad1cd3881a83e17c
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-08-17 02:02:27 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: b12bab664322b5668ba25c5a01cbe56af3fa9e2f 
Package: TCGAbiolinks
Commit: 6751178614b712856df70ce71e26775a748503df
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-08-17 02:02:14 -0300
Commit message:

 removing example


Former-commit-id: 43d5a6c64c65504b5adfc454d161f974b2f1608a 
Package: TCGAbiolinks
Commit: 3881eb0b266afb4e7bc51ca9ef49c820bfc13813
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-08-12 21:51:56 -0700
Commit message:

 Closes #125


Former-commit-id: 9a3af647146965085fda8782c53013175d927d67 
Package: TCGAbiolinks
Commit: 278edc8f7ec20d6a433a98eaff3cce88a147d57b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-08-11 11:38:57 -0700
Commit message:

 Merge pull request #127 from romagnolid/patch-1

fixed typoes and message

Former-commit-id: 7b6af61505322a6c97b37f9bdc741e1398e8251d 
Package: TCGAbiolinks
Commit: 1b8e32a6d575962c3b7557872b11bf3cd4512ac0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-08-11 11:38:09 -0700
Commit message:

 Merge pull request #130 from romagnolid/patch-2

Update internal.R

Former-commit-id: d2bec9b5af8923b8ee624aafead2d7048ac775c4 
Package: TCGAbiolinks
Commit: 1685aebac9ce76cdd4f3b38d266c6f5efa1f89c9
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-07 17:14:04 -0700
Commit message:

 Increasing time for build


Former-commit-id: a2fe4720a2359447d82856bd43c9818059bae706 
Package: TCGAbiolinks
Commit: b2a18604c2a427f89fa8de8e641334e8da40a3c3
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-07 17:01:51 -0700
Commit message:

 Move folder was not working correcly for client download.As it used folder instead of the file.
Closes #131


Former-commit-id: 07575c33fb74ee6eaa9eb53e403efc4b362f0ba1 
Package: TCGAbiolinks
Commit: 39b8217852a027933d761d0b7eae41eb48166b41
Author: Dario Romagnoli <dario.romagnoli87@gmail.com>
Date: 2017-08-07 10:29:20 +0200
Commit message:

 Update internal.R

Former-commit-id: 9c9c7c41eb399cee3c1a9518f79a248d61653c86 
Package: TCGAbiolinks
Commit: 68a1ca449be5d8bdf3c6c3f82c64c86d545ab088
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-08-04 14:00:57 -0700
Commit message:

 Updating prepare and query to consider Protein expression archives


Former-commit-id: 4ef302f90d75d6676501983973e782ad3c4b0d72 
Package: TCGAbiolinks
Commit: 3634a6c9ad5a20f8ccb2df5aca025fd4697f54e3
Author: Dario Romagnoli <dario.romagnoli87@gmail.com>
Date: 2017-08-04 11:50:48 +0200
Commit message:

 fixed typoes and message

To avoid the display of confusing messages like "Downloading chunk 0 of 0"

Former-commit-id: a74f40fe98f85b284fb7e44e85acd05c6d8dcdda 
Package: TCGAbiolinks
Commit: 4c324677cb2c446ce4adefa37ac623bb6f52ef5a
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-31 17:52:07 -0700
Commit message:

 Improving gistic function from firehose


Former-commit-id: d1cd118b214d038e737274b585f8c80eb431676e 
Package: TCGAbiolinks
Commit: c74fdff3a1ebf2b4f38402cc5c1ff0997ce93734
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-31 12:01:09 -0700
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: ccd12e4fbf8465cffe34a1e59bfde1ccd6afce81 
Package: TCGAbiolinks
Commit: a46fd71bf738c0aabf9e9020fd0a25a5a0ebb65a
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-31 12:01:04 -0700
Commit message:

 Adding function to get data release.
It can be accessed with getGDCStatus()$data_release
Closes  #125


Former-commit-id: 030a5ffb9388a3bbe06a5e2e8ef8aa96a22beb82 
Package: TCGAbiolinks
Commit: c62979eaff31f2d3101a914f858e9cd706d48266
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-07-31 15:26:58 -0300
Commit message:

 Testing repeat if chunk failes


Former-commit-id: aa17162deec376a1b3e93e180b725e47a6872878 
Package: TCGAbiolinks
Commit: 2a6c7b37f29a63a0af53edd02087b4e4577f80ac
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-07-29 00:57:02 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 2e8265e74de546b7aaece49de11225cb8fe2947c 
Package: TCGAbiolinks
Commit: 5e3cda91f39af4284af92237e2317be03baa1bb9
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-07-29 00:56:45 -0300
Commit message:

 Closes #124


Former-commit-id: a1dfa3bce8dd094e866cf05e121b570141e856d4 
Package: TCGAbiolinks
Commit: 0929135b6c11463536cfbec3a04f2ec9aa023b71
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-21 16:57:51 -0700
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: d7eb94c5b51218eaa2c6d4608b5b0773144da5ce 
Package: TCGAbiolinks
Commit: 353b6c5cb803d15e65b7a9b625564cff3f93a099
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-21 16:57:47 -0700
Commit message:

 Give option to change the ggtheme


Former-commit-id: e614a6e169df18d2c4821b7321f4568f3845f5ae 
Package: TCGAbiolinks
Commit: 7ee91eb8606a8831a5d1effc2dd5a668f3b0379c
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-07-19 17:21:20 -0300
Commit message:

 Travis fix


Former-commit-id: a2456db68eb56e9df6183ba710b0e9bbe6fc865a 
Package: TCGAbiolinks
Commit: 6f13d9acf7f5638c3e3b40798f2c8a480a868ced
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-07-19 15:31:18 -0300
Commit message:

 Adding another try to get barcode information


Former-commit-id: 402953d2b8b11647e0b95f10b3a19ffeea07b247 
Package: TCGAbiolinks
Commit: 705e816cb73b8274299bb4c9ac18a3056dee33f5
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-17 17:15:54 -0700
Commit message:

 Removing


Former-commit-id: c8679628f88d3134fddbdb50b11255b9a52ce70d 
Package: TCGAbiolinks
Commit: ba593a66e742303b6ecd135ede9cfff58e486479
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-17 16:46:47 -0700
Commit message:

 Adding elmer.data from github


Former-commit-id: e44046700c67550962d609bc0501c4fa40fe1e8d 
Package: TCGAbiolinks
Commit: 1e9ea03c11226f53fbfd7a79beae7f99c7c72eec
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-17 16:43:24 -0700
Commit message:

 Changing osx image


Former-commit-id: 3eef6ae1e3803bf946a5a2cb2a838996261a3dc6 
Package: TCGAbiolinks
Commit: 73bd8b495fbd823e3f92661c7133ea8095aea3aa
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-17 15:31:57 -0700
Commit message:

 Fixing travis


Former-commit-id: 2dfbb215dc5f2de840c35b8389292b1505e12f9f 
Package: TCGAbiolinks
Commit: d97f748122ac4b4e8d28aee47b679ad016aa9dde
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-17 14:47:37 -0700
Commit message:

 Fixing namespace


Former-commit-id: 42e1b3fe5f7f0e644e065348f0c327b54787cce3 
Package: TCGAbiolinks
Commit: 407d140af2f706e484751d5d98d4e33a18147864
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-10 17:07:31 -0700
Commit message:

 Changing the logic, if input was incorrected just request without filtering data. Closes #114


Former-commit-id: f762c37652914c33a6cfef7ad0af226942b4df33 
Package: TCGAbiolinks
Commit: 5df04909211f11a7451bd1be82d4109cc27f20fb
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-10 16:55:33 -0700
Commit message:

 version bump


Former-commit-id: 85f787294899cbdbd45da745194f04d718d8eec8 
Package: TCGAbiolinks
Commit: 6202a8f291ae8dc9e6ffe13732954c8d481b63bd
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-07-10 21:01:20 -0300
Commit message:

 Fixing moving file due to cross link device. Closes #112


Former-commit-id: 8e2084a6e1fa2eb239b10ea7d97759be98df35d8 
Package: TCGAbiolinks
Commit: 2e18f0a0f8950cc4edf1b829bc1142c86e96ddc6
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-10 16:33:45 -0700
Commit message:

 Adding error message if file to move is not found


Former-commit-id: bb03cc77eed1a0d414a44c7803414cc5f2f994ad 
Package: TCGAbiolinks
Commit: e61b8d1599ce232132b15aec2317fb1834c2ea00
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-10 16:07:56 -0700
Commit message:

 Fixing name


Former-commit-id: 990508ef168bd4d5eb31abaabadbe7d47542731e 
Package: TCGAbiolinks
Commit: b6ed3993ad11adda48e32f7cd81624ce3a417c35
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-08 13:40:35 -0700
Commit message:

 Removing examples


Former-commit-id: f36faad3e8d4dd2bcf03ab2aca52528a8e825f3e 
Package: TCGAbiolinks
Commit: 5a4a6eaa927971ba504ef6a637f63643728313e0
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-08 13:05:27 -0700
Commit message:

 Version bump


Former-commit-id: 0eb9835fd7a06a4a69a4b6dc1154d5c2ffc95e64 
Package: TCGAbiolinks
Commit: bf3fa6d21f96e3cbde31f738db22d60e84f6c75f
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-08 13:05:06 -0700
Commit message:

 Adding functions to suggest


Former-commit-id: c8da6d6bd5f66095490160fb1b49eaf4a5903553 
Package: TCGAbiolinks
Commit: 79af500f29f231a7d081d01cff905705f61e4fc0
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-07-08 12:51:06 -0700
Commit message:

 Bug fix


Former-commit-id: 7202d9f60f669c2c555f7d6713669d56fd774a28 
Package: TCGAbiolinks
Commit: d79ae74e9ee84c02ee41f48fd59058afd5307a8d
Author: tiago <tiagochst@gmail.com>
Date: 2017-07-02 07:51:59 -0700
Commit message:

 closes #111


Former-commit-id: 07f507793235980076a3dd3cb658c27e09a9a656 
Package: TCGAbiolinks
Commit: 468f6f5a805efb164fd789cce95d54ab62591d40
Author: tiago <tiagochst@gmail.com>
Date: 2017-06-28 15:51:28 -0700
Commit message:

 Reducng request


Former-commit-id: 6be557a8924e44a87463d05027e982adee356951 
Package: TCGAbiolinks
Commit: 21795ca09e885c29bde3dcb46d0d4a01a313b282
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-06-13 17:09:13 -0700
Commit message:

 Removing useless line


Former-commit-id: 2c60481926592ce1a0c08c6229835d4eadd2b57c 
Package: TCGAbiolinks
Commit: 668475a1e54a3e8301258b66e4d1baee1f6fe650
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-06-13 16:51:45 -0700
Commit message:

 Fixing appveyor


Former-commit-id: 81a7825076b48b2a2a20b56620d807bbf86103e1 
Package: TCGAbiolinks
Commit: eac91ea5f7bf2e38e7cce3acffef0c5a1f69b681
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-06-13 16:42:25 -0700
Commit message:

 Packages in only one function were moved to suggests. This will make the package load less DLL


Former-commit-id: 104b45bf7c93801e480c0603b93ca338bb29c3b1 
Package: TCGAbiolinks
Commit: dd0fa36ccc402c6198ba48c1d992318985233bff
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-06-05 12:48:54 -0700
Commit message:

 Fixing vignette


Former-commit-id: 5cffda960de6fc77c02b1995256ca973dcc24f41 
Package: TCGAbiolinks
Commit: 75868d4bc3439142557badd099d1f022b1931af4
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-06-05 12:41:40 -0700
Commit message:

 adding message for genome of reference.


Former-commit-id: d05c97d39fd874bf0ea648208698eeb059d50967 
Package: TCGAbiolinks
Commit: 0360b2f679f3ab728dec5e0a52987180fed4c7d8
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-06-02 15:47:59 -0700
Commit message:

 Reducing json request size


Former-commit-id: 10d1c58c486050c5d07e611cdba62eee6f4db6c1 
Package: TCGAbiolinks
Commit: 7add10c06aa1615e464284b4094880a098bf3ef2
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-31 14:41:55 -0700
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 92aff4a1b36638004cbf3634ccc3d09aa67abbfb 
Package: TCGAbiolinks
Commit: 8031e8e8a137bedbc06eac2e03a823e1414ddc5f
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-31 14:41:50 -0700
Commit message:

 Adding message for error in trycatch


Former-commit-id: 52a38b107caa743430c7c00968dfce4e63dc6605 
Package: TCGAbiolinks
Commit: 98b4fb90166d4faa63f677ce0cc59d6054b76dc3
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-23 20:21:29 -0300
Commit message:

 version bump


Former-commit-id: 66e9cbaaac01b3398bac0c0d9f844e64e9a15ef0 
Package: TCGAbiolinks
Commit: 2b1dc68e7d5814acb3d77d101bdf47fb2e17901a
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-23 12:24:54 -0700
Commit message:

 Changing parsing for follow ups. It will parse all versions and identify the version on the first column.
closes #93


Former-commit-id: 55408ea5df08f7636616bd291217a754a37ad2fe 
Package: TCGAbiolinks
Commit: 14183c828f8fb0c1e236b0c8aba36959a5bf7485
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-18 15:41:49 -0700
Commit message:

 Adding information for annotations #91


Former-commit-id: c6e277ed1776cbec19398a33737923b202d38569 
Package: TCGAbiolinks
Commit: 576f511eb91ce2f2f20e23f29fccc1c3f4decc52
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-17 09:38:43 -0700
Commit message:

 Using same nomenclature for target and tcga.


Former-commit-id: fc11e2d15fafa34ba21e1c4fcfe591e6e505b0cc 
Package: TCGAbiolinks
Commit: 7639f4298d846257ab85edddbcfc14d4acbb26c2
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-16 17:44:06 -0700
Commit message:

 Bug fix in colors for ggrepel.


Former-commit-id: 365704889f8568d680839ebc1367eec991536724 
Package: TCGAbiolinks
Commit: b0fbb33bebdf301a20cba2d03aa865a229c7486a
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-15 14:07:13 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: ac0d57df545425051fc40e2f06d4c4653e8a3d31 
Package: TCGAbiolinks
Commit: 5068fb5efcd2768151a08882a8f6746b2c4dff13
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-15 14:04:54 -0300
Commit message:

 fix man


Former-commit-id: eadee5a7020b99c30424740d89921dbc0a351f69 
Package: TCGAbiolinks
Commit: a68f1e26879eda5bedfc476a26117af5b1901f94
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-12 09:07:29 -0700
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 192ac18e34b8e71816c00f02cfda0257640fd66f 
Package: TCGAbiolinks
Commit: a010ff753eb4832620b8f45278fbb5fbe4f15107
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-12 09:06:01 -0700
Commit message:

 Removing redundant info


Former-commit-id: 1ce05194fb9e299aed296a4f1bc82f6b1298e94e 
Package: TCGAbiolinks
Commit: 78f77660e6d6509b7bc5973dcd30536e057b09c1
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-05-12 09:06:01 -0700
Commit message:

 Removing redundant info


Former-commit-id: e6ca5a926e6fde07c53ae554a7ff25ad5b8a2b62 
Package: TCGAbiolinks
Commit: ea186a8f22abdb1189e709c312dd27614593f4da
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-11 20:31:32 -0300
Commit message:

 TARGET pipeline was fixed. Closes #87


Former-commit-id: 6ee66c148ed8fcef1d0077ade9059019efb3702c 
Package: TCGAbiolinks
Commit: 91a05f4c6d7fa6c1f1566547b6c0d309fd169a75
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-11 20:30:07 -0300
Commit message:

 Fixing preprocessing plot


Former-commit-id: a36f4f8fd244e19b471b04b95f86155a815675a6 
Package: TCGAbiolinks
Commit: bfb92dc9019d112c5327e716d2d5c3bfa6a9c977
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-11 19:41:56 -0300
Commit message:

 parsing TARGET barcode for TCGAquery_SampleTypes #87


Former-commit-id: 92d1d54b5f9c97ff079706801b1f1c173d9f6c9f 
Package: TCGAbiolinks
Commit: a00773140d0065eefd5769c3fb9806148055246c
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-11 18:17:52 -0300
Commit message:

 Update version to same numbers as biocondcutor


Former-commit-id: 8d47f60d939c9a5b10e0cb8eb6b417181e3abddb 
Package: TCGAbiolinks
Commit: 90a976bf8e35c31a3edd6edbf031c5d1effceae0
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-09 10:56:07 -0300
Commit message:

 Fixing target Coldata information. Merging was duplicating lines, that way object was not created.


Former-commit-id: 09c8ee6d138c22c35c2302fbe29752c74f69eb62 
Package: TCGAbiolinks
Commit: 41d3e060b0bf0a083f5da080a03bac172b251bb8
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-08 13:52:09 -0300
Commit message:

 bug fix. adding gene name


Former-commit-id: e88ce06c98d1a1eb15da73c5a3cd8f3a9102a73c 
Package: TCGAbiolinks
Commit: 2cc0b3a7d876cc71bdfd15021542803eb16d8246
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-05-07 19:48:11 -0300
Commit message:

 mapping ENSG


Former-commit-id: f4955d11849c57ef669fae43c3a83dca2048b9d6 
Package: TCGAbiolinks
Commit: f0cb5a26ade4273c94c27feabedba718f35dfe1e
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-04-20 15:01:16 -0300
Commit message:

 version bump


Former-commit-id: ed0e66875570a625f66499e7c69e4e4fd4b5916f 
Package: TCGAbiolinks
Commit: 4b15c562504ea809a3b8cdd3b17f1551215c0baf
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-20 10:55:11 -0700
Commit message:

 Fixes #83


Former-commit-id: 9f5b689a710f0fe8aee10e13772a4512ce1a47e4 
Package: TCGAbiolinks
Commit: e7c6d1f77f72f32a25374b724f4913ec2a23e259
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-19 11:28:30 -0700
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 2a2497ec54031ea7412756d91202ccff34b895f7 
Package: TCGAbiolinks
Commit: 95e8693ea0210e678980b33ed110836dba48b94d
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-19 11:28:25 -0700
Commit message:

 Get gene info as granges


Former-commit-id: 15ef37be419cec8c649fd61a71da0ffeff5ff212 
Package: TCGAbiolinks
Commit: a41508eb3d7bd956c1af3d670521c205a16c981a
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-04-18 20:15:26 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: b661dc835d1729f6c0bad61f3539d7d8d1455caa 
Package: TCGAbiolinks
Commit: a6b72a4a58b3d8f00b4e84b7bb1fdc9595258c88
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-04-18 20:14:52 -0300
Commit message:

 Fixing description


Former-commit-id: 1bc84c330003f1cdca726674f8e3ef1adaecb8a5 
Package: TCGAbiolinks
Commit: a30e0bcea9abd44c370b87e8f2f4510c4004a067
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-17 13:14:11 -0700
Commit message:

 Fix prepare if add.gistic2.mut is used for multiple projects


Former-commit-id: b6cb5c5170fb5bb24e4758caf999f9233d00cb45 
Package: TCGAbiolinks
Commit: 66db635d076079cb071c45037dfeb1055f63159a
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-11 10:37:15 -0700
Commit message:

 Adding missing man


Former-commit-id: 4e562e39c61d980bf19dbe922330024499dd3283 
Package: TCGAbiolinks
Commit: 4e31efc3d36d4ac7f86508beb1d67b30fc0f7fc8
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-11 10:28:40 -0700
Commit message:

 Remove warning and version bump


Former-commit-id: b57e16455471e9c16fb64c0321fdf5d1a821653f 
Package: TCGAbiolinks
Commit: 956e17cc4e7642e1036ab73cf9a3d7cb11acb16f
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-11 10:16:54 -0700
Commit message:

 Bug fix


Former-commit-id: 5ee8863cc59cfa4040a186b8ed7d1a4dbc257e9d 
Package: TCGAbiolinks
Commit: 42c275fe128939ca4abadf14fe6178063d1645e8
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-11 09:26:06 -0700
Commit message:

 Removing function


Former-commit-id: 04e75a0bc796294befe8e6423df281f9c459c985 
Package: TCGAbiolinks
Commit: e1d0e5d494ac58f1f57a9f532a56476ebcfac41f
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-11 09:12:24 -0700
Commit message:

 Automcatic downloads per chunck if files are too big.


Former-commit-id: c9cda569f459a106efcfca8c2766e3b309c7abf4 
Package: TCGAbiolinks
Commit: 4a4ffa7a6b51ca985a480589250c46e4550715ff
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-11 08:57:17 -0700
Commit message:

 Code refactoring


Former-commit-id: bb8890c3a370a6c40d7c24736e8c5964bf72472e 
Package: TCGAbiolinks
Commit: 2ef8919a797f06452c8b5375300f62bd34bda153
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-10 15:40:34 -0700
Commit message:

 Set secondary host


Former-commit-id: 39265220f7cfeb677c3133f13214ffc4abf6df91 
Package: TCGAbiolinks
Commit: 523612e0de0c1b3aead8d6c9b8f49474fb563368
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-10 15:31:06 -0700
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: f014cd85d816966d1b0d2092ba74f56a3ce4ed45 
Package: TCGAbiolinks
Commit: 4817f77037d9235ef7252c77fea273df616684ab
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-04-10 15:30:48 -0700
Commit message:

 Improving speed by requesting smaller jsons.


Former-commit-id: ca69ecd3abdc1b26e623de9923b05fa2bc16778f 
Package: TCGAbiolinks
Commit: 6bfd34129efd304360a7b1bcb2709e7edf258dd0
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-04-10 15:55:27 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: e830244746bcea5d343edfb63e630c1eb78ab027 
Package: TCGAbiolinks
Commit: 98968c94be90e5089ac88fbb038e7b789fb8b280
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-04-10 15:55:15 -0300
Commit message:

 Fixes #79


Former-commit-id: 278509788c87cfdc82db60ae2094a36f62806d94 
Package: TCGAbiolinks
Commit: b0d320eab7030959d2371846be4efa629ea7e3e0
Author: torongs82 <antonio.colaprico@gmail.com>
Date: 2017-04-07 22:02:56 +0200
Commit message:

 Reducing size of the figures


Former-commit-id: 24a05a36712f4481342547619f6cdbe82ba23935 
Package: TCGAbiolinks
Commit: 7e014a8cbc1b9def95de47dc36f8718b6aedb4cf
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-04-06 13:11:13 -0300
Commit message:

 Adding support to MSI-Mono-Dinucleotide Assay


Former-commit-id: e87d8ce21ed31d2507fdfe16fd81e324ff80df5e 
Package: TCGAbiolinks
Commit: 28df6386e0247d8e7520bcebb32446d09c8fa85d
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-04-03 00:42:20 -0300
Commit message:

 Improving table in documents


Former-commit-id: 41861653116a13e489929a9ec0c2721c50268f5f 
Package: TCGAbiolinks
Commit: df8d4121f00e4002fc9ab914cc033d1df650f41e
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-04-01 13:05:23 -0300
Commit message:

 Fixing test


Former-commit-id: 06d3a5963d224d64d8819612dba43d0c8ff238b6 
Package: TCGAbiolinks
Commit: b07d4a041912ba741054ca88cd23efebc4a48744
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-31 16:26:35 -0700
Commit message:

 Version bump


Former-commit-id: c8745796b838461e03b06893a17391807e94d765 
Package: TCGAbiolinks
Commit: 855c31efda0b15e027efba462fbe9ff00d76c610
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-31 16:16:54 -0700
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks


Former-commit-id: 134857886747f5004d6d3212c67efbfb13a9246e 
Package: TCGAbiolinks
Commit: 8fa028bf05530b601e04e5f9fecc8d8465a3c6cb
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-31 16:16:45 -0700
Commit message:

 Adding fucntiosn from the workflow


Former-commit-id: 0c8ea4d88238ff5804bfb62346ea6881a6b8f6ba 
Package: TCGAbiolinks
Commit: 09f9e1a1a44bce844a663a054028e5ca9dc7b0dd
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-03-29 22:54:09 -0300
Commit message:

 Typo fix


Former-commit-id: a2d13002346dcfe1b049c6f434e0cdf73d138d5b 
Package: TCGAbiolinks
Commit: b9a3c9518e2b54190d09dd9c584e5eea22689517
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-03-29 22:26:22 -0300
Commit message:

 doc update


Former-commit-id: 6cf9332df12eefe4e946e228ecdb2c34f16f07f5 
Package: TCGAbiolinks
Commit: 4ac771fa0b0775e70cbdd0150df6bdde6848317b
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-03-29 21:18:25 -0300
Commit message:

 update doc


Former-commit-id: 8efe8cb77224e3451ba37d46110989da77ca225a 
Package: TCGAbiolinks
Commit: d78a41412190d70f8e2916d2d8250db6ea5192ec
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-03-29 20:59:41 -0300
Commit message:

 Update docs


Former-commit-id: ee06ebd407c4936a25a7f51561f7f912a43ad2c6 
Package: TCGAbiolinks
Commit: 08e235de841e2ecfacd325a892045941347a8521
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-29 16:12:38 -0700
Commit message:

 Update for clinical biotab


Former-commit-id: 19a80b598134804a6cf2af54631ed84c73535e12 
Package: TCGAbiolinks
Commit: 69920f91dd0bbf90d72f0654cb978d0b5d0286f5
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-29 14:55:21 -0700
Commit message:

 Removing block appveyor


Former-commit-id: 5ba06c79ad47ba9e2cc2d93604b76b9c30bc694c 
Package: TCGAbiolinks
Commit: 230261b3fdec786dc3917cd89da7624083f07da0
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-29 14:54:25 -0700
Commit message:

 Fixes #76


Former-commit-id: 68c279e7af37362f767b79bcd61224fbfe00038c 
Package: TCGAbiolinks
Commit: 2c8bc864d332c2ec740ecdda819869722ea5dbf6
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-23 13:21:27 -0700
Commit message:

 Closes #74 (Thank you @sahilseth)


Former-commit-id: cf103129a882164167ab8959d565247487e43aad 
Package: TCGAbiolinks
Commit: 48c2a3dad5ebd877c9a83248fbdef544cce8352e
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-22 15:04:36 -0700
Commit message:

 Update vignettte links


Former-commit-id: 7ee86cf14585f29b4fc096d6326914da05b2fbe9 
Package: TCGAbiolinks
Commit: 29a412d849ea76c29937d8190e7e872a0335dfe5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-03-20 22:33:25 -0700
Commit message:

 Update query.R

Former-commit-id: 4668c962cfba65fb4c3fc24ec681a5346e425f89 
Package: TCGAbiolinks
Commit: 0b79f47874e729f6384b55b0b6aebf0d9d2a856d
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-20 11:25:31 -0700
Commit message:

 Try catch to maf


Former-commit-id: 3dd9aef9eac4a8246d4a6167a380eb4847ac1588 
Package: TCGAbiolinks
Commit: be368122a3a0c6ed1e23bc268a085be43297e5c5
Author: Tiago Chedraoui Silva <tiagochst[at]gmail.com>
Date: 2017-03-20 11:24:23 -0700
Commit message:

 Removing second way of download of maf


Former-commit-id: 6a8e14faf1ba930600823465432b41448e68102a 
Package: TCGAbiolinks
Commit: 00ad8bf0de351954131fcec1907c689b27767ea1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-03-19 18:02:02 -0700
Commit message:

 Update internal.R

Former-commit-id: ecc102de265953421ca88d02ff54d0eee1ecf70a 
Package: TCGAbiolinks
Commit: e1c7fddb0720e99707350c70af86d87446419176
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-03-14 17:17:48 -0700
Commit message:

 Update prepare.R

Former-commit-id: a21c68e417ac8e96b9ce5d2b70cbc782d4130d4b 
Package: TCGAbiolinks
Commit: ce2cb08bc8c7da70695a6e57643da7b8d36f5e1c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2017-03-14 17:16:15 -0700
Commit message:

 Update download.R

Former-commit-id: 8621e882969fee69af7df2c86ce5bee65fbad7d6 
Package: TCGAbiolinks
Commit: b1c613efafbcc7500fd51fb89ba34c78316a5545
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-03-12 16:59:05 -0300
Commit message:

 trying to debug appvyeor


Former-commit-id: 94c5502811511b9dbea89d321419d991ffb70226 
Package: TCGAbiolinks
Commit: 471ecc03aa212b4bdfcb72f31e7b5ff4f7398dff
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-03-12 16:25:25 -0300
Commit message:

 Version bump


Former-commit-id: 405efd3d938f1686425706a5e87fd81f7e2e948d 
Package: TCGAbiolinks
Commit: 0abeb09ae946a9f5d7ce340ee88742fa0e5983f2
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-03-12 16:11:26 -0300
Commit message:

 Typo fix doc


Former-commit-id: d0d9178394e8a80728a5f1935f8e15e9425d6be4 
Package: TCGAbiolinks
Commit: 710491f1e00dba95ecb035cdac907d055bb8bb2a
Author: tiagochst <tiagochst@gmail.com>
Date: 2017-03-12 15:48:35 -0300
Commit message:

 Updating doc


Former-commit-id: b0fec191fb81a2aa8d408a8449d2f12139a8ee38 
Package: Rdisop
Commit: 3d8a66ec4488600019e6635d4f1cf049060c923b
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2019-04-18 15:33:28 +0200
Commit message:

 Explicitly cleanup *.o files
 
Package: Rdisop
Commit: 9a1c26e0c3e944dde8c68c2205e4e74f221bab45
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2019-04-18 15:26:10 +0200
Commit message:

 recover the clean: target in Makevars
 
Package: epivizrChart
Commit: 3ff08b55d6514b35ad64e0bdb7344fdb499ce3fe
Author: hcorrada <hcorrada@gmail.com>
Date: 2019-04-18 09:28:57 -0400
Commit message:

 version bump v1.5.1
 

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