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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: beachmat
Commit: b42a3e899e1ad3211978aa39bf44847aec25c60e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-20 13:33:46 +0100
Commit message:

 Updated CITATION.
 
Package: EnrichedHeatmap
Commit: 9b7331b14106102243067f944afe3bbb411a7a6b
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2018-05-20 17:47:28 +0800
Commit message:

 the legend labels for the discrete heatmaps are correct now
 
Package: EnrichedHeatmap
Commit: 0624bdb56a60827c3d31a87e2685861902a7a9f7
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2018-05-20 17:22:27 +0800
Commit message:

 adjust the print message
 
Package: EnrichedHeatmap
Commit: 10c76c9c2b8ec9f6e9bde381c763406abb07257b
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2018-05-20 17:11:44 +0800
Commit message:

 bump version number
 
Package: EnrichedHeatmap
Commit: 801f102b02abebf791f4ce6f72d5a3db50efb786
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2018-05-20 17:10:52 +0800
Commit message:

 update
 
Package: stageR
Commit: f99eb6e952111f3403af759f49cfaa91cdab433b
Author: statOmics <lieven.clement@ugent.be>
Date: 2018-05-19 14:49:54 -0700
Commit message:

 version bump
 
Package: stageR
Commit: 5982e9eb7d9900a5fa8d875cef7d4cbaeefbccf0
Author: statOmics <lieven.clement@ugent.be>
Date: 2018-05-19 14:35:14 -0700
Commit message:

 fix vignette engine
 
Package: csaw
Commit: 89b9a46dd094107b48b9e63f47696e9624f4da4b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 22:25:16 +0100
Commit message:

 Added warning if weight.list not specified for statistics consolidation.
 
Package: PureCN
Commit: 0ae9c2695dbd96482bdcd30de6dc16563d5fc0db
Author: lima1 <mriester@gmx.de>
Date: 2018-05-19 15:43:29 -0400
Commit message:

 Warn when score column in mappability or reptiming data is not numeric (#35)
 
Package: PureCN
Commit: 2b60cf8b19a82e977e5dd50051e555c9fd8e3893
Author: lima1 <mriester@gmx.de>
Date: 2018-05-19 14:46:40 -0400
Commit message:

 Move reptiming tiling from IntervalFile.R to preprocessIntervals (#31).
 
Package: MLSeq
Commit: b599876b34d83ec872c131c780f28d39969606d2
Author: Dincer GOKSULUK <dincer.goksuluk@gmail.com>
Date: 2018-05-19 22:09:38 +0300
Commit message:

 DESCRIPTION is modified to remove warnings from imported packages. Version is set to 1.99.2
 
Package: MLSeq
Commit: 164c8c16e5a7f7a0d2cc0bdff293705381bbce38
Author: Dincer GOKSULUK <dincer.goksuluk@gmail.com>
Date: 2018-05-19 15:06:18 +0300
Commit message:

 Generic functions are debugged and version moved to 1.99.3.
 
Package: MLSeq
Commit: 63a99f1d8320e4d57f8eeee1eda627dff78430fd
Author: Dincer GOKSULUK <dincer.goksuluk@gmail.com>
Date: 2018-05-19 13:23:57 +0300
Commit message:

 Updated build ignore list.
 
Package: MLSeq
Commit: dd9ae8b3e4830a0e760dded935298c5f4908f8b6
Author: Dinçer GÖKSÜLÜK <dincer.goksuluk@gmail.com>
Date: 2018-05-18 16:58:00 +0300
Commit message:

 version moved to 1.99.2
 
Package: MLSeq
Commit: da55e2a3f2314f61d6f4982a86b7871e96752516
Author: Dinçer GÖKSÜLÜK <dincer.goksuluk@gmail.com>
Date: 2018-05-18 16:57:29 +0300
Commit message:

 gitignore & buildignore added.
 
Package: GenomicRanges
Commit: b050bae4a06fdcb30d56ea19e785a4233484a48e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-19 11:44:28 -0700
Commit message:

 trying one more time
 
Package: GenomicRanges
Commit: b217fb0181912a0f3fd75522d59079dcd9732e78
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-19 11:11:57 -0700
Commit message:

 Resync with rbind() enhancement on DataFrame objects in S4Vectors 0.19.5
 
Package: S4Vectors
Commit: fc0dca1d16148d3bc031fc05632fe8d3ac9b6102
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-19 10:37:09 -0700
Commit message:

 Small tweaks to "cbind" and "c" methods for DataFrame objects

- The "cbind" method now accepts (and ignores) NULLs in the input.
- The "c" method now supports the 'ignore.mcols' argument.
 
Package: csaw
Commit: ea494d35a2fd6408d56cd122f210ba6c2a84c988
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 16:39:30 +0100
Commit message:

 Extra comment.
 
Package: csaw
Commit: 5f49fa80c8cbbcac249446c2d0c1e8b5b09f9888
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 16:39:18 +0100
Commit message:

 Streamlined calculateCPM test with log=TRUE.
 
Package: csaw
Commit: 197fbe25301f219ef05a2f567e6eefea984eecbf
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 16:10:04 +0100
Commit message:

 Updated NEWS.
 
Package: csaw
Commit: b3d30851261f22b5bef1f2e8fe925b8fb51910a6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 16:09:54 +0100
Commit message:

 Removed unnecessary *.Rout.save file.
 
Package: csaw
Commit: 6a0df1b2ebc0f6f1554f0d35206978464183ed01
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 16:01:27 +0100
Commit message:

 Updated NAMESPACE to export new functions.
 
Package: csaw
Commit: 2b365e38308be0b097b1d5b8f0007d16608987d5
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 16:00:36 +0100
Commit message:

 Switched consolidate* function tests to use testthat.
Added separate tests for consolidateTests, consolidateOverlaps.
 
Package: csaw
Commit: 83984590dc3d6f97447d28b9c06377f63d430d5a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 15:59:28 +0100
Commit message:

 Fixed bugs to pass CHECK.
 
Package: csaw
Commit: 32285041e47391e66d7ac4f44fc8a7afb2df51b2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 15:45:06 +0100
Commit message:

 Added docs for consolidateTests/Overlaps.
 
Package: csaw
Commit: 7dfc3a124e5f5101f16b26a59df62a177f255330
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 15:29:16 +0100
Commit message:

 Added consolidateTests/Overlaps functions.
 
Package: csaw
Commit: bfec495df26d1d1ee3098d8b9808a568773142f5
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 14:42:48 +0100
Commit message:

 Updated docs for new consolidateWindows function.
 
Package: csaw
Commit: 4eb15c60d96baa566b9c087384ef1ae5e85b10a2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 14:38:56 +0100
Commit message:

 Refactors window consolidation function.
 
Package: csaw
Commit: 5679097c415a63118cfd94812546600807a2d2ea
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-19 11:45:53 +0100
Commit message:

 Added tests for asDGEList, empty scaledAverage.
 
Package: csaw
Commit: a95e2cb8fe5298a87539380d9fa80481186e4233
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 17:34:26 +0100
Commit message:

 Docfix.
 
Package: csaw
Commit: 13ed17f9c93139bdb5bb7559ae5c91667380b635
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 17:28:52 +0100
Commit message:

 Updated basic tests, NEWS.
 
Package: csaw
Commit: 0b533d86224992ff75406ac34e07b19699d7cb7f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 17:04:44 +0100
Commit message:

 Bumped version, date.
 
Package: csaw
Commit: 29bd8a446aadc5f2b7463ea2616fc32bac4d9617
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 17:02:47 +0100
Commit message:

 Added docs, tests, minor edit to calculateCPM.
 
Package: csaw
Commit: c3b25f81aaaf496135f061ccd46955dba07367b7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 16:18:16 +0100
Commit message:

 Added calculateCPM convenience function.
 
Package: csaw
Commit: 121e0ceaffa3dc2be4a54c1fa900deea4af5b209
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 15:19:35 +0100
Commit message:

 Moved tests for scaledAverage to separate file, with testthat.
 
Package: csaw
Commit: 0e0f8045a191e11ea05f556c108df51086f979a6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 15:00:40 +0100
Commit message:

 Transitioned normalization tests to use testthat.
 
Package: csaw
Commit: 355baf6284a11e82a0e34fe9e1c80ccf85cc2447
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 14:50:42 +0100
Commit message:

 Fixes to examples in docs, depracation warning.
 
Package: csaw
Commit: 741eb06552ac998331134673df9e42f86b901d67
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 14:50:13 +0100
Commit message:

 Switched normFactors to a normal function, not S4 method.
 
Package: csaw
Commit: 67aa92197d721fb6239efef0b9ffdb6c13c9d399
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 14:20:39 +0100
Commit message:

 Docfix.
 
Package: csaw
Commit: dc8de7fd7820cac3593b435a69662870fe646755
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 14:19:51 +0100
Commit message:

 Updated some test results.
 
Package: csaw
Commit: 8f389a80b068418343c21ee7852af809ca89566c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 14:12:48 +0100
Commit message:

 Updated tests for new normFactors.
 
Package: csaw
Commit: 626968b3bdbb8b5d369499c228389b60f840c170
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 10:52:00 +0100
Commit message:

 Split TMM normalization into normFactors function.
 
Package: csaw
Commit: 190b29f63c0e02e573fb9fb2e4f3bc9cc9818f3c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 10:07:30 +0100
Commit message:

 Updated tests for new scaledAverage input.
 
Package: csaw
Commit: 8b716938d8ece4ff16717c45f39e0f71d9afac6d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 10:03:31 +0100
Commit message:

 Minor fix to asDGEList.
 
Package: csaw
Commit: 6946a3f886fa416d7deb054fd8f1650eaa936aab
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 09:31:32 +0100
Commit message:

 Updated documentation.
 
Package: csaw
Commit: fe930918f3544bc311f249f0e7184b08c2862720
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 09:27:19 +0100
Commit message:

 Small fixups to asDGElist.
 
Package: csaw
Commit: 74e89dbad4f9c1f38bcf66f11b1c5417d9222057
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 09:26:35 +0100
Commit message:

 Updated filterWindows to pass SEs to scaledAverage.
 
Package: csaw
Commit: c19fb29d7d1513183402eae0d0ce5cf92869c650
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 09:21:58 +0100
Commit message:

 Switched scaledAverage to accept SE objects directly, deprecated DGEList input.
 
Package: csaw
Commit: ac0beffa1dd82b4d20e36cb2a81f130c9740bd04
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 09:07:57 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/csaw
 
Package: csaw
Commit: bb0feea09215a87394dd82a1326434eb37273b31
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-03-15 21:17:26 +0000
Commit message:

 Updated expected test output for new GRanges show().
 
Package: Trendy
Commit: 65305227d7e56e8f7b63ac609794227da1fd5090
Author: rhondabacher <rhonda.bacher@gmail.com>
Date: 2018-05-19 11:26:17 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/Trendy
updates to vignette
 
Package: Trendy
Commit: f0966069b71a85503285f7b1f9ffa55ba1890262
Author: rhondabacher <rhonda.bacher@gmail.com>
Date: 2018-05-19 11:25:27 -0400
Commit message:

 updates to vignette
 
Package: MSBdata
Commit: 3635d235e45e69fbc539acf691d2d4554945247c
Author: Wolfgang Huber <wolfgang.huber@embl.de>
Date: 2018-05-19 11:34:31 +0200
Commit message:

 Updated Description
 
Package: IRanges
Commit: 3126abcf76b4536d5010c5afd08ed550614efc70
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-18 21:57:48 -0700
Commit message:

 Resync with enhancement of rbind() on DataFrame objects in S4Vectors 0.19.5
 
Package: S4Vectors
Commit: 1664d3f14e811324d462f25ced935a90764b7758
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-18 21:53:17 -0700
Commit message:

 2 fixes and 1 enhancement to the "rbind" method for DataFrame objects

Most of the logic that used to be implemented in the "rbind" method for
DataFrame objects is now in a new "bindROWS" method for these objects.
The "rbind" method for DataFrame objects now is just a thin wrapper
around a call to bindROWS().

This new "bindROWS" method for DataFrame objects fixes the following long
standing bugs:
  1. rbind() now properly handles DataFrame objects with duplicated
     colnames. Note that the new behavior is consistent with
     base::rbind.data.frame().
  2. rbind() now properly handles DataFrame objects with columns that
     are 1D arrays.

It also provides the following enhancement:
  3. rbind() now supports DataFrame objects with the same column names
     but in different order, even when some of the column names are
     duplicated. How rbind() re-aligns the columns of the various objects
     to bind with those of the first object is consistent with what
     base:::rbind.data.frame() does.
 
Package: scmeth
Commit: 1737d8609f78099002841a9a78266bf3e6535146
Author: Divyagash <sdivyagash@yahoo.com>
Date: 2018-05-18 23:35:06 -0400
Commit message:

 Updated all functions not to output plots
 
Package: runibic
Commit: d1e39d289dadb6ae4f67f08a0cee50ead5800748
Author: Artur Pańszczyk <a.panszczyk@cad2cad.com>
Date: 2018-05-11 19:04:27 +0200
Commit message:

 Improvements of results for sets with a small number of columns
+ fix for correct order in initializer list
 
Package: matter
Commit: be1659cb2639ba0363b211ea4ee9dc42d805074d
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2018-05-18 14:25:20 -0400
Commit message:

 v1.7.1 bump w/ file.exists() bug fix
 
Package: matter
Commit: 417542e475594b95fd1c22b6d93726fd3088e19a
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2018-05-18 14:23:45 -0400
Commit message:

 fixed file.exists() warning
 
Package: BiocCheck
Commit: cdec6d15d48c44a73b4380223943d2dbaad175bf
Author: lshep <shepherl@gmail.com>
Date: 2018-05-18 13:09:29 -0400
Commit message:

 Vignette Engine check enhancement

  - catch edge case where multiple vignette engines are
    specified in vignette
 
Package: stageR
Commit: d94cf5b648ea1c8548cfd1a3db3f98b1518d4949
Author: statOmics <lieven.clement@ugent.be>
Date: 2018-05-18 10:08:01 -0700
Commit message:

 version bump
 
Package: S4Vectors
Commit: 0fcc86844852f7c1379c7a7c7a3ea010dfccc5b5
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-18 10:03:08 -0700
Commit message:

 Add 'nodup' argument to selectHits()
 
Package: pkgDepTools
Commit: c9f8a9e582b0d8314d32bedbdbfdaa705230872c
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-05-18 12:11:27 -0400
Commit message:

 version bump
 
Package: pkgDepTools
Commit: 25c9fcb6358ed4b9cac956a75ae20abee8574895
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-05-18 11:43:33 -0400
Commit message:

 update Bioc maintainer
 
Package: AnnotationFilter
Commit: 80e465e0353fee5ad9f0c3dbc161032569f1ba1c
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-05-18 11:41:45 -0400
Commit message:

 correct Bioc maintainer
 
Package: rhdf5client
Commit: 7f51f1891c80e53d3dbb74445d3fa511b167d369
Author: User-Zero <User-Zero@user-zeros-air.dfci.harvard.edu>
Date: 2018-05-18 11:07:08 -0400
Commit message:

 Increment version number after merge
 
Package: rhdf5client
Commit: 16de2981ebf72b40cad78319f427608074afd46e
Author: sampoll <sampoll@users.noreply.github.com>
Date: 2018-05-18 10:39:32 -0400
Commit message:

 Merge pull request #14 from vjcitn/master

simplify by omitting BiocSklearn references, and move away old vignette 
Package: rhdf5client
Commit: ca7d29f972a57baae905fdce784067b0ef8b74ee
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-05-15 22:08:59 -0400
Commit message:

 getting rid of old vignette that had too many details...
saved in inst/oldvig
 
Package: rhdf5client
Commit: 58223ce2a6af0930d55335d80e6c197b5853c306
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-05-15 21:52:38 -0400
Commit message:

 deal with triple-colon
 
Package: rhdf5client
Commit: a0c9179fd07eed76fc50d8db019d5db7945ef5ea
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-05-15 21:49:27 -0400
Commit message:

 HSDS_Matrix man page
 
Package: rhdf5client
Commit: e179b8acf638087455a47d72876b99141f8aebf0
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-05-15 21:34:43 -0400
Commit message:

 adding simple example for reading hdf5 in package
 
Package: rhdf5client
Commit: 27661667fa39886f11cbf172c5f71dc81df448c5
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-05-15 21:33:13 -0400
Commit message:

 purging BiocSklearn
 
Package: rhdf5client
Commit: 4aa5bbc7ddbf9069e3421d9cac652127e9307b4e
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-05-15 21:27:48 -0400
Commit message:

 adding HSDS_Matrix.R
 
Package: rhdf5client
Commit: 3e0dbc36c26289b78d97344aef2ce6a2d3790ca5
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-05-15 19:46:07 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/rhdf5client
 
Package: rhdf5client
Commit: d81567b28c6e6b091031847049437b88b7e1cc19
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-05-15 19:45:20 -0400
Commit message:

 drop the BiocSklearn dependence
 
Package: CATALYST
Commit: 485c2542fc146b85f4394c362d2080e58dc4c115
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-18 16:23:30 +0200
Commit message:

 change exmpl
 
Package: CATALYST
Commit: f56d85ab95d2887b26e2c50818f3231cecad30f8
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-18 16:20:18 +0200
Commit message:

 updt dox; ver bump
 
Package: CATALYST
Commit: 95932caa7fb926412010e32f3d096dff832cbbec
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-18 16:03:28 +0200
Commit message:

 updt dox
 
Package: CATALYST
Commit: a90535ca11ecb2f7bac8a24503e83af93a000554
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-18 09:28:53 +0200
Commit message:

 updt dox
 
Package: CATALYST
Commit: 5d6a68bfe09b491d6bd3a4a7996232465bd1245e
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-18 09:28:41 +0200
Commit message:

 updt dox, fix color_by=NULL
 
Package: CATALYST
Commit: d8129cf0398b486f56e7c7184e5b85eadff6a1f7
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-18 09:28:19 +0200
Commit message:

 updt dox
 
Package: CATALYST
Commit: c04b9f3895142e3a786d3d2e81e127d66838cfed
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-18 09:27:42 +0200
Commit message:

 store cofactor in metadata
 
Package: CATALYST
Commit: 6e3c4ff8c0ece85c76bd1855640dbe03662e0512
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-18 09:27:26 +0200
Commit message:

 + extractClusters()
 
Package: CATALYST
Commit: 8c0dcff07d16799a9b4a21930ce84cbd97fefb0a
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-17 09:03:24 +0200
Commit message:

 add validity check for `custom_isotope_list`
 
Package: CATALYST
Commit: 39c82c2255afa49561fb86531bf554cc31b37dcb
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-17 08:35:38 +0200
Commit message:

 +opt to specify custom_isotope_list prior to launchGUI
 
Package: CATALYST
Commit: 91d2c4339d14b0267c1af999dd2aebc96d944d2b
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-16 22:23:03 +0200
Commit message:

 code cleaning
 
Package: CATALYST
Commit: ec91df245a1d2929e1aec12cd8978365e6a46630
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-15 20:25:50 +0200
Commit message:

 updt dox
 
Package: CATALYST
Commit: bb87c224014f39f9996fda807ca6b8b065cd6dba
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-15 20:08:13 +0200
Commit message:

 fix issue #35: + option to specify custom isotope list
 
Package: CATALYST
Commit: ea177ec93711083de9f5f5b37a7d1e8e979e5705
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-15 19:37:20 +0200
Commit message:

 rmv git link
 
Package: CATALYST
Commit: 4735ec59535a61fa92422e09185a010e1b690e76
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-15 19:35:53 +0200
Commit message:

 fix path to logo
 
Package: CATALYST
Commit: 3d5bce078a32c0e3a7e0b63d4342fda6ee28aee5
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-15 19:34:34 +0200
Commit message:

 add logo
 
Package: CATALYST
Commit: fbef299da78f8d140a3bf8e40c5867afeba3d004
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-15 19:34:06 +0200
Commit message:

 updt README.md
 
Package: CATALYST
Commit: d695526431bd039ff54ab6a397ecfc155862e92e
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-15 19:33:03 +0200
Commit message:

 updt author details
 
Package: CATALYST
Commit: 71028b09ad36d039c3886a2a5003e6e8d212ebaf
Author: HelenaLC <crowellh@student.ethz.ch>
Date: 2018-05-15 18:32:05 +0200
Commit message:

 add .travis.yml
 
Package: MLSeq
Commit: 210d939b33c30ae084a280c8c78f8882f3d498b3
Author: Dinçer GÖKSÜLÜK <dincer.goksuluk@gmail.com>
Date: 2018-05-18 16:23:32 +0300
Commit message:

 Version numbering is fixed.
 
Package: MLSeq
Commit: 743a30d547498058b1242e6c7201e72390954b7d
Author: Dinçer GÖKSÜLÜK <dincer.goksuluk@gmail.com>
Date: 2018-05-18 16:13:32 +0300
Commit message:

 NEWS & README added.
 
Package: MLSeq
Commit: 285db4dd4d7a3db6012e38e0a7ccc3b0152be9f9
Author: Dinçer GÖKSÜLÜK <dincer.goksuluk@gmail.com>
Date: 2018-05-18 15:09:43 +0300
Commit message:

 Major Changes in MLSeq, version moved to 2.x.y from 1.x.y
 
Package: netSmooth
Commit: 6fe54337b3ddcedb5cda9ae1d30ef69779582d56
Author: jona <yablee@gmail.com>
Date: 2018-05-18 15:22:08 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: netSmooth
Commit: 56be2893238112376f6bbb3f2d84230c7a93e4a6
Author: jona <yablee@gmail.com>
Date: 2018-05-18 14:56:56 +0200
Commit message:

 Add inst/CITATION file, pointing at the F1000 article
 
Package: netSmooth
Commit: 8c7af8bbe7ba78b13a99d34a8e4bcc234c37be5b
Author: jona <yablee@gmail.com>
Date: 2018-05-08 18:52:58 +0200
Commit message:

 emph netSmooth
 
Package: netSmooth
Commit: 330648d58dcb8cbf192dfc4ffbee83dd16295fdd
Author: jona <yablee@gmail.com>
Date: 2018-05-08 18:50:14 +0200
Commit message:

 Add bioconductor and f1000 references to readme
 
Package: netSmooth
Commit: 93b97541c491abf2e51c174e9e7827e50e62f406
Author: jona <yablee@gmail.com>
Date: 2018-05-08 17:36:52 +0200
Commit message:

 Another...
 
Package: netSmooth
Commit: 11cd410446f34f57ce9a3ad8e2c0de2e96ca5928
Author: jona <yablee@gmail.com>
Date: 2018-05-08 16:57:10 +0200
Commit message:

 Another..
 
Package: netSmooth
Commit: 18fd1bcd39ef5ecf6108c4b7cb6695634cd608bb
Author: jona <yablee@gmail.com>
Date: 2018-05-08 16:19:10 +0200
Commit message:

 Another
 
Package: netSmooth
Commit: f73319a88db9eb8e62431412188546e81ca53521
Author: jona <yablee@gmail.com>
Date: 2018-05-08 16:04:52 +0200
Commit message:

 More packages to be installed from CRAN and not apt-get (travis-ci)
 
Package: netSmooth
Commit: 887bcf6b84bb499d6a746862765770bb0dd76777
Author: jona <yablee@gmail.com>
Date: 2018-05-08 15:29:37 +0200
Commit message:

 Another package renaming
 
Package: netSmooth
Commit: c28469250356e1d3599716e6be572298407c5cc1
Author: jona <yablee@gmail.com>
Date: 2018-05-08 15:18:20 +0200
Commit message:

 More on packages for travis..
 
Package: netSmooth
Commit: 42fc340da35ed9145924964600c2641212f8b76b
Author: jona <yablee@gmail.com>
Date: 2018-05-08 14:46:39 +0200
Commit message:

 Fix package names (in R world camelCased, in apt-get world all lower). For travis build.
 
Package: netSmooth
Commit: 5a54fc088b6a5fae4fde4727d7437e00cafed0c8
Author: jona <yablee@gmail.com>
Date: 2018-05-08 14:34:34 +0200
Commit message:

 More.
 
Package: netSmooth
Commit: 39fd95d6a342849d3b626342f35629c816cfb8f6
Author: jona <yablee@gmail.com>
Date: 2018-05-08 14:31:48 +0200
Commit message:

 Move some packages from r_binary_packages to r_packages to fix travis build
 
Package: netSmooth
Commit: 64d5da39ca6a1d02c8dc6a58c518b689bf08c478
Author: jona <yablee@gmail.com>
Date: 2018-05-08 14:26:02 +0200
Commit message:

 Travis to build on release R
 
Package: simpleSingleCell
Commit: 8543d48cb70c3bc4fab6b5cb1bca8900dfd2690e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 14:04:13 +0100
Commit message:

 Updated pancreas HVG analysis to use multiBlockVar.
 
Package: simpleSingleCell
Commit: c1c7f07f4fdb83912121c680338750b6b9e7f975
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 10:23:58 +0100
Commit message:

 Fixed cluster mention.
 
Package: simpleSingleCell
Commit: aa344149cbd52219f1da45b0507b60503643b544
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 10:14:40 +0100
Commit message:

 Switch to FTP path for GEO resources.
 
Package: simpleSingleCell
Commit: f72b2ff8a8040c4230fd2ad3d791b82e871f01f1
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 09:00:58 +0100
Commit message:

 Switched to BiocFileCache for local file management.
 
Package: simpleSingleCell
Commit: b6f53cb81a0528c3b9b2074f02ae3be5f4a421e7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 17:59:59 +0100
Commit message:

 Added an ignore file.
 
Package: simpleSingleCell
Commit: 61cd1e2ab1ed3e20012cb4a970db9747554c3073
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 17:49:05 +0100
Commit message:

 Bumped version number.
 
Package: simpleSingleCell
Commit: 92dfac6bb19ac084fd83d5a79b0e8faa87462a85
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 17:48:45 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/simpleSingleCell
 
Package: simpleSingleCell
Commit: 184d9bbbc68b99c1a3b30b78340c9ac41338c9cf
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 17:48:42 +0100
Commit message:

 Exposed download scripts in MNN workflow.
 
Package: simpleSingleCell
Commit: 652d3474b08408e20c0c8a51c6320a2a751db50b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 17:46:58 +0100
Commit message:

 Exposed download chunks in miscellaneous workflow.
 
Package: simpleSingleCell
Commit: e27aa88ffb946a839cc3c7340b24fd7517be88ea
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 17:19:59 +0100
Commit message:

 Bug fix for edge widths.
 
Package: simpleSingleCell
Commit: 75082c2e532c0c979800aaf4c66a1864edc47049
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 17:10:15 +0100
Commit message:

 Exposed download in 10X workflow.
 
Package: simpleSingleCell
Commit: 4fd8135dd225a809b435b73ae8fc27c80826acf9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 17:07:53 +0100
Commit message:

 Added layout plot for cluster similarities, exposed download info.
Added graph abstraction citation.
 
Package: simpleSingleCell
Commit: 080bae8785289ddc51755e68a22b12d6e9046bc7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 13:29:46 +0100
Commit message:

 Turned off titlecaps in read workflow, exposed download.
 
Package: simpleSingleCell
Commit: bb59f34960874c1950ea186b18fed5e6e12c83a3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-10 17:02:18 +0100
Commit message:

 Merge branch 'master' of https://github.com/MarioniLab/simpleSingleCell
 
Package: simpleSingleCell
Commit: 60f736418abe1704ab7de5b05685a17941c7218c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-10 17:02:09 +0100
Commit message:

 Code cleanup, elaborated on alternative QC methods.
 
Package: TCGAbiolinks
Commit: 5b0e23257589377d172a6c96646ffe8c8a94b861
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-05-18 09:45:42 -0300
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks
 
Package: TCGAbiolinks
Commit: c995d07f9ae7240af597042175b9097798dac5bc
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-18 09:24:27 -0300
Commit message:

 bug fix
 
Package: TCGAbiolinks
Commit: 7afbe3a314a8d6c5197c94cfdd363bd71f727aa3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-16 10:07:36 -0300
Commit message:

 Fix vignette
 
Package: MLSeq
Commit: ff3e4a8a1f755e707afc30a7131ec8a332ad8cc3
Author: Dinçer GÖKSÜLÜK <dincer.goksuluk@gmail.com>
Date: 2018-05-18 15:06:23 +0300
Commit message:

 Remove author from description.
 
Package: scran
Commit: 111d2d92ab54932f6a47d2014a10934b30897994
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-18 13:00:02 +0100
Commit message:

 Protect against non-informative blocks in multiBlockVar.
 
Package: scmeth
Commit: 77854c66812bc8341f1aa722023ac371982066af
Author: Divyagash <sdivyagash@yahoo.com>
Date: 2018-05-17 23:26:00 -0400
Commit message:

 removed devel from travis
 
Package: scmeth
Commit: 8f339200672a73b1bc651b3d9e4cbf7e464f7a7f
Author: Divyagash <sdivyagash@yahoo.com>
Date: 2018-05-17 22:50:14 -0400
Commit message:

 updated input parameter in qcrReport
 
Package: S4Vectors
Commit: 2557ea9064046e78dcea8ca0cd82e9404dd2ab6c
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-17 17:45:56 -0700
Commit message:

 Rename some variables

These are leftovers from the renaming of queryLength/subjectLength ->
nLnode/nRnode on Feb 22, 2016.
 
Package: dmrseq
Commit: a53af90309dd9a982e4c5dccb82ee719186b313a
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-17 18:24:01 -0400
Commit message:

 Version bump
 
Package: dmrseq
Commit: cab042ffc0f1c72b66520014cd73c89cf0744da6
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-17 18:23:37 -0400
Commit message:

 Bug fix for error if only 1 column of pData
 
Package: AnalysisPageServer
Commit: df066559e9978dd758defad9a8c15bb1f86206b5
Author: Brad Friedman <friedmab@gene.com>
Date: 2018-05-17 15:15:11 -0700
Commit message:

 latest changes to handle more local reports and gene selectors; also update for minor changes in SVG format
 
Package: BiocStyle
Commit: db7bf82e3e0af03ac5f7393439211c5868ccc5eb
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-05-18 00:12:12 +0200
Commit message:

 Remove defunct functions (closes https://github.com/Bioconductor/BiocStyle/issues/50)
 
Package: compEpiTools
Commit: 93a0ac2e00278e9e5ca21f2716b6a2f2d1e73650
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2018-05-17 23:01:07 +0100
Commit message:

 GRbaseCoverage
 
Package: dmrseq
Commit: 53cc922728dcbac0a4985d29fe000266bf4191ee
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-17 17:44:16 -0400
Commit message:

 Make custom plot attributes (col,lty,lwd,label) more robust
 
Package: dmrseq
Commit: 1c8bcd601df9804cfd85f3ebb03275068b97c1d5
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-17 16:55:14 -0400
Commit message:

 Version bump
 
Package: dmrseq
Commit: 598557669f6b9aef2db58d9a58cce1eb92b65c64
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-17 16:55:08 -0400
Commit message:

 Bug fixes for minNumRegion &  multiple covariates

Fixes error that was being thrown for minNumRegion = 3. In addition, updates support to adjust for multiple covariates with adjustCovariates. Restrict to a single covariate for matchCovariate.
 
Package: biomaRt
Commit: b3dca7931ecd4630606d30a88495b2221e95bf2f
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-05-17 22:34:29 +0200
Commit message:

 Modified error message when Ensembl is down.
 
Package: gCrisprTools
Commit: 7d36c693c0090deceed8d9d18b942c28750d1337
Author: OscarBrock <russ.bainer@gmail.com>
Date: 2018-05-17 13:12:51 -0700
Commit message:

 updated description file
 
Package: gCrisprTools
Commit: 195c567c203a4265218f22aad64123249fac90ed
Author: OscarBrock <russ.bainer@gmail.com>
Date: 2018-05-17 13:12:29 -0700
Commit message:

 added additional input checks
 
Package: BiFET
Commit: 61e002f1321a7b2cb02bcf7c5b27dc8ba68d1a27
Author: Ahrim Youn <youna@mlg-jgm164.local.jax.org>
Date: 2018-05-17 15:51:21 -0400
Commit message:

 updated vignette
 
Package: BiFET
Commit: d697fed2fe3cf05fa43b33abc52e78003bfd4c78
Author: Ahrim Youn <youna@mlg-jgm164.local.jax.org>
Date: 2018-05-17 15:27:55 -0400
Commit message:

 updated Vignette and Rcode
 
Package: rRDP
Commit: f3f8642c5cba6fe6cd755e2700b27828d8001084
Author: Michael Hahsler <michael@hahsler.net>
Date: 2018-05-17 13:51:03 -0500
Commit message:

 Fixed problem with fixrank.
 
Package: rRDP
Commit: daad18ec2886dd487d6663bb4c290c3369edc315
Author: Michael Hahsler <michael@hahsler.net>
Date: 2018-05-17 13:50:26 -0500
Commit message:

 Added missing import.
 
Package: rRDP
Commit: 9ff656147c19e04f59a74a99c4b9b4f3369e897d
Author: Michael Hahsler <michael@hahsler.net>
Date: 2018-05-17 13:50:06 -0500
Commit message:

 New version.
 
Package: ggcyto
Commit: 117735ff11806771c774175992c868e61a1f67b7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-17 11:10:15 -0700
Commit message:

 Merge branch 'trunk' into devel
 
Package: ggcyto
Commit: 14b1db7dbc9097722e7daf178f044afd29771bc4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-17 11:06:04 -0700
Commit message:

 bump
 
Package: ggcyto
Commit: 43993bcaa807f3a51387914fca2169c64e568e78
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-17 11:05:37 -0700
Commit message:

 update vignette build
 
Package: ggcyto
Commit: 75e3fa86a4239a0b0461f71ff7cbb3978da8698d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-17 10:35:13 -0700
Commit message:

 fix error when non-abstract geom_gate is added to gs. #33
 
Package: eegc
Commit: afe1642e64be17f2968ba342f9eabe7baabc2cf2
Author: Xiaoyuan <xiaoyuan@github.com>
Date: 2018-05-17 10:15:24 -0700
Commit message:

 Version bump
 
Package: GENESIS
Commit: eac328d851ddfb57f85156adb8ed0589bd316548
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-05-17 09:44:14 -0700
Commit message:

 bump version number
 
Package: GENESIS
Commit: ea9c39cea642b051e6c237e495189c60e0100498
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-05-17 09:42:44 -0700
Commit message:

 update comments in vignette

Be more clear about the distinction between genes and transcripts.
Note that the example given is simplistic.
 
Package: signeR
Commit: 86ca84c3c97ea7b384eb24d324bd82c6a0b02e9f
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2018-05-17 11:14:45 -0300
Commit message:

 optimization of genCountMatrixFromVcf function
 
Package: iSEE
Commit: 18a3214d1f17c4e042c10f9a0315aa80e47c7711
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-17 15:05:27 +0100
Commit message:

 Merge pull request #198 from csoneson/furtherfix

Get rid of Enhances. 
Package: iSEE
Commit: ac0837f247a9438c57d480a6ee0539af2039087e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 14:42:50 +0100
Commit message:

 Merge branch 'master' into furtherfix
 
Package: iSEE
Commit: a1fa6035f2ca73fca156378c0e557d5bbd9ef7c2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-17 14:42:22 +0100
Commit message:

 Removed ExperimentHub from Enhances.
 
Package: iSEE
Commit: 82f95dbe9b886ebc4555d5178a257ccd185fc1e0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-05-15 13:44:51 +0200
Commit message:

 Merge pull request #197 from csoneson/heatfix

Fix heatmap issue if all values in the matrix are identical. 
Package: iSEE
Commit: 08684b2d412c91041c86bbbfa16f1b22ff257a87
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-05-15 13:15:27 +0200
Commit message:

 Merge branch 'master' into heatfix 
Package: iSEE
Commit: 6d74f3b3b85f7853a452f197a795875e2f8d62e6
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-05-15 12:31:32 +0200
Commit message:

 Merge pull request #196 from csoneson/standardizetour

Standardizetour 
Package: iSEE
Commit: a2e2d7a8eac06d7bd65282814f8b04af02f10141
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-05-15 12:14:44 +0200
Commit message:

 Merge branch 'master' into standardizetour 
Package: iSEE
Commit: 9e45144ef68879e9742bd9919605762cc20ecb64
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-15 11:12:22 +0100
Commit message:

 Merge pull request #194 from csoneson/datatable

 preserve column names in datatables 
Package: iSEE
Commit: 49b0853a9187d15159fbcd7d3ebb50c8c2d63849
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-05-15 12:03:46 +0200
Commit message:

 Fix heatmap issue if all values in the matrix are identical.
 
Package: iSEE
Commit: a50e1bbd03a7f879a764ee2358cccb701062d4eb
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-15 10:53:03 +0100
Commit message:

 Merge branch 'master' into datatable 
Package: iSEE
Commit: 92c199fd015da7c69841103eb3828c26dfb8469d
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-15 10:52:41 +0100
Commit message:

 Merge pull request #193 from csoneson/quotes2

bugfix: deparse size factor names 
Package: iSEE
Commit: 2e3141097af962e1ce4ffae16e052088796b9f78
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-15 10:34:42 +0100
Commit message:

 Fixed bug in UI code.
 
Package: iSEE
Commit: 7cf28b43be7d757f86df3f0a44adfec51e3c7ab2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-05-15 11:32:19 +0200
Commit message:

 Remove disclaimer from firststeps tour
 
Package: iSEE
Commit: e621e7a25a08f3dd2d621e1d4e3834a443d8ec3a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-15 10:29:31 +0100
Commit message:

 Fixed SE sanitation test.
 
Package: iSEE
Commit: 87ce3ef269beee10e7c04a871cdd21a463ae00ea
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-15 10:28:51 +0100
Commit message:

 Removed reliance on tmp_se during SE sanitation.
 
Package: iSEE
Commit: 3b817a4dbe987199e00a77badea37a1a160ef39d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-05-15 11:21:09 +0200
Commit message:

 Standardize firststeps tour
 
Package: iSEE
Commit: f0b0e29a79314c3fec9d67ac6020b41a4166b5c3
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-14 22:16:41 +0100
Commit message:

 Revert "single & to avoid shortcut"

This reverts commit 469e857d911d178bcb1b66bcd768f1a7144c62bc.
 
Package: iSEE
Commit: fcefd55b5fc38b718312dcf579078ac72f511b2a
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-14 22:07:14 +0100
Commit message:

 funky error: sanitize_SE_input fails to add the last nested column
 
Package: iSEE
Commit: 469e857d911d178bcb1b66bcd768f1a7144c62bc
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-14 22:00:29 +0100
Commit message:

 single & to avoid shortcut
 
Package: iSEE
Commit: f0faad4d16b07304050eb030a281ab2005a624ae
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-14 19:24:10 +0100
Commit message:

 extra test dedicated to nested DataFrames
 
Package: iSEE
Commit: f79d4779de3ce3795c4c9bca9c81156355fa0ecd
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-14 19:18:45 +0100
Commit message:

 Merge branch 'master' into quotes2 
Package: iSEE
Commit: c3f0c34afd0647ab89596226e2170d5a23b29b8f
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-14 18:24:38 +0100
Commit message:

 cover unit tests that involved nested colData
 
Package: iSEE
Commit: 669beb427549427cba2f67cc383b72ae897366a4
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-14 17:23:44 +0100
Commit message:

 Merge pull request #195 from csoneson/furtherfix

License fix and assorted sundries 
Package: iSEE
Commit: 84eaa115d9034ebd149507dbc9e1ebbe94735bc4
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-14 13:39:17 +0100
Commit message:

 Updated LICENSE for more sobriety.
 
Package: iSEE
Commit: ef79c2bc4190faf8eec04632451fcc56062d5bd0
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-14 00:06:28 +0100
Commit message:

 clear spikes to test empty rowData
 
Package: iSEE
Commit: 8a4484a1c6f8e3fd4df10c4e45d3715e9f2fdb19
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-13 23:57:41 +0100
Commit message:

 more honest test name
 
Package: iSEE
Commit: af09f28c35adf1fbba1206f80bce052a6534ff70
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-13 22:23:14 +0100
Commit message:

 add spike and size factors
 
Package: iSEE
Commit: 1272b6fc2ce73041b8de45c84733e5c12c5f3d1f
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-13 22:23:03 +0100
Commit message:

 update doc
 
Package: iSEE
Commit: 67b042ea12db3f229cb6de958293c98b1175e6b2
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-13 19:21:53 +0100
Commit message:

 preserve column names in datatables
 
Package: iSEE
Commit: 0e49d9db1abec0f08bf7a7c0522d3a9f54e02c4f
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-13 18:22:27 +0100
Commit message:

 bugfix: deparse size factor names
 
Package: iSEE
Commit: bc0d5bba9c66a5888e875efdba35c6667c9e731a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-09 18:25:44 +0100
Commit message:

 Merge branch 'master' into furtherfix
 
Package: iSEE
Commit: b7168a7c1ade50397305eddc6fbf7cd0391dd958
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-09 18:25:29 +0100
Commit message:

 Merge branch 'furtherfix' of https://github.com/csoneson/iSEE into furtherfix
 
Package: iSEE
Commit: 1f2c1b4b05bc11f3a154535cccf5b685c8fce6c7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-09 18:25:24 +0100
Commit message:

 Deleted unused variable.
 
Package: iSEE
Commit: 862bf2c61bcde01618fac522be2c7cb1dfbf72de
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-07 21:19:31 +0100
Commit message:

 Merge pull request #191 from csoneson/furtherfix

Additional miscellaneous fixes 
Package: iSEE
Commit: 3b7bbb806c187b74df824d303a25326cbaa5577e
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-07 20:41:57 +0100
Commit message:

 Merge branch 'master' into furtherfix 
Package: iSEE
Commit: b33f5c88a0dfed684c725050bc54591b5f470148
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-07 19:28:16 +0100
Commit message:

 Merge pull request #190 from csoneson/categorical

Clarify instances of 'discrete' that mean 'categorical' 
Package: iSEE
Commit: 3c8bdccb46ffa12e8e7e995ff6a35e18b95305c0
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-07 19:06:56 +0100
Commit message:

 's'
 
Package: iSEE
Commit: 0d89f5f9cf05981cbc240aea64814d542a5930ed
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-07 19:01:16 +0100
Commit message:

 Merge branch 'master' into categorical
 
Package: iSEE
Commit: 8b65699aab5bdc86635ca316765da32ca826e18e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-07 14:51:57 +0100
Commit message:

 Merge remote-tracking branch 'origin/categorical' into furtherfix
 
Package: iSEE
Commit: d9c10fb778d4816dfaaaa5cc7bfb80990a136a3a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 18:26:59 +0100
Commit message:

 Switched to numericInput for reddim dimension choice.
 
Package: iSEE
Commit: 84a619a04c954af8e9854892e320061630679354
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 18:19:45 +0100
Commit message:

 Fixed bug, added test for code reporting for initialPanels.
 
Package: iSEE
Commit: eedde0bfce76919c6826929a46d1042e17386022
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-06 18:13:12 +0100
Commit message:

 Merge pull request #189 from csoneson/customplot

Allow user-specified functions for dynamic coordinate generation 
Package: iSEE
Commit: 20ce903264bbd01ede44f4c74f63c8c88fbc4b8f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 17:52:17 +0100
Commit message:

 Fleshed out custom plot example.
 
Package: iSEE
Commit: ca58c915eb424f1308a1a8f32fb0484c27285a2e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 17:22:43 +0100
Commit message:

 Added tests for custom plot generation.
 
Package: iSEE
Commit: 3a88db6f57d0c398e459557811d67ca679ca77fa
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-06 16:46:25 +0100
Commit message:

 Merge branch 'customplot' into categorical
 
Package: iSEE
Commit: 04d65122370ce7358e8271daf3313e84a5968346
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-06 16:45:29 +0100
Commit message:

 4 space indent; discrete -> categorical documentation
 
Package: iSEE
Commit: c24ea48e66b9ea4281e81e350abee8eb19e7b80a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 15:02:42 +0100
Commit message:

 Fixed iSEE documentation.
 
Package: iSEE
Commit: 7cbbc00e855513d322d1438e92b814fad3327381
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 15:02:19 +0100
Commit message:

 Fixed tests for the existence of custom column plots.
 
Package: iSEE
Commit: 2db2ce950281e3fc9bb61ad89b767d378e8912f6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 13:34:01 +0100
Commit message:

 Merge branch 'master' into customplot
 
Package: iSEE
Commit: e8069c063f8bd02b6101fa0756359e57a6d66d2f
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-06 13:33:32 +0100
Commit message:

 Merge pull request #188 from csoneson/renamed

Restrict generation of certain variables in code tracker 
Package: iSEE
Commit: 66abd2dcf8e321c3489cc746ee6fda426ceeaa81
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 13:30:04 +0100
Commit message:

 Clear brushes upon reselect in a custom col plot.
 
Package: iSEE
Commit: 72677803845629c246702ec4d064a2b230a48351
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-06 13:28:31 +0100
Commit message:

 Ensure .make_customColPlot always returns, even with '---' function.
This is necessary to fill all_coordinates for receiving plots.
 
Package: iSEE
Commit: fa38e104256c87f48e5923be6ce82a911e1d7737
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 19:09:18 +0100
Commit message:

 Minor comment changes, avoid unnecessary newline in commands.
 
Package: iSEE
Commit: aadbc01115b79ed868fba62a01931a08fc9762c3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 18:59:25 +0100
Commit message:

 Reorganized code blocks for easier reading, renamed cached variable.
 
Package: iSEE
Commit: 2642dc43231f8f7cea4e064252932504e678766f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 18:49:32 +0100
Commit message:

 Ensure custom plot functions work with the code tracker.
 
Package: iSEE
Commit: cc657bb2c90c1fddf81c462660201babc78b1382
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 18:43:53 +0100
Commit message:

 Added an ugly colour for the custom col plots.
 
Package: iSEE
Commit: 503b2b2bef02a128ad70284756024da7ed387967
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 18:43:40 +0100
Commit message:

 Rebuilt NAMESPACE, docs.
 
Package: iSEE
Commit: 957e3765cf623afd70907c886f6bde705c3ff400
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 18:43:04 +0100
Commit message:

 Bug fixes to custom plot function, documented custom fun requirements.
 
Package: iSEE
Commit: c50f20c6a58f8320a151c3ef1fecbcf92c4e207e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 18:42:32 +0100
Commit message:

 Try to initialize custom col plot, observe function changes.
 
Package: iSEE
Commit: 98ca2c9841909a91725a79d8aeef429d015d7faf
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 17:49:07 +0100
Commit message:

 Cleaned up iSEE doc page.
 
Package: iSEE
Commit: 6be4211cad8e6164bdb84791bb01b972b86fdd85
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 16:33:59 +0100
Commit message:

 Added function for generating custom column plots.
 
Package: iSEE
Commit: b4f7288058a0bab92e85e2f37d68c93208d1c357
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 16:32:08 +0100
Commit message:

 Integrated customColPlot into observers, select/table link setup.
 
Package: iSEE
Commit: b2ac0753fa770bfb53644bbaef1fb876b26fc8ad
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 16:10:05 +0100
Commit message:

 Broke up large plotting functions for general use.
Enforced character vector returns for commands.
 
Package: iSEE
Commit: 40cd539f70038932584b11e122bd1a01619c3748
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-05 14:35:26 +0100
Commit message:

 Set up basic infrastructure for custom column plots.
 
Package: iSEE
Commit: 7f182d9e10aae6fd1e0f837eef4f31aaa44e3105
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-05 13:52:53 +0100
Commit message:

 Merge branch 'master' into renamed 
Package: iSEE
Commit: 9be7d9dcbad7e1f2749c8202d6cb0c67eb4521e7
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-04 23:32:19 +0200
Commit message:

 Merge pull request #187 from csoneson/kevinrue-release-badge

Release badge 
Package: iSEE
Commit: 45cb38d9468754baf762316f9e99683217a9f991
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-04 20:01:23 +0100
Commit message:

 Various fixes to pass CHECK, edit comment.
 
Package: iSEE
Commit: dbc35593bfd24a0b1d8a1752c3c6f48829980f0b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-04 19:48:08 +0100
Commit message:

 Simplified handling of plot.data.all in horizontal violins.
 
Package: iSEE
Commit: a1ce882d874b8df95fbb997e7cf96082dc772a34
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-04 19:40:13 +0100
Commit message:

 More selective generation of plot.data.all and plot.data.pre.
Adapted functions to use *.all or *.pre only when available.
Moved geom_blank out of create_points, into individual plotfuns.
Minor fixes to internal docs formatting.
 
Package: iSEE
Commit: d6fab9ead236808dfc7c8b60712a3d4509575ae4
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-03 19:01:15 +0100
Commit message:

 Release badge 
Package: iSEE
Commit: ede3521954b60017726b08253e4fb6449d7d0a28
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-02 17:43:43 +0100
Commit message:

 Merge pull request #186 from csoneson/renamed

Renamed feature expression to feature assay, for generality. 
Package: iSEE
Commit: 1e935f4a1dcf486d8f3129ba8d3e10f064a27eff
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2018-05-02 18:10:48 +0200
Commit message:

 rename completed in the tour section
 
Package: iSEE
Commit: 56c4370f88c4a087e74aca785316e028a1d4d27a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-02 16:38:43 +0100
Commit message:

 Updated version number, date, NEWS.
 
Package: iSEE
Commit: 17fac19c26ee72a7c60d799971445713cb06e0cf
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-02 15:26:42 +0100
Commit message:

 Merge branch 'master' into renamed
 
Package: iSEE
Commit: 514e330b56aa4974436d04a4e4107c631db2cac3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-05-02 14:55:36 +0100
Commit message:

 Changed 'Feature expression' to 'Feature assay' plot name.
Changed 'featExpr' to 'featAssay' in variables, arguments.
 
Package: iSEE
Commit: b55fd05b14fafc1a14b19c87fb7cf759be50c05b
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-01 16:49:20 +0100
Commit message:

 Merge pull request #185 from csoneson/bump

Bumpy bump 
Package: iSEE
Commit: 73bc4cc05665c8403e60bd8f04abe5ba8635e12b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-01 16:31:02 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master' into bump
 
Package: iSEE
Commit: f0f7c301f944972e5775111e52c00b8170c36489
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-05-01 16:20:46 +0100
Commit message:

 Merge pull request #184 from csoneson/RELEASE_3_7

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch 
Package: iSEE
Commit: af82c9695ac95f66f231888cb4ac289d86c50c14
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-05-01 16:04:08 +0100
Commit message:

 Merge branch 'master' into RELEASE_3_7 
Package: iSEE
Commit: 2ba7a5d8deb4a755de1658c134860d08dcb2b9a4
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-04-30 10:06:26 +0100
Commit message:

 Merge pull request #183 from csoneson/more_devel

Fixed downsampling for violin plots. 
Package: iSEE
Commit: 7da9ee49976f82fdc90b6df27af55cafda059b9f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-04-30 09:24:35 +0100
Commit message:

 Fixed downsampling for violin plots.
 
Package: BiocCheck
Commit: 2b0db51bd0244c8fc84e2237e6c095a497480a73
Author: lshep <shepherl@gmail.com>
Date: 2018-05-17 10:01:29 -0400
Commit message:

 Add check for set.seed in R/*.R files

   - Also generalized the wrapper around codetools findGlobals
 
Package: BiocCheck
Commit: 33747ee70be3ba8f7aaba7cfd0132c0bbce63be5
Author: lshep <shepherl@gmail.com>
Date: 2018-05-17 09:33:13 -0400
Commit message:

 Update class() == check to Warning instead of Note
 
Package: BiocCheck
Commit: c1c2bbc364a1bed42808c946c90cfc9495a012a8
Author: lshep <shepherl@gmail.com>
Date: 2018-05-17 09:31:15 -0400
Commit message:

 Add check for global option in vignette closes 22

   - catch if global option for vignettes using knitr is eval=FALSE
 
Package: BiocCheck
Commit: 132fbc5019bd88239b31e60deea8ba849eec3bab
Author: lshep <shepherl@gmail.com>
Date: 2018-05-16 14:31:28 -0400
Commit message:

 Add check for system vs system2
 
Package: BiocCheck
Commit: de82310260955d3503ac7c410da1d54ff7e71753
Author: lshep <shepherl@gmail.com>
Date: 2018-05-16 13:37:00 -0400
Commit message:

 Add check for class()== / class()!=

  - use is() over class()==
  - use !is() over class()!=
 
Package: trackViewer
Commit: 23eef5c62f881201fcefa05bf461e18be10cd768
Author: Jianhong Ou <jianhongou@riboimager.research.duhs.duke.edu>
Date: 2018-05-17 09:45:22 -0400
Commit message:

 add smooth function
 
Package: multiClust
Commit: 24233f60ca1e093b9b5f0f0f720d2f615383f3c7
Author: Nathan Lawlor <lawlon@mlg-jgm144.jax.org>
Date: 2018-05-17 09:01:38 -0400
Commit message:

 Updated NEWs file and pushed package version to 1.11.1
 
Package: hipathia
Commit: f13f723fc6ea1cf82aed8a3d9b830e72ea65be9f
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2018-05-17 10:50:30 +0200
Commit message:

 Bumping to version 1.1.1
 
Package: hipathia
Commit: 1322da09af9a78dd0d6182a0be64e3e1e74944ca
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2018-05-16 17:06:53 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'

Merge para traer los primeros cambios desde Bioconductor
 
Package: hipathia
Commit: 0a72802eeb8de291f4cc727171a1b528c05c7f6d
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2018-05-16 15:08:48 +0200
Commit message:

 Add top_pathways & simplify get_pathways_summary
 
Package: clusterProfiler
Commit: 8255e9faf1118a04179c1972e3965abb68fd8f36
Author: guangchuang yu <guangchuangyu@gamil.com>
Date: 2018-05-17 11:20:50 +0800
Commit message:

 color scheme
 
Package: Rsubread
Commit: 023e914e3f073144fea2f868f63d8eb6e4df5ea7
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-05-17 11:16:02 +1000
Commit message:

 (1) changed screen output in flattenGTF (not relevant to Rsubread, but anyways)
(2) fixed a bug in featureCounts
 
Package: CytoML
Commit: 76055b89ca6c410343cbfbd673a95aefa2b501f1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-16 15:56:06 -0700
Commit message:

 Merge branch 'trunk' into devel
 
Package: CytoML
Commit: ba474fc0bf507b6d23cafe54d78e58750233ba94
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-16 15:55:49 -0700
Commit message:

 bump
 
Package: CytoML
Commit: 74dfcc1cce39bcda513e2ed685a16cc3f68da7fc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-16 14:59:40 -0700
Commit message:

 import transform_gate from ggcyto
 
Package: ggcyto
Commit: e3a633d7e383c7f20aabb92d19c1d1a5cc5ccf8c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-16 15:53:51 -0700
Commit message:

 Merge branch 'trunk' into devel
 
Package: ggcyto
Commit: d872cef22cf87ce456a7629020f8e99111019113
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-16 15:53:07 -0700
Commit message:

 bump
 
Package: ggcyto
Commit: c56cba1099943b29cd14911668f3f79644f1da6e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-16 13:27:47 -0700
Commit message:

 transform data and gates properly before compute_stats for in-line scale layer. #33
 
Package: ggcyto
Commit: af3564c69a3120b4e06386f911cf9511323bb0b3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-16 11:54:12 -0700
Commit message:

 add transform methods for gates. #33
 
Package: ggcyto
Commit: 0a8a2b30eb697fa441057321c54086804db5dcdb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-15 12:51:35 -0700
Commit message:

 bump
 
Package: ggcyto
Commit: ffc40a38d96a5b1174549a06e697c01d275838b8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-05-15 12:51:05 -0700
Commit message:

 support flowCore::quadGate. #33
 
Package: dmrseq
Commit: f7b00c57b5219200c15f118a674ceadd391a21e5
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-16 18:11:37 -0400
Commit message:

 Version bump
 
Package: dmrseq
Commit: c5f881c8529ca9d79ff42a3ca77e8948743b3fd4
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-16 17:55:21 -0400
Commit message:

 Bug fixes for smoothing lines

Adding constrained smoothing so that smoothed lines can't extend
beyond the range of (0,1) by smoothing logit-transformed proportions
and plotting inverse-logit predictions. Also adding an adaptive
smoothing span parameter that uses a larger span for regions with
fewer points plotted (ranges from 1 to 0.75 for regions with up to
40 points (after that, span is fixed at 0.75)). In addition, adding
a check that at least two points exist before trying to plot a line.
 
Package: dmrseq
Commit: c595048b25b87bf3e191e95597caf849030afb99
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-16 16:33:59 -0400
Commit message:

 Add check for extreme beta values (unstable fit)

Also ensure that meanDiff calculation is in the same direction as beta values.
 
Package: dmrseq
Commit: 363e7ba60e7f77ea53ff6d79b19cb99972ba5e8c
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-05-16 10:57:37 -0400
Commit message:

 Check for replicates within candidate regions

This commit adds a check to ensure that candidate regions have
replicates (with coverage at least 1) in each group for at least
two CpGs within the region. This is only in
effect for factor comparisons.
 
Package: affycoretools
Commit: 53b3a070934a2497a3bc578c27ef07ec7895f0ad
Author: Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu>
Date: 2018-05-16 11:42:49 -0700
Commit message:

 Changed to use colored plotting symbols in makeImages, similar to how the lattice plots looked.
 
Package: epivizrServer
Commit: 0ec8b3ad5a8d437ebee30af19e9b804cd53cd171
Author: hcorrada <hcorrada@gmail.com>
Date: 2018-05-16 13:46:59 -0400
Commit message:

 version bump v1.9.1
 
Package: epivizrServer
Commit: baf94024c9963c036cb68fa01acfdcf23fac01b7
Author: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: 2018-05-07 11:16:34 -0400
Commit message:

 fix for changes in httpuv package (>= 1.4.0)
 
Package: MAST
Commit: 1f0c9e6fb79def478e46d55c1314d9857c1cfb1b
Author: Andrew McDavid <amcdavid@fhcrc.org>
Date: 2018-05-16 12:51:50 -0400
Commit message:

 start of vignette demonstrating interoperability
 
Package: MAST
Commit: 0df3abb5a123e3a5992eb990b17cdb410ba688b5
Author: Andrew McDavid <amcdavid@fhcrc.org>
Date: 2018-05-16 12:51:26 -0400
Commit message:

 import some missing methods to quell check() NOTES
 
Package: MAST
Commit: ba5f0b3b35cbaeb03a7d3ee10aa5735b64aa341f
Author: Andrew McDavid <amcdavid@fhcrc.org>
Date: 2018-05-16 12:48:33 -0400
Commit message:

 add coercion method from SingleCellExperiment
 
Package: BiocCheck
Commit: 4378c8af90391aab319c00426184dce5217e387c
Author: lshep <shepherl@gmail.com>
Date: 2018-05-16 11:52:27 -0400
Commit message:

 Update test for T/F usage

  - complaint that $T  or [T,] usage was being treated as TRUE/FALSE.
  - knitr moved to imports instead of suggest as need purl to check Rmd
  - namespace update for codetools::findGlobals, knitr::purl
  - move T/F check to best coding practices
  - fix indentation of messages that indicate affected files
  - separate sapply, 1:n and T/F check into individual functions for unit testing
  - checkLogicalUseFiles get all Rnw, Rmd, man, and R (not in R/*) scripts for testing
  - findLogicalFile searches a file for T/F usage
  - safeFindGlobals to encapsulate findGlobals in tryCatch for assignment error cases
  - findLogicalRdir check R/*.R scripts for global These are handled separate for two reasons:
       1. to output function rather than file name.
       2. to avoid errors with class and global assignment
  - makeTempRFile function to encasulate Rnw, Rmd, and man code into a dummy function for use
    with codetools::findGlobals
  - clean whitespace
  - update tests
 
Package: graphite
Commit: 9ed2276deb99885b80710aba4c862cf56df61f14
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2018-05-16 17:14:48 +0200
Commit message:

 Test markMultipleEdges()
 
Package: compEpiTools
Commit: a669c79ecf9f284b109b160a472b693306f53dac
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2018-05-16 15:03:34 +0100
Commit message:

 updated GRbaseCoverage
 
Package: compEpiTools
Commit: 6df7547fec44e618d60990f90a9f217cfac6f68a
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2018-05-16 14:59:59 +0100
Commit message:

 updated heatmapPlot
 
Package: Rhdf5lib
Commit: e385f9d455acc14af33070583b25d7e472e76a0a
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-05-16 14:13:55 +0200
Commit message:

 Updated COPYRIGHT notice
 
Package: baySeq
Commit: 3e1303b1849f487550aeeb5bcc55578ff1d37178
Author: t.hardcastle <tjh48@cam.ac.uk>
Date: 2018-05-16 11:06:34 +0100
Commit message:

 Added 'flatten' method for reducing countData object to a data.frame.
 
Package: plyranges
Commit: 92a195cec710e411eeb51f5d76eaa56b75989751
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-16 15:55:58 +1000
Commit message:

 doc fixes
 
Package: plyranges
Commit: ac4d090812781dd956e3e901f790d4d4cbf6b978
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-16 11:46:52 +1000
Commit message:

 add endomorphic tile/window method, fix doc typos, version bump
 
Package: plyranges
Commit: d84996a4bfe4738afd3fda4bd66756ce7dd6e58a
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-16 10:01:44 +1000
Commit message:

 endomorphic tile/slide methods
 
Package: plyranges
Commit: 83c96abc8b6ccb0237a62ebecbce32855651bcd7
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-15 14:42:06 +1000
Commit message:

 safer n and export chop_by methods
 
Package: plyranges
Commit: 71c66f17bc36698f9f7c2b684fc8cb63290afb58
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-14 14:45:56 +1000
Commit message:

 version bump
 
Package: plyranges
Commit: 7c953cec53a2b76749dad230ffdf65bdc6efe5eb
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-14 14:45:30 +1000
Commit message:

 add in get_genome_info methods for files
 
Package: plyranges
Commit: 51b3df00943606f2598badaf898ff0bb115545f2
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-14 14:30:16 +1000
Commit message:

 update to docs
 
Package: plyranges
Commit: 516d0cee80fd936f1ee8fe16cf40845a24daf1e7
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-14 14:21:41 +1000
Commit message:

 merge operators class
 
Package: plyranges
Commit: 3a8e546a55cda7e1d4ebcc5d3ed6ef5c63e95136
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-14 14:03:32 +1000
Commit message:

 improvements to BAM reading
 
Package: plyranges
Commit: 2d1ffc0b1b68198e18470a998f52e5f23a0aa856
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-10 18:22:30 +1000
Commit message:

 rlang has deprecated overscopes, replace with new_data_mask, testthat can't find the BiocGenerics versions of mean so causing errors in test - need to look into this more.
 
Package: plyranges
Commit: db63968e1a8db2ee1c698029bbb989d5f2c8b63b
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-10 16:35:35 +1000
Commit message:

 wayward print message
 
Package: plyranges
Commit: 9df6fba2989b9893f72bc660b38fdd2c8a0490ca
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-10 16:02:35 +1000
Commit message:

 prelim optimisation of group_by for summarise and filter
 
Package: plyranges
Commit: c73c4937ee5c4cce49c5d16e879f4a37c705d85d
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-10 14:08:23 +1000
Commit message:

 remove white space
 
Package: plyranges
Commit: c8a82fc144ba8f14bc9b31f3acfe6f7253feb265
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-10 10:08:15 +1000
Commit message:

 chop by works like grglist
 
Package: plyranges
Commit: ae02a75984eb1c966092b2956a59498a3c97ba45
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-09 14:45:07 +1000
Commit message:

 add chop_by functions
 
Package: plyranges
Commit: 5396b2b3256dfb2f6abfff72b631a23d50c6644b
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-09 14:02:13 +1000
Commit message:

 fix tests
 
Package: plyranges
Commit: d54e57a2fc8ffb235cd2764ae89176fa84ecad25
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-09 11:45:52 +1000
Commit message:

 merge in master
 
Package: plyranges
Commit: 3746c5a12d8b7a60fafe556bcc3f04ee73f27792
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-05-09 11:40:50 +1000
Commit message:

 better bam reding
 
Package: plyranges
Commit: 1c557cf53236103e7e8d19c3fd48c5e86cdf7977
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-04-29 22:21:26 +1000
Commit message:

 experiments with operators
 
Package: S4Vectors
Commit: fe33ed13de08128c02259044a492a8ee89d4ce95
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 21:53:01 -0700
Commit message:

 Small tweak
 
Package: S4Vectors
Commit: b15b5b451e43f1b9dc8a1350ee1b5c9996df71d8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 21:51:07 -0700
Commit message:

 Remove no more needed "bindROWS" method for matrix objects
 
Package: S4Vectors
Commit: 372f8d5438cf2dac742776352d2d99fa656f34c8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 17:37:39 -0700
Commit message:

 Add alias
 
Package: S4Vectors
Commit: 6ba6a367096073d163daea28f95a063c7092f020
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 17:35:35 -0700
Commit message:

 Fix bindROWS() on 1D arrays
 
Package: GenomicAlignments
Commit: 23c1870b24c97082b8ed35e60fe8983bbb252d3b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 15:49:13 -0700
Commit message:

 concatenateObjects() was renamed bindROWS() in S4Vectors 0.19.4
 
Package: InteractionSet
Commit: cf0389ab63b5fb997ec0c05fad4e7847bd854550
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 15:41:57 -0700
Commit message:

 concatenateObjects() was renamed bindROWS() in S4Vectors 0.19.4
 
Package: GenomicRanges
Commit: 87f0ac9af8cf90adfdfebcbbd7c64bc7d217316f
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 15:39:32 -0700
Commit message:

 concatenateObjects() was renamed bindROWS() in S4Vectors 0.19.4
 
Package: XVector
Commit: 76869afdc93b5b30739b95e265a7ed9c3be12b61
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 15:33:52 -0700
Commit message:

 concatenateObjects() was renamed bindROWS() in S4Vectors 0.19.4
 
Package: doppelgangR
Commit: 04b2b5124f39421fa8b007a1525f2b0fdf992b74
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-05-15 18:20:16 -0400
Commit message:

 move examples to examples field
 
Package: doppelgangR
Commit: 0fb24e46b39b09d709011b9ec2c1c5254777cdcd
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-05-15 16:30:51 -0400
Commit message:

 minor changes to resolve notes
 
Package: doppelgangR
Commit: 4416e1bd001153ddc72b76253935ddbfb43f6989
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-05-15 16:17:27 -0400
Commit message:

 import SummarizedExperiment functions
 
Package: doppelgangR
Commit: 8491bfa58c0bdcda9b0ace90be8acdc3461169c5
Author: Marcel Ramos <LiNk-NY@users.noreply.github.com>
Date: 2018-05-15 16:07:23 -0400
Commit message:

 Merge pull request #18 from maddahi93/master

Add colFinder and update doc with roxygen2 
Package: doppelgangR
Commit: d9bcb8fc4a31951ecb0d972c810121e224aae57c
Author: Fabio Da Col <fabiodacol.93@gmail.com>
Date: 2018-05-15 15:56:47 -0400
Commit message:

 Update documentation
 
Package: doppelgangR
Commit: 8b6aea344f184c123322ecfe9bf5cc1098358232
Author: Fabio Da Col <fabiodacol.93@gmail.com>
Date: 2018-05-15 12:30:11 -0400
Commit message:

 Update doc to roxygen2
 
Package: doppelgangR
Commit: 53a566ee7bd94d14a5ed31771dec5ab11a5df497
Author: Fabio Da Col <fabiodacol.93@gmail.com>
Date: 2018-05-15 11:11:48 -0400
Commit message:

 add colFinder function
 
Package: IRanges
Commit: ee0673ff30648946be13f927bbf9f493d8a09ea7
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 15:07:57 -0700
Commit message:

 concatenateObjects() was renamed bindROWS() in S4Vectors 0.19.4
 
Package: S4Vectors
Commit: 4a70d6103f0a7cd8076be30e2a0296c43fac9287
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 14:58:36 -0700
Commit message:

 Rename concatenateObjects() -> bindROWS()
 
Package: BiocStyle
Commit: 0585174e3af9eecb04e8c7b28d763e402e6b8532
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-05-15 23:11:12 +0200
Commit message:

 Make footnotes work with Pandoc 2.0 (fixes https://github.com/Bioconductor/BiocStyle/issues/48 and closes https://github.com/Bioconductor/BiocStyle/issues/49)
 
Package: flowCL
Commit: 0f79509ef52506d58e932faad99a569383538f6b
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-05-15 13:57:08 -0700
Commit message:

 Fixed conflickts in DESC
 
Package: flowCL
Commit: 136a955876569d77b57df9b837910ac052ff8592
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-05-15 13:32:18 -0700
Commit message:

 itemized NEWS
 
Package: flowCL
Commit: 4238d3384124ff52c6e0d8adcc86acd5a25daa13
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-05-15 13:31:53 -0700
Commit message:

 bumped
 
Package: ELMER
Commit: 1e3b4104d9407a2e15ee70186a4dbb4aaf26ea2e
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-05-15 15:04:39 -0300
Commit message:

 Warning remove
 
Package: ELMER
Commit: 721df1f7c7ea0a4ebab1de786603e47a5e8ae69d
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-05-14 16:39:11 -0300
Commit message:

 Adding dir.out option
 
Package: ELMER
Commit: 0061598ed397f8446d5475b0ad9ad04bc6fd8c8f
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-05-14 14:16:08 -0300
Commit message:

 Merge branch 'master' of https://github.com/tiagochst/ELMER
 
Package: ELMER
Commit: bf1856cb4ddae0e805709b5a96546c980d09fa9c
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-05-14 14:15:53 -0300
Commit message:

 improving heatmap gene plot
 
Package: ELMER
Commit: b3068956e4ee33e230c81edc6c31a62ec794076e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-11 17:00:41 -0300
Commit message:

 Adding missing file
 
Package: ELMER
Commit: 46d9a879d4ae2abf2e09540759863edc1230519c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-11 16:58:22 -0300
Commit message:

 Improving documentation
 
Package: ELMER
Commit: 725334e15d1210b325d07a82857399e3f49dcefa
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-05-11 16:41:37 -0300
Commit message:

 Updates in doc
 
Package: eegc
Commit: 55ec651ae22dd237bfe15bac5642a1e219e81f57
Author: Xiaoyuan <xiaoyuan@github.com>
Date: 2018-05-15 10:33:52 -0700
Commit message:

 Version bump
 
Package: gep2pep
Commit: bed8dc9938b4c1e266aba3b5ea30df078792ad01
Author: ciccio <franapoli@gmail.com>
Date: 2018-05-15 19:17:06 +0200
Commit message:

 updated README
 
Package: gep2pep
Commit: 426659218695fcd3a1c707ce1141709212a6ab2b
Author: ciccio <franapoli@gmail.com>
Date: 2018-05-15 18:58:48 +0200
Commit message:

 metadata fixes for new devel version
 
Package: gep2pep
Commit: a6e6181c7780b609ee2a5879eba0c718a9ea4e26
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-05-15 17:53:02 +0200
Commit message:

 fixes and added subset to pathSEA
 
Package: gep2pep
Commit: 2d26790c6735851078dde895b2e3e2baee3cf052
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-02-23 13:48:32 +0100
Commit message:

 removed CondSEA merging method from tests
 
Package: gep2pep
Commit: 0e67c628ae88aeb7586d398fa767dce003a0a5c4
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-02-16 17:47:38 +0100
Commit message:

 exported and documented createMergedRepository, BiocCheck clean
 
Package: gep2pep
Commit: 6c2d930175b1b3a8b3e3981c3c472279b9787fa5
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-02-16 17:10:24 +0100
Commit message:

 Final raw mode - BiocCheck clean

CondSEA now uses the new function .getPEPRanks to compute
HDF5-cache-enabled ranks from HDF5.

Added createMergedRepository

Fixed collection names. Special characters are lost in
file raw-mode file names, but now they are recovered using gene set
collection names.

as.CategorizedCollection not needed anymore for example pathways.

Added missing documentation
 
Package: gep2pep
Commit: 4d479570cd4c238c6e5643858b06a94fdb1bedd0
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-01-24 12:14:45 +0100
Commit message:

 This version includes an experimental merging method with caching that is probably going to be replaced with a less automatic method
 
Package: gep2pep
Commit: 9072fb9540bbe10d73b2bbfff0c90754ca87a347
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-01-19 12:42:44 +0100
Commit message:

 added organism option for importMSigDB.xml, added minsize and maxsize for computing KS statistic, changed rawmode datasets, added PEPs ranking function as a parameter, minor bug fixes
 
Package: gep2pep
Commit: 802e77201d425fae5cb2ee372c1dd56bbb37a1b5
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-01-01 21:46:39 +0100
Commit message:

 Merge branch 'untested' of github.com:franapoli/gep2pep into untested
 
Package: gep2pep
Commit: 261fe7355101156312712fb5a9b89c4dc17b0201
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-01-01 21:46:27 +0100
Commit message:

 restoring rownames and colnames as chunk size solves the problem of huge file size
 
Package: gep2pep
Commit: 062134e2d4b3f44e339388ff45a217702b5c83b3
Author: ciccio <franapoli@gmail.com>
Date: 2018-01-01 20:58:22 +0100
Commit message:

 added .loadPEPs for raw mode
 
Package: gep2pep
Commit: 0fbdae6554eaf29d0a3b1f05db59f04254b4cc05
Author: Ciccio <f.napolitano@tigem.it>
Date: 2018-01-01 20:22:16 +0100
Commit message:

 changed _ to # in raw mode file names
 
Package: gep2pep
Commit: ea12838aa181ea975a9d2baa1dcfaf6497d4f69a
Author: ciccio <franapoli@gmail.com>
Date: 2017-12-26 19:28:38 +0100
Commit message:

 raw mode: temp file directly into repository
 
Package: gep2pep
Commit: 2af81ba2b3d209d8621060592d79f9388e643dd4
Author: Ciccio <f.napolitano@tigem.it>
Date: 2017-12-26 18:53:17 +0100
Commit message:

 added slection of collections in raw mode import
 
Package: gep2pep
Commit: f44f37feafbbd7f4d86b512e377e3c7916a76ab3
Author: ciccio <franapoli@gmail.com>
Date: 2017-12-26 13:01:32 +0100
Commit message:

 importFromRawmode working
 
Package: gep2pep
Commit: 41af8cf45be93c6e3a109feac424c14f05be3a11
Author: Ciccio <f.napolitano@tigem.it>
Date: 2017-12-23 15:55:55 +0100
Commit message:

 added hdf5 composition, fixed version number to comply with bioconductor
 
Package: gep2pep
Commit: 9096611ea9a11a91bcb3a7b8c44e1d66df587336
Author: Ciccio <f.napolitano@tigem.it>
Date: 2017-12-20 15:49:38 +0100
Commit message:

 updated version number
 
Package: gep2pep
Commit: 2e701c0ecea5792f09f252a153a20be3ea775dd6
Author: ciccio <franapoli@gmail.com>
Date: 2017-12-20 15:47:00 +0100
Commit message:

 added raw mode
 
Package: gep2pep
Commit: dd193279ff4a3e87795b08643d074f37d9285b50
Author: ciccio <franapoli@gmail.com>
Date: 2017-11-22 17:29:51 +0100
Commit message:

 couple minor changes to vignette
 
Package: xps
Commit: 0d3ccd05a653119a496a2b1f72b9ead4f5f3aec5
Author: cstrato <cstrato@aon.at>
Date: 2018-05-15 19:08:54 +0200
Commit message:

 Fixed conflicts in version change
 
Package: DESeq2
Commit: 50070e7a32c1d66e5d7f72d17cbb9c0841118d21
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-05-15 12:48:10 -0400
Commit message:

 add fix from nalcala
 
Package: IRanges
Commit: a8bfc8ef91011534521f846030252d68b5e464b9
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 08:37:55 -0700
Commit message:

 Fix DF[IRanges(...), ] on a DataFrame with data.frame columns

This is fixed by adding an extractROWS,data.frame,RangesNSBS method.
Also move extractROWS,array,RangesNSBS method from the S4Vectors package.
 
Package: S4Vectors
Commit: ebd0e1ac8cd5cda79274b55a077b87e4f754fef8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-05-15 08:31:11 -0700
Commit message:

 Fix window() on a DataFrame with data.frame columns

This is fixed by adding an extractROWS,data.frame,RangeNSBS method.
Also move extractROWS,array,RangesNSBS method to the IRanges package.
 
Package: pathVar
Commit: 0e1729b6758d782795b7fcf929f341479a6fd5be
Author: Sam Zimmerman <SamEZ@Samuels-MacBook-Pro.local>
Date: 2018-05-15 10:39:16 -0500
Commit message:

 update NEWS file
 
Package: attract
Commit: dccd14b12a96ca12d5482b41f962e9a828c97cef
Author: Sam Zimmerman <SamEZ@Samuels-MacBook-Pro.local>
Date: 2018-05-15 10:27:40 -0500
Commit message:

 update NEWS file
 
Package: SRAdb
Commit: 66e4ba1d5c1833b4d3f63038267333645e058821
Author: zhujack <zhujack@mail.nih.gov>
Date: 2018-05-15 10:24:06 -0400
Commit message:

 remove unspoortedsystem win in .BBSoptions and bump the version
 
Package: MEAL
Commit: ca5a092af0d380a3770412c1de5cd8ceb98b0e10
Author: Carlos Ruiz <yocra3@gmail.com>
Date: 2018-05-15 15:48:59 +0200
Commit message:

 Export deprecated functions
 
Package: podkat
Commit: 3912e716be54f8411920a5f39b990a33a209b3b4
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 15:19:46 +0200
Commit message:

 added GitHub URL to DESCRIPTION
 
Package: podkat
Commit: 5d43d8e75300728f1ccaf98546086251e5c6c73c
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 15:16:40 +0200
Commit message:

 added README.md and .gitignore
 
Package: MDTS
Commit: 149285cf124c2c4190daca2f89a348760ac5714c
Author: Jack Fu <jmfu@jhsph.edu>
Date: 2018-05-15 08:50:33 -0400
Commit message:

 bug fix: subsampling, filtering bug fix
 
Package: MDTS
Commit: b41c9914619be58d35e8e39ab24e043694e9cb12
Author: Jack Fu <jmfu@jhsph.edu>
Date: 2018-05-15 08:35:31 -0400
Commit message:

 Merge remote-tracking branch 'origin/master'
 
Package: MDTS
Commit: 773315fe9a109343b65c2d90f974dfccca4cc9cc
Author: Jack Fu <jmfu@jhsph.edu>
Date: 2018-05-15 07:46:37 -0400
Commit message:

 Update denovoDeletions.R 
Package: MDTS
Commit: 8253d1710cb3c0e8557899e5bc51655ede46e35e
Author: Jack Fu <jmfu@jhsph.edu>
Date: 2018-05-15 07:45:38 -0400
Commit message:

 Update denovoDeletions.R 
Package: MDTS
Commit: 8e18c49f0deebaee49f559bcb6ccaf66c97c5d6c
Author: Jack Fu <jmfu@jhsph.edu>
Date: 2018-05-15 07:44:30 -0400
Commit message:

 Update denovoDeletions.R 
Package: msa
Commit: c635f4fd2819174147dc984597aa6e0d7c32d039
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 14:29:11 +0200
Commit message:

 added README and .gitignore
 
Package: kebabs
Commit: 013971c0ad3ae049d050ebac179a84cdd8eb0b9a
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 14:23:51 +0200
Commit message:

 updated DESCRIPTION (add GitHub URL)
 
Package: kebabs
Commit: 9e4130c9e70d890d232d5b4167f49a02ca356e08
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 14:17:07 +0200
Commit message:

 updated README
 
Package: kebabs
Commit: 147986d3061d6ee48238df0fa623548277ea6cd9
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 13:46:58 +0200
Commit message:

 corrected README
 
Package: kebabs
Commit: ee8f6bd0a174fa6d9926dd8e3c5ea613d70566ad
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 13:25:31 +0200
Commit message:

 added README
 
Package: kebabs
Commit: 19b2387a1a75f4100edb1455a55a9dde9a869c64
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 13:21:41 +0200
Commit message:

 added .gitignore
 
Package: procoil
Commit: 96ca73350efa31544c1caa454dd8a17b0adb0de1
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 14:22:46 +0200
Commit message:

 updated DESCRIPTION
 
Package: procoil
Commit: 59a7d4ae0f729898834c732780a648859a2d76f0
Author: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Date: 2018-05-15 14:14:58 +0200
Commit message:

 added README
 
Package: xps
Commit: 4121457fa6e63add414ea90243d7cdae3f701492
Author: cstrato <cstrato@aon.at>
Date: 2018-05-15 13:00:24 +0200
Commit message:

 update for NEWS
 
Package: xps
Commit: cf326be13344052e7c1b3ee1eae822fca0349f1b
Author: cstrato <cstrato@aon.at>
Date: 2018-05-14 19:48:32 +0200
Commit message:

 update for NEWS
 
Package: xps
Commit: 7616d6070720cf6a7b929e1014154f9e62c6fbbb
Author: cstrato <cstrato@aon.at>
Date: 2018-05-12 11:11:37 +0200
Commit message:

 update for NEWS
 
Package: SummarizedExperiment
Commit: 4b6465c02825c30d8322a32eb5582ce50b975856
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-05-15 05:54:30 -0400
Commit message:

 closes #11, fix 'getter' example in 'Extensions' vignette
 
Package: SummarizedExperiment
Commit: 50d165e5f100681a201c4bb72b81a8daedcf32c1
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-05-15 05:54:16 -0400
Commit message:

 version bump
 
Package: SummarizedExperiment
Commit: df1bfefa7f6a8a64b24b32fae42f480d52e5f601
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-05-14 19:18:41 -0400
Commit message:

 Fix 'getter' example in 'Extensions' vignette
 
Package: gdsfmt
Commit: 7f8146f6ca7e46e54138580b155b5f93ef98d0a3
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2018-05-15 01:56:28 -0700
Commit message:

 bug fixed: put.attr.gdsn() fails to update the existing attribute
 
Package: DMRcaller
Commit: ca459c035644a56b44a7f0a5a3473e9fee1c6588
Author: nrzabet <n.r.zabet@gen.cam.ac.uk>
Date: 2018-05-15 09:04:55 +0100
Commit message:

 bug fix: error with betareg when less than 3 samples are used
 
Package: DMRcaller
Commit: 8a32249291be76be22e8c8e12c2b0badc95fb2b8
Author: nrzabet <n.r.zabet@gen.cam.ac.uk>
Date: 2018-05-15 09:02:26 +0100
Commit message:

 bug fix: error with betareg when less than 3 samples are used
 
Package: clusterExperiment
Commit: 7dfbdc543140422a394f024077a25a415fc33ed3
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2018-05-15 08:50:22 +0200
Commit message:

 release bug fix
 
Package: clusterExperiment
Commit: ae5ae67e78aa894fe7fac6b8dba00215f17a3dd8
Author: Davide Risso <dar2062@med.cornell.edu>
Date: 2018-05-03 14:50:20 -0400
Commit message:

 Fix version in master
 
Package: clusterExperiment
Commit: 13d3aefffb8a907d77660ebef2fb285ca4bacf59
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2018-05-02 14:58:55 +0200
Commit message:

 update rbuild ignore
 
Package: clusterExperiment
Commit: f1e48df364db61bd4fd932ac8e8c30b3bcc042fc
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2018-05-02 14:51:48 +0200
Commit message:

 fix merge
 
Package: clusterExperiment
Commit: c2bda2dadc37de2f0d94b6007a9001b38dd7c283
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2018-05-02 14:51:05 +0200
Commit message:

 update README description
 
Package: clusterExperiment
Commit: 148544a71a7c8d3115e5ed4e3b033ec9ebed433f
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2018-05-02 14:44:16 +0200
Commit message:

 add update on 2.0
 
Package: RCy3
Commit: b00d54118bd8ee2bbcdd396e93b9299548dc1195
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-05-14 23:17:16 -0700
Commit message:

 version bump
 
Package: RCy3
Commit: 4631ea54a6d0e6cfda411effcc9c5d478f0357e6
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-05-14 23:16:11 -0700
Commit message:

 bug fix: #21
 
Package: Rsubread
Commit: 41301c099ab0a6d0db52c88b4ca009a074f17f57
Author: Wei Shi <shi@wehi.edu.au>
Date: 2018-05-15 13:15:56 +1000
Commit message:

 Provide download link for human reference genome.
 
Package: doppelgangR
Commit: b869ad9d95837cf4d3c9e2b1aea26a3e5587e5a1
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-05-14 20:08:39 -0400
Commit message:

 version bump
 
Package: doppelgangR
Commit: 8cffeb6a9a23cbcfd8c7acfd2aefe96c54cb9d11
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-05-14 19:37:10 -0400
Commit message:

 use apply with margin = 2, closes #17
 
Package: doppelgangR
Commit: ad7446ecb4c6b77841d380e4abe6cb5d9f6f7e21
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-09-28 14:53:33 -0400
Commit message:

 Updated unit tests for change in ExpressionSet behavior.
 
Package: doppelgangR
Commit: 3f25e384c4f431349fb58e7bcc98868203dde27c
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-03-07 12:21:29 +0100
Commit message:

 Fix errors caused by auto-formatting, version to 0.99.0
 
Package: doppelgangR
Commit: 87de32e07abebf6ae8ad83f1be5d20924571f8a6
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-03-07 11:41:54 +0100
Commit message:

 Code re-formatting.
 
Package: doppelgangR
Commit: 0c960d81074e658a767ae6cbdb49ac38877ccf4f
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-03-07 09:59:27 +0100
Commit message:

 Minor updates to DESCRIPTION, NEWS, vignette.
 
Package: doppelgangR
Commit: 35b314aac0e3f1aa6c22fe63ed9c41d852e814a5
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-03-07 01:58:45 +0100
Commit message:

 Improvements to vignette, fix outlierFinder.Rd example.
 
Package: doppelgangR
Commit: c8bc722d7f0e3b1dda30755cc4a9d502cd819664
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-03-02 16:02:51 -0500
Commit message:

 add entries to vignette
 
Package: doppelgangR
Commit: 217e33415836e3b3cef45fcaf8e11303a2f5e915
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-03-02 10:48:19 -0500
Commit message:

 shorten examples in phenoDist
 
Package: doppelgangR
Commit: 65dc08ea83d8ec1b2fb0d396018aac664be10ff4
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-03-02 14:06:37 +0100
Commit message:

 Remove some apparently spurious aliases from summary-methods.R:

-\alias{summary,ANY-method}
-\alias{summary,diagonalMatrix-method}
-\alias{summary,sparseMatrix-method}
 
Package: doppelgangR
Commit: a64ad1de51e95b0e5d8d3ab62b1057ceba72d96c
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-03-02 13:54:09 +0100
Commit message:

 Add example for phenoDist().
 
Package: doppelgangR
Commit: 21cdcf9613d6db0511d6ff9d133927ad3eafa8b0
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-03-01 18:21:04 -0500
Commit message:

 either method works, use bpparam consistent with docs
 
Package: doppelgangR
Commit: b7ed20f001f5c1a46ec5d9f82e0fbb28fe3c9aa1
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-03-01 18:10:36 -0500
Commit message:

 add examples and edit bpparam
 
Package: doppelgangR
Commit: fbbc9dc4b7cd31fbaaf114459b9872f16a2efeea
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-29 19:31:06 -0500
Commit message:

 add examples, fix docs, organize DESC
 
Package: doppelgangR
Commit: 173beda034bd9adcd4a3fdf83b6bfe79611a7bc9
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-29 11:54:14 -0500
Commit message:

 update upstream with origin merge changes
 
Package: doppelgangR
Commit: 6b328cfc9ef5ca131d06c3584d92b9c61dd793be
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-29 10:24:48 -0500
Commit message:

 Merge branch 'master' of github.com:LiNk-NY/doppelgangR
 
Package: doppelgangR
Commit: a40bd24c8cf0418fe6eb95fecd2c3b68d22cc899
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-29 10:26:55 +0100
Commit message:

 Add example for vectorHammingDistance.R, add Marcel as package author.
 
Package: doppelgangR
Commit: 40384d649814f37a9d4ba28d783fcce03a5d313c
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-28 17:11:34 -0500
Commit message:

 add examples to docs
 
Package: doppelgangR
Commit: 1c91f765d843c113e62abd7629c4eb962d1fee77
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-23 18:37:45 +0100
Commit message:

 Remove duplicates from TCGA ovc study. Make AUC-annotated suitability table.
 
Package: doppelgangR
Commit: 8fddad1ac7d8a632b4153f1c271a91337ac35f17
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-23 11:23:20 +0100
Commit message:

 Syntax fixes, uncomment loading of tcga.res.
 
Package: doppelgangR
Commit: a2ca05e70163158699e7e89a25c34894c665e6d5
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-23 11:18:14 +0100
Commit message:

 ROC plots for microarray-rnaseq matching, use primary samples only.
 
Package: doppelgangR
Commit: 4c8a82415d8d7037479633ab75a7188af5220250
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-23 11:10:29 +0100
Commit message:

 Save esets with primary tumors only.
 
Package: doppelgangR
Commit: 5dca31033803d5aa1e44fd5288346b050fdcfbef
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-22 22:46:31 +0100
Commit message:

 log(x+1) for RNA-seq data.
 
Package: doppelgangR
Commit: c4f7fce0d065ab44cda62c4c40a597da53716417
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-22 21:41:20 +0100
Commit message:

 modified:   TCGA_microarray_RNAseq.R - turn off all but correlation doppelgangers
 
Package: doppelgangR
Commit: 0551937f70325f173e494417b5cdd4dcfc453739
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-22 14:06:59 -0500
Commit message:

 update pkg to pass checks
 
Package: doppelgangR
Commit: 7305179442df9d0745e8f4e2405b9a5e66a387db
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-22 19:40:13 +0100
Commit message:

 Microarray / RNA-seq paired datasets from TCGA.
 
Package: doppelgangR
Commit: 58a6d6b2b6edefd36ceb8a91c044a3732f86d7f9
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-12 16:24:05 -0500
Commit message:

 add changes
 
Package: doppelgangR
Commit: 872478172a787d2ef65bc05a1168c67321be0fd1
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-03 17:29:15 -0500
Commit message:

 minor edit to vignette
 
Package: doppelgangR
Commit: daea4d590916c3fed2e1cbd15c214062cab38b0e
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-03 14:10:10 -0500
Commit message:

 Merge with upstream master
 
Package: doppelgangR
Commit: 809b569c94773e6901d8231fa56353e3cbae4b96
Author: LiNk-NY <mramos09@gmail.com>
Date: 2016-02-03 14:07:11 -0500
Commit message:

 Rename class file
 
Package: doppelgangR
Commit: d3cdd6147e8b7c9ce081f77b13e348f8c1cb7eca
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2016-02-03 14:52:32 +0100
Commit message:

 Minor vignette updates (ROCR::prediction) and fixes to .Rbuildignore.
 
Package: doppelgangR
Commit: aaff7dc52dde2adca3cbbfdc78dd8b1ecf88329e
Author: lwaldron <lwaldron.research@gmail.com>
Date: 2015-12-03 18:22:20 -0500
Commit message:

 New Supplemental Figure 1.
 
Package: doppelgangR
Commit: 72d74e7c72e43de2efa69c92a3927c44405c1b19
Author: lwaldron <lwaldron.research@gmail.com>
Date: 2015-12-02 16:32:54 -0500
Commit message:

 TCGA.R: fix to work with updated cancer table, don't eliminate
emargoed (last embargo ends 12/18/2015).
 
Package: doppelgangR
Commit: afcc169972c518b1c276f066c0735c81ec2c323a
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-28 17:55:41 -0500
Commit message:

 Merge branch 'master' of github.com:lwaldron/doppelgangR
 
Package: doppelgangR
Commit: 218b7c4a5d01e46fe4cfca58ac45fd7c7e96d5ac
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-28 17:55:26 -0500
Commit message:

 Case study clean-up.
 
Package: doppelgangR
Commit: 02ef317300a2c7386b9b007d95d85e9c3829bdc4
Author: lima1 <mriester@gmx.de>
Date: 2015-11-28 16:24:32 -0500
Commit message:

 Merge branch 'master' of https://github.com/lwaldron/doppelgangR
 
Package: doppelgangR
Commit: 69fa8372b871862cfe26945f240a69f45824130a
Author: lima1 <mriester@gmx.de>
Date: 2015-11-28 16:24:13 -0500
Commit message:

 added two more cell-lines
 
Package: doppelgangR
Commit: c45bea752516d9d4aac4bf3baa3d0e1dfcd97949
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-28 13:37:05 -0500
Commit message:

 Performance on small ovc datasets.
 
Package: doppelgangR
Commit: 7b2cf9d028020fe3957ad56ab4170b63993fb37a
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-28 12:29:34 -0500
Commit message:

 Fixed "doppelgangR(esets[[1]]) :  Intermediate pruning off but no addCols shortcut available. error."
 
Package: doppelgangR
Commit: 928971d94648f3020a6714bb0c47d1a58261bb48
Author: lima1 <mriester@gmx.de>
Date: 2015-11-28 00:08:25 -0500
Commit message:

 fix merge
 
Package: doppelgangR
Commit: 329e941efc861e0a13ed534519eff23cdc64124b
Author: lima1 <mriester@gmx.de>
Date: 2015-11-28 00:05:32 -0500
Commit message:

 fix merge
 
Package: doppelgangR
Commit: f81135707a2c31716b901746a18766241d62b14f
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-27 23:30:06 -0500
Commit message:

 esets -> eset.pair in phenoFinder.R (fixes bug)
 
Package: doppelgangR
Commit: 38efe1e087e730bc610202aca0f9a8ac5e35af83
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-27 23:09:23 -0500
Commit message:

 Remove browser() line...
 
Package: doppelgangR
Commit: 66f67a8f75ed8750d241a0d41f116c20f72583f3
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-27 23:07:34 -0500
Commit message:

 New function to check whether pair of esets are "close enough".
 
Package: doppelgangR
Commit: 7853b83de8a7ee7765fb93961e11efce77b89b6b
Author: lima1 <mriester@gmx.de>
Date: 2015-11-27 21:39:36 -0500
Commit message:

 merge
 
Package: doppelgangR
Commit: 710ccf4e72898f98d0cf4f24efda4552be790fe0
Author: lima1 <mriester@gmx.de>
Date: 2015-11-27 21:38:32 -0500
Commit message:

 Merge branch 'master' of https://github.com/lwaldron/doppelgangR
 
Package: doppelgangR
Commit: 62266983bcdfb9a89e00f408d30c4c323f40bf57
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-27 21:35:22 -0500
Commit message:

 Analysis of GSE44104, get rid of _1.0 in filenames for *.R.
 
Package: doppelgangR
Commit: 054d1f2ba2a85657ca6b234f471269d505f221c2
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-21 15:47:13 -0500
Commit message:

 Leaving only confirmed duplicates.
 
Package: doppelgangR
Commit: a788000ca85674f269b5b66b02d2cf1c687f4ca0
Author: lima1 <mriester@gmx.de>
Date: 2015-11-21 14:58:38 -0500
Commit message:

 refactor corfinder: moved combat into private function
 
Package: doppelgangR
Commit: d7f19febcc00ca7ac079762a565f5b5d20301733
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-21 14:24:24 -0500
Commit message:

 smoking gun-finder no longer calls NAs matches.
 
Package: doppelgangR
Commit: 0e3cfc3f224453bb88d24397ef01ea70b5f5002e
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-21 14:09:13 -0500
Commit message:

 File of confirmed doppelgangers.
 
Package: doppelgangR
Commit: d6efbcc0303abd080e2425963d5de1d6634eab54
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-15 19:47:46 -0500
Commit message:

 Merge branch 'master' of github.com:lwaldron/doppelgangR
 
Package: doppelgangR
Commit: 7d8472388fbdf937b4e2555087a3cc6411e37651
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-15 19:47:31 -0500
Commit message:

 Spearman's correlation examples to vignette.
 
Package: doppelgangR
Commit: a61d46621e2f9b49e11e950c22514a5e9b2b684e
Author: lima1 <mriester@gmx.de>
Date: 2015-11-15 17:37:39 -0500
Commit message:

 added NCI60/CCLE analysis
 
Package: doppelgangR
Commit: d3266fe805bffcad00d59a54a6b6dcad69e5416e
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-14 22:43:46 -0500
Commit message:

 Unit test for missing one or both pData.
 
Package: doppelgangR
Commit: 7bd23aac0bfff9acd775bec83645c42f1ad59249
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-11-14 22:42:41 -0500
Commit message:

 Bugfix so now runs when pData missing for both ExpressionSets.
 
Package: doppelgangR
Commit: 622e5adfa25e779f5cdd7b30a54d33ed2eaf8dcf
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-09-26 17:05:41 -0400
Commit message:

 Test all databases for smoking guns only, convert vignette to Rmd, add unit test for checking smoking guns only.
 
Package: doppelgangR
Commit: 3e2c04c4fea58a2215294d37aca02c1d9e9b6f5b
Author: lwaldron <lwaldron.research@gmail.com>
Date: 2015-09-09 13:27:20 -0400
Commit message:

 added biocViews, NEWS, renamed vignette to vignettes.
 
Package: doppelgangR
Commit: 32b14e6707859a1e7a040435ee59a2e3b1577372
Author: lwaldron <lwaldron.research@gmail.com>
Date: 2015-09-09 10:58:38 -0400
Commit message:

 Fix documentation warnings for plot-method.
 
Package: doppelgangR
Commit: 656b4ea1cb4a8e3f6a5a566d973842780fd364c3
Author: lwaldron <lwaldron.research@gmail.com>
Date: 2015-09-09 10:30:25 -0400
Commit message:

 Fixed imports, ExpressionSet method. All unit tests passing. V. 0.11.
 
Package: doppelgangR
Commit: f0e02bca770efab4671a8290cd2580f0ec5cc674
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-15 22:04:54 -0500
Commit message:

 Put three ROC plots panels into one plot for RNA-seq vs microarray in ovarian.
 
Package: doppelgangR
Commit: 3ae1fd7107a758a3783404cc73cc7c1e724e4b03
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-15 21:12:50 -0500
Commit message:

 HR vs. % duplication example.
 
Package: doppelgangR
Commit: 6388fc4b5723a9023cab8516aa2c1e81f7f1804e
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-15 19:16:52 -0500
Commit message:

 Added .Rbuildignore.
 
Package: doppelgangR
Commit: a0813f324b628765d295f4082f334ccadf500013
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-15 18:10:46 -0500
Commit message:

 Forgot to bump version number.
 
Package: doppelgangR
Commit: 19a81a44e4ad9fa1db1973c876df2786a7091e8d
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-15 18:09:23 -0500
Commit message:

 Fixed plot method so density line is scaled correctly.
 
Package: doppelgangR
Commit: 4d48bbf8c556265e24b53d807de9e85891761475
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-14 22:26:55 -0500
Commit message:

 Now look at samples instead of sample pairs for ROC plots in four cancer types.  AUC goes from 0.98 to 0.97.
 
Package: doppelgangR
Commit: 04df578ba4d7dc3a1db164b9b87fa48eec85e659
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-14 19:57:58 -0500
Commit message:

 Merge branch 'master' of github.com:lwaldron/doppelgangR
 
Package: doppelgangR
Commit: 55f6aa1b29b2ab24fdfd6d7aadb7491249b44369
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-14 19:57:35 -0500
Commit message:

 Fixed doppelmelt in vignette.
 
Package: doppelgangR
Commit: 6e68f2bcb2c5c4fe98e9c7893f02f3c180f661fc
Author: lima1 <mriester@gmx.de>
Date: 2015-02-14 18:33:39 -0500
Commit message:

 removed sweave syntax
 
Package: doppelgangR
Commit: f31a5a77df6cf1ec5c099a15cd24f3ab33dae31d
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-12 14:55:43 -0500
Commit message:

 Added missing library(ggplot2).
 
Package: doppelgangR
Commit: 14819ac0baa304d87f35b75ee3ad6213e91b8098
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-12 14:53:43 -0500
Commit message:

 Switch to Marcel's fork of RTCGAToolbox to use his extract function,
and get rnaseq / rnaseq2 in every case (whichever has more samples).
 
Package: doppelgangR
Commit: a108aee83cb80ea9d5fc12b6dae11f8471f4fc89
Author: lima1 <mriester@gmx.de>
Date: 2015-02-10 10:58:14 -0500
Commit message:

 used quantile, not median to sort
 
Package: doppelgangR
Commit: 6370659237b0a739aa8a325d7c4557deae74386d
Author: lima1 <mriester@gmx.de>
Date: 2015-02-09 23:35:14 -0500
Commit message:

 violin plot
 
Package: doppelgangR
Commit: 96e6a97cffc217bc2f99ef109274d7b350589eb8
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-08 18:02:08 -0500
Commit message:

 Analyses for paper - TCGA table updates, ROC plots for 4 cancer types.
 
Package: doppelgangR
Commit: 69bca55a30a6a61e9f5f547c038c7e003dfa369a
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-08 07:01:37 -0500
Commit message:

 Add summary table of all samples.
 
Package: doppelgangR
Commit: bf1fd467fa6318fece44b41e1ab741703e28d5c3
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-08 06:44:45 -0500
Commit message:

 Added suitability.table to TCGA.R.
 
Package: doppelgangR
Commit: 180490e363d9f7d68b48820420fc59449ab28c5c
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-03 11:33:59 -0500
Commit message:

 Working analysis of within-dataset expression correlations for all TCGA data types.
 
Package: doppelgangR
Commit: 223f4bf16ed337b4aacd0ae1aef4b54cae0a2b54
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-03 08:03:47 -0500
Commit message:

 Merge branch 'master' of github.com:lwaldron/doppelgangR
 
Package: doppelgangR
Commit: 1ce809c23480aafe89452d77245c1996af97544b
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-03 07:46:44 -0500
Commit message:

 Oops, re-add inst/*.R.
 
Package: doppelgangR
Commit: 30753235da3a88c2f160c38a626b573f51e31a65
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-02 16:51:45 -0500
Commit message:

 Merge branch 'master' of github.com:lwaldron/doppelgangR

Conflicts:
	inst/TCGA.R
 
Package: doppelgangR
Commit: d2b9fec5ab0eb0eb1335a3fb50310803cbe5aea8
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-02-02 16:49:00 -0500
Commit message:

 Extractor function for RTCGAToolbox data.
 
Package: doppelgangR
Commit: 6ae59ca2700f58505dc69f5604fbf350f71e3761
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-31 11:44:26 -0500
Commit message:

 Saving bonf.prob=1.0
 
Package: doppelgangR
Commit: dcf420af7c323d7443226d8793a4cf60783d1b8e
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-31 10:21:29 -0500
Commit message:

 Catch errors in TCGA.R
 
Package: doppelgangR
Commit: 796bb514bca085d256e695c08f1834db6c19c057
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-31 10:19:11 -0500
Commit message:

 Merge branch 'master' of github.com:lwaldron/doppelgangR
 
Package: doppelgangR
Commit: 2b7c5876315d1129cea319d3806874d236999035
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-31 10:18:57 -0500
Commit message:

 Threshold at bonf.prob=1.0.
 
Package: doppelgangR
Commit: 7eaa6a8451abb09cdefd1e1819065d0e54510552
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-31 10:16:04 -0500
Commit message:

 Doppelganger summarizer script (countdops.R) and TCGA downloader (TCGA.R).
 
Package: doppelgangR
Commit: 317f5e4cf0977bdb77cdcc20baf22c4e13b0d780
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-30 22:09:59 -0500
Commit message:

 Save esets lists.
 
Package: doppelgangR
Commit: 2a2e670a4c077f81eaa3827060e5f025761efeb3
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-30 15:46:44 -0500
Commit message:

 Fix error in CRC caused by infinite expression values.
 
Package: doppelgangR
Commit: 13d5b28d786003609d53bea52a9b25b34db6333d
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-30 08:44:19 -0500
Commit message:

 Slight correction to unit test.
 
Package: doppelgangR
Commit: f5995d8bc01bb74677d46fd2cfd56184e3b7d896
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-28 20:56:03 -0500
Commit message:

 More unit tests.
 
Package: doppelgangR
Commit: 2486ad9f0ef92d363edbb9fcedc3271e2d56dcb3
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-28 17:46:41 -0500
Commit message:

 Add esets[c(i, j)] to digest arguments for caching, since now these
are added after digest call, which had broken caching.
 
Package: doppelgangR
Commit: 2300f9aa32d6ff1eeb838ed2aa3996d9cafaa17d
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-28 14:50:45 -0500
Commit message:

 Passes R CMD check with only documentation and IMPORTS notes/warnings!  Still need to document BiocParallel and cache.dir.
 
Package: doppelgangR
Commit: d663afd22288e5d8df23e63716f485c6f4536232
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-27 22:48:29 -0500
Commit message:

 Housekeeping checkin.  Added support for BiocParallel, unit tests, lots of code cleaning.
 
Package: doppelgangR
Commit: bb7e29867b9cf5f54abb35d09564f3f1356fb702
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-04 16:51:00 -0500
Commit message:

 Fixed cases with one smoking gun or one row of output, return untransformed Pearson correlations so plots now show red lines again.
 
Package: doppelgangR
Commit: 329d0c18c67eba9032cd3c78c068a9e12900035f
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2015-01-01 22:06:37 -0500
Commit message:

 Scripts for running on CRC, bladder, breast and ovarian, with link to results for all but breast in README.md.
 
Package: doppelgangR
Commit: 4740a3301a9855e2920d144ad105a531059aeebd
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-10-12 18:04:15 -0400
Commit message:

 Fix summary() method and put this in vignette.
 
Package: doppelgangR
Commit: 43885d71e247a1b3872c4ca22206d95aea6adc96
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-10-12 15:02:18 -0400
Commit message:

 Overdue version bump to 0.9.0, point to print() method in show() method fixes one of the issues.
 
Package: doppelgangR
Commit: a80e8781d33d2eddf93aafd2c8a23d07eeb5f5ca
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-10-12 13:09:42 -0400
Commit message:

 doppelgangR is building.  Fix to CRC.R and addition of RUNME.sh to run
CRC, breast and bladder examples.
 
Package: doppelgangR
Commit: 9b73d43238fd62839665e20b716488123514badb
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-08-28 12:34:59 -0400
Commit message:

 Fixed corner case in corFinder when a feature has non-finite values
(by removing that feature for ComBat).  Added scripts to run
doppelgangR on CRC, bladder, and ovarian.
 
Package: doppelgangR
Commit: 5bbb04bfa7fc34dce98a24774e03e0b266b55548
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-08-28 09:12:27 -0400
Commit message:

 removed one more deprecated reference to eset.pair
 
Package: doppelgangR
Commit: 3997cf4c71935c4b57a20cf04f7756eef8b2a4a2
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-08-28 09:07:39 -0400
Commit message:

 fixed na.output, got rid of eset.pair object so big lapply loop now seems to work?
 
Package: doppelgangR
Commit: 3362966d83d560b5a4325a180b663f6b60f965fc
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-04-27 15:21:33 -0400
Commit message:

 Attempt to fix case when a pair of esets gets skipped for phenotype or smokinggun checking.  Not sure if it works.
 
Package: doppelgangR
Commit: 0afce6486cd2558efb57e29613ed72ca14a06a30
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-04-27 14:13:39 -0400
Commit message:

 Merge branch 'master' of github.com:lwaldron/doppelgangR
 
Package: doppelgangR
Commit: bd59b1c5f2ddc53714482752c110a8bfa967b982
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-04-27 14:13:30 -0400
Commit message:

 outer2df.R: stop unless x is a matrix or x and y are both vectors.
 
Package: doppelgangR
Commit: 4de75e03547e13b64eef1466c5ab42281a6285fb
Author: lima1 <mriester@gmx.de>
Date: 2014-04-27 14:05:19 -0400
Commit message:

 Merge branch 'master' of https://github.com/lwaldron/doppelgangR
 
Package: doppelgangR
Commit: bfb96626d118aa99a8572477557be6a18804e4c6
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-04-27 14:04:14 -0400
Commit message:

 Increased verbosity.  Code clean-up in outlierFinder.R.
 
Package: doppelgangR
Commit: d4267e6349b794591a1480b04b96f439fbc47ba4
Author: lima1 <mriester@gmx.de>
Date: 2014-04-27 12:59:32 -0400
Commit message:

 runinline.sh: remove alias automatically
 
Package: doppelgangR
Commit: 6e4818a9f13357e089b4a887a02934b8200ffda2
Author: lwaldron <levi.waldron@hunter.cuny.edu>
Date: 2014-04-26 22:01:32 -0400
Commit message:

 Overhaul of smoking gun finder so it fits the same API.  Fixed plot.pair option to plot.
 
Package: doppelgangR
Commit: d005e069a73d8240216cbbca47e453bb979520cd
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-04-23 21:53:56 -0400
Commit message:

 Change outlierFinder to use skew-t distribution instead of normal distribution.
 
Package: doppelgangR
Commit: f117390258771ea0726846cd146e4ed9396e48e6
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-04-23 13:40:35 -0400
Commit message:

 housekeeping checkin: added skew-normal functions, but not yet used.
 
Package: doppelgangR
Commit: ae7ad08b5aee4f1880ba7ba383af0cce4be2f8db
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-04-20 17:36:31 -0400
Commit message:

 Fixed ?doppelgangR and plot method for doppelgang-class
 
Package: doppelgangR
Commit: 3178469040df184d80254278c3dbf87ecefdc01f
Author: lima1 <mriester@gmx.de>
Date: 2014-03-30 14:06:18 -0400
Commit message:

 added phenoDist function to phenoFinder.args
 
Package: doppelgangR
Commit: 8b4700a27dcd79a9581cfd7986ca7fc6617cb845
Author: lima1 <mriester@gmx.de>
Date: 2014-03-30 12:27:15 -0400
Commit message:

 fixes in weighted dist
 
Package: doppelgangR
Commit: 8ac2ab08a15bedb72806aac1d3a2eed7db2f5417
Author: lima1 <mriester@gmx.de>
Date: 2014-03-30 11:02:24 -0400
Commit message:

 digest package
 
Package: doppelgangR
Commit: b5a60a47a03ed6ee251f585e14f1f971556f66dc
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2014-03-30 01:23:10 -0400
Commit message:

 Flatten nested output@fullresults structure, add caching for phenotypes, update documentation.
 

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