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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: TCGAbiolinks
Commit: 6bcb7d82fa587214c1e54d64075af84613884cea
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-20 23:59:53 -0300
Commit message:

 fix figure 1
Package: TCGAbiolinks
Commit: ddfcac264377b17e283987e20b3448eeea442e54
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-20 23:58:37 -0300
Commit message:

 fix figure 1
Package: TCGAbiolinks
Commit: 9c749b6e6e3771dd667acf1306288461a497c94d
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-20 21:02:07 -0400
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinks
Package: TCGAbiolinks
Commit: 1d5e548a7fc6261bd3a5810b3662749eebdb4c11
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-20 21:02:00 -0400
Commit message:

 Update TCGA's wiki to GDC in query

Update TCGA's wiki to GDC in query
Package: universalmotif
Commit: da95d507d56303a1b3108e78f60ba225b22b0e18
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-20 22:50:53 -0400
Commit message:

 adjusting default make_DBscores params
Package: Rsubread
Commit: fd34ea4af7593f7a591363b888da5696cb58820e
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-05-21 12:35:25 +1000
Commit message:

 Add check on dup files
Package: universalmotif
Commit: 04278a2622907f30cf42b096de533b22acad0a81
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-20 22:14:37 -0400
Commit message:

 fixed min.overlap < 1 not working
Package: universalmotif
Commit: a85fe826643755d2055be5af5be3e2a87f48f514
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-20 21:59:48 -0400
Commit message:

 changed default min.overlap
Package: universalmotif
Commit: aa43b612f217e2a0b1b9a3ee3deec3402d6fa67e
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-20 21:49:51 -0400
Commit message:

 fixed merge_motifs() not getting right offset
Package: singleCellTK
Commit: a1272fbb4d74a6e89c298f62ca6787d8818abb66
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-05-20 21:45:33 -0400
Commit message:

 Merge branch 'mmkhan19-master'
Package: singleCellTK
Commit: de9d67fd56786db8b1538ec567202a588331fe5e
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-05-20 21:45:07 -0400
Commit message:

 version bump
Package: singleCellTK
Commit: a6353488aa508d3379a028fa11e2cfc09b1f9f89
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-05-18 22:05:11 -0400
Commit message:

 Issue #185 - helptext for reducedDim naming convention
Package: singleCellTK
Commit: 2249eadb8b2a41a59ea133fd7c209f7f35370c59
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-05-18 21:35:13 -0400
Commit message:

 Issue #182 - changed the grep pattern
Package: singleCellTK
Commit: 20806dbc0782530b07727dc44e5ed05fad1ba1b0
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-05-05 20:13:24 -0400
Commit message:

 removed UI_biomarker from the code(Jasons part) will work on this in the next PR
Package: singleCellTK
Commit: 9f7a016c4a17c02b16d9a9a325c1b5ec2f8d1a10
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-05-05 20:10:17 -0400
Commit message:

 helptext in Visualize and annotation data sections, updated all methods in visplot to take more than 1 and less than 25 genes with distinct colors for each gene
Package: singleCellTK
Commit: 5321ff5f9f6944ed71e4caf089ae1dad294000f7
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-05-05 16:52:35 -0400
Commit message:

 Merge branch 'master' of github.com:mmkhan19/singleCellTK
Package: singleCellTK
Commit: 32c5a61bed24e5e0540318de078816576ef1ae9b
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-05-05 16:50:58 -0400
Commit message:

 minor changes
Package: singleCellTK
Commit: f007ee56c76fa45b13363197ee946990e872afcd
Author: mmkhan19 <39277690+mmkhan19@users.noreply.github.com>
Date: 2019-05-05 16:27:29 -0400
Commit message:

 Merge pull request #5 from compbiomed/master

new changes
Package: singleCellTK
Commit: 5294b818d1bd65f68e3e159fc7214619361689ed
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-05-05 14:32:25 -0400
Commit message:

 version bump
Package: singleCellTK
Commit: ffebf31c6aa4745bc9270ce35c085703eac5f0b5
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-05-05 14:32:00 -0400
Commit message:

 Default condition is NULL
Package: singleCellTK
Commit: fde369a6a41266aa64cf17ad49f505e086a3a8d8
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-05-05 13:41:43 -0400
Commit message:

 don't fail travis build on warnings
Package: singleCellTK
Commit: 7056e6094fa35a985b16f1b81288a15845815907
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-05-05 12:08:00 -0400
Commit message:

 Don't build vignettes on travis
Package: singleCellTK
Commit: 134b8afaf38c112ed79122d95c5bd0c7e61b396d
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-05-04 17:08:23 -0400
Commit message:

 Update the readme with new bioc versions
Package: universalmotif
Commit: 3e87163b39364ed3a6ff7ce51321832e6831d70a
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-20 21:35:57 -0400
Commit message:

 get rid of pseudocount in final figure
Package: universalmotif
Commit: a487c555db7e86ba2035c4ac8e92e10bb39824da
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-20 21:30:44 -0400
Commit message:

 various fixes to make_DBscores(), merge_motifs(), view_motifs(), compare_motifs(); using logistic distributions for comparison P-values
Package: apeglm
Commit: ef3d59f7f55700947b5c81a38c0133acbeae7de9
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-05-20 21:04:07 -0400
Commit message:

 turn off second run of C for betabin
Package: tximport
Commit: 9e200393ce27339ecf11e2b7b7d155f9ad288813
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-05-20 20:55:49 -0400
Commit message:

 bump version, thank Aaron
Package: tximport
Commit: bb38fa1e8840ed5e166c09a31311b30751e6adb4
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2019-05-20 20:51:40 -0400
Commit message:

 Merge pull request #28 from LTLA/master

Minor edits to edgeR part of the vignette.
Package: tximport
Commit: 31687072175252a52a998f4cdcd0ba583d48712e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-05-20 13:51:47 -0700
Commit message:

 Minor edits to edgeR part of the vignette.
Package: tximport
Commit: 6b35bb868ec2e570951c59c036b69046e75c81b0
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-05-20 09:39:58 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 488b938b48e02ce1919a57abe5535b9a106bb327
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-05-06 10:14:46 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: d1a195b41f92489562f451ecf99f8fd6d47bb112
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-03-07 07:36:19 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: b5b5fe11b0093b4b2784f982277b2aa66d2607f7
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-12-03 09:40:45 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 7f7b85e16d5e948862c8ae1b3835e039280460c6
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-11-28 11:00:47 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: ec78ce0e8a467b3c67414273aa8312bba85ab8a2
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-11-27 13:33:17 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 9ca3dda9718cf25c8c9ed2f91237c12257fda344
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-11-19 20:32:41 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: daebcb711ddc477fc24d4dbf147fb76e25ee5cd0
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-11-13 15:14:15 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: b8f2640b728226dfa067f816e07ec6eea067eebc
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-11-05 13:27:25 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 125d77db350bb15b7327c0ed18e15dfc1f711ec8
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-10-31 16:17:37 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: d4f8f31cb7d03373b1f4a3f37bb500912eea9779
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-08-30 10:32:49 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 0a39cd91e5c3f6a86fb6e84afaea1b1e429d6ab8
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-08-03 09:56:44 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: ee304e2ee6da239da10e431430387c395b2bd042
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-08-02 15:31:01 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 94b08d7ff0b4647b07cd1933fd220dc8e8974087
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-07-14 08:38:57 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: c0638f597f82b5c17e766c52342d4d09584a650b
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-06-29 10:38:41 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 12d28328d95b2290eb96d42df9990cdf9e2b194a
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-06-26 08:59:09 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 868ee60e7507a1911827dcee498ce81bfa55723a
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-06-25 09:32:58 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 32f218f548cea2661808bec5dcd147a801cbd56d
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-06-08 11:41:31 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 846804f7b9052fc78d0342c4a9e4f5b2d0df4b32
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-06-08 10:24:40 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 6daf3d3233b7bcff5c66a680f894993ebe844590
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-05-25 12:05:14 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 60e5d6f5086ccf82de989dacab10e0195b4bffec
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-05-04 20:29:19 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: f0c6d4e09863f70e25601d3a0301001c95329f18
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-04-01 22:36:54 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 47fd7f8b5ad4de56ac8332cdfb205323420b161c
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-02-24 11:09:11 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 5337e0b8d4258dbd46b1f74d6b137822e067b89e
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-02-18 21:46:56 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: cb214cd8b6a86033b48eac8a692c00d252dfa2a0
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-02-18 21:44:12 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: 22a5f2a1175e71254536cce17be29b22fd6d1b56
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-02-13 08:28:49 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: b7c784ea6d000a87d1c02c2023940ce010dde639
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-02-08 10:02:14 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: a74573921fa9befa2382100a8b2ed192ef69edf1
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-02-07 12:54:28 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: eb316e8afc825fd42ca6a020c45b2b2e166a19eb
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2017-12-11 10:56:17 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: ba001f18961e3c1139c6b502c8f8a4f6bf3eb9a6
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2017-12-08 15:23:00 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: e5957dd86ea246e9eec64759c677d1b7c19bc4de
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2017-12-08 15:21:34 -0500
Commit message:

 add to thanks
Package: tximport
Commit: bc1b5936810c44ab9aa922d015655064d73627ec
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2017-12-08 15:16:24 -0500
Commit message:

 merge
Package: tximport
Commit: 9b9d3e6e0d0843cfec2048e5dbd0a8ddca189a71
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2017-11-29 14:03:44 -0500
Commit message:

 remove old file
Package: tximport
Commit: 1493eec7b1a26486abf33e5a88a79c6a8bfac29d
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2017-11-29 14:02:13 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: tximport
Commit: b674022cf959705c80dc8fd7676f92b56f050303
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2017-03-08 11:29:26 -0500
Commit message:

 replace README with warning
Package: tximport
Commit: d04d7bc722933e541918446a2b6728a7866426ab
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2016-12-12 21:09:12 -0500
Commit message:

 Update tximport.R
Package: tximport
Commit: cc3e00fad860dd3a6d18591988c7618b49a0c25d
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2016-12-12 21:07:59 -0500
Commit message:

 Update README.md
Package: tximport
Commit: cd8bdefc5e730924309894a411647157f6f14cee
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2016-02-15 11:41:53 -0500
Commit message:

 Update README.md
Package: tximport
Commit: 6541898c1d3d4393a01d19a023ce52b68f92df9b
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2016-02-12 07:11:11 -0600
Commit message:

 Update README.md
Package: tximport
Commit: 78c270516cdf57f633917a771d4bd53c5ec84654
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2016-02-12 07:09:58 -0600
Commit message:

 Update README.md
Package: tximport
Commit: e02f4d4d0ac302e3cb99f6409c3aa648c8a425c7
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2016-02-12 07:09:11 -0600
Commit message:

 Update README.md
Package: tximport
Commit: ce7cf2d2f8511636f0ffa5edf728cdf63ad913e1
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-02-12 07:06:30 -0600
Commit message:

 startup message
Package: tximport
Commit: 3e926e8c00fa058bc2e7d9b36056e24083e310b9
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-02-10 07:21:46 -0500
Commit message:

 add biocviews and imports
Package: tximport
Commit: 288c9fbec2c4e3961f96a16a34549ff7a50d3905
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-02-09 13:02:28 -0500
Commit message:

 remove travis
Package: tximport
Commit: 345772a63703c0ee58ee482226953f6ba3fc4c18
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-02-09 13:01:37 -0500
Commit message:

 rm travis
Package: tximport
Commit: 95e26fd65748bc8b5655e6079f00b0c7ce1086eb
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-02-09 11:06:56 -0500
Commit message:

 update as per Bioc code review
Package: tximport
Commit: a6f8cabc3e87a93087981f2568c1db93b520e6bd
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-02-02 13:27:17 -0500
Commit message:

 update vignette
Package: tximport
Commit: b985242737a2f6bd0c7c184e3830974479772783
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-01-29 14:01:52 -0500
Commit message:

 try removing biocviews?
Package: tximport
Commit: 31a9f2613bfa84db3e4fa906caf6127f7f4b8255
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-01-29 13:46:01 -0500
Commit message:

 updating for bioc submit
Package: tximport
Commit: f76438b356e347e63adb7f62595f09e4fd49efae
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-01-26 14:57:18 -0500
Commit message:

 update docs
Package: tximport
Commit: 78fc215f97728a79fdac3ffafddb90441bf0d338
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-01-26 14:49:59 -0500
Commit message:

 break out summarizeToGene
Package: tximport
Commit: 8f31541991c08ad3fe71145987ea4c4b1424ad67
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-01-18 11:41:19 -0500
Commit message:

 changing gene2tx argument to tx2gene
Package: tximport
Commit: 7e0084443af05575252a6fd9595bae0545b32b78
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-01-07 14:09:26 -0500
Commit message:

 change usage of voom
Package: tximport
Commit: 90350562e61bd2e2bfe91ca221f442614f656e0b
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-01-03 12:31:08 -0500
Commit message:

 update
Package: tximport
Commit: 492e1dbb24bd0e83a2391224214abbe27e190c57
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2016-01-03 12:21:54 -0500
Commit message:

 allow none
Package: tximport
Commit: 4d0447762d5558826573acae685685039f79ddca
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-30 10:47:22 -0500
Commit message:

 add citation
Package: tximport
Commit: 518d381c4f7500110bb3892b88df193b592abdbb
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-16 13:21:50 -0500
Commit message:

 consistency
Package: tximport
Commit: 2bb232c101cc7f82800a4ded9a9c6ac31fe3a997
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-16 13:20:12 -0500
Commit message:

 update docs
Package: tximport
Commit: 4e2a3b223c1d80f58656879381a194d96ce78281
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-16 12:28:05 -0500
Commit message:

 reworking the detection of older salmon/sailfish versions
Package: tximport
Commit: ec87631ed82f8d23a754be7b58a8077a1291fc5f
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-16 11:37:57 -0500
Commit message:

 update docs
Package: tximport
Commit: 7b9f5d3cca45c7696ae72e3d8b03c5cead2dcec6
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2015-12-16 10:00:07 -0500
Commit message:

 Merge pull request #9 from rob-p/master

Support for new sailfish and salmon formats
Package: tximport
Commit: 438358c2f8b669c406098fb84dab1bf6e9d1e5a0
Author: Rob Patro <rob-p@users.noreply.github.com>
Date: 2015-12-16 08:28:00 -0500
Commit message:

 Update tximport.R

Only grab the first file rather than the first 6.
Package: tximport
Commit: ea05af8851b15bbeea837143f14e69d933f0a48c
Author: Rob Patro <rob.patro@gmail.com>
Date: 2015-12-15 22:06:18 -0500
Commit message:

 remove rogue call to head
Package: tximport
Commit: c234045a1be6819391ae8f8c0cb98d8536ab472c
Author: Rob Patro <rob.patro@gmail.com>
Date: 2015-12-15 22:05:33 -0500
Commit message:

 support the new salmon and sailfish formats
Package: tximport
Commit: 7c8a481e95f8ae1e4714c1ac3c01375ed888482d
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-14 10:59:45 -0500
Commit message:

 link in vignette
Package: tximport
Commit: 478ae5324b1d4480f2a8a22938a7124d07149ad3
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-14 10:52:40 -0500
Commit message:

 travis take 3
Package: tximport
Commit: edb03cf5ab53e8f1b1d1c9cdd15e527a480cd8fd
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-14 10:47:04 -0500
Commit message:

 travis take 2
Package: tximport
Commit: 7df97710028dc22a98d27b859c79df8c141f6c15
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-14 10:36:49 -0500
Commit message:

 travis take 1
Package: tximport
Commit: e60d696ae91e523f74a728d32ab38cfa3c99b677
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-14 08:05:43 -0500
Commit message:

 skip => comment for readr
Package: tximport
Commit: c01a1a00b7cdb9f2899a04b39da96a2d7df8d004
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-11 15:04:33 -0500
Commit message:

 fix typo in vignette
Package: tximport
Commit: 390ddd8735c8ad142fd1c8ae587b0c088fcc4346
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-11 15:02:01 -0500
Commit message:

 adding reader arg, allows plug in of read_tsv
Package: tximport
Commit: be06f774f62621f0d228454bd3dcf2f25a5dcaf9
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 16:39:41 -0500
Commit message:

 link to travis build log
Package: tximport
Commit: cc003471e433b3545a50b70f810cfdf90d5eda15
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 16:28:10 -0500
Commit message:

 add travis badge
Package: tximport
Commit: d0bc3ccfc5d3eb57912e5549eaf43e7087ff2592
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 16:14:09 -0500
Commit message:

 rename arg, more travis CI
Package: tximport
Commit: 2ddcc2cfc688cc73a744ab3b43110b2aded6c1dc
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2015-12-10 16:03:37 -0500
Commit message:

 Merge pull request #6 from mdshw5/master

Option to ignore transcript version numbers for gene merge
Package: tximport
Commit: 14ea5db33fb18c0366db6932f72a75aa20929f56
Author: Matt Shirley <mdshw5@gmail.com>
Date: 2015-12-10 15:53:57 -0500
Commit message:

 Transcript to gene mapping ignore version numbers
Package: tximport
Commit: 2e546519857bc4552b225d43343bf50a52d83602
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 15:43:34 -0500
Commit message:

 travis take 5
Package: tximport
Commit: 6355669ecc17af8e7fa5b8ff8a6774d02a812e6b
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 15:34:21 -0500
Commit message:

 travis take 4
Package: tximport
Commit: 08d48e2c71a78f620a4aadaab54d248abadb7267
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 15:28:04 -0500
Commit message:

 travis take 3
Package: tximport
Commit: 014c317955fd8e104e23c69924652598d1440a38
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 15:23:43 -0500
Commit message:

 travis yml take 2
Package: tximport
Commit: 2c384741843440558e2d948d20a027d7491c6048
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 15:15:43 -0500
Commit message:

 add sudo to travis yml
Package: tximport
Commit: acbc8733db8bf5f059b0c1c3ceec063217c7a121
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-10 15:13:02 -0500
Commit message:

 adding tests, trying travis CI
Package: tximport
Commit: 547fb6070b6f366976c686311646b4876387c9f0
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-09 10:59:58 +0000
Commit message:

 salmon eff len needs more work...
Package: tximport
Commit: 7d442e986cc9366643ab44dd727ce64c07b27d7b
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-09 10:41:15 +0000
Commit message:

 adding extra code to salmon imported
such that it will by default get effective lengths from stats.tsv files.
also fixing the shape of outgoing matrices with a single input file
Package: tximport
Commit: 1648defccd30d1492fd3cc998ef1bdb643c5ecca
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-08 23:17:17 +0000
Commit message:

 add drop=FALSE for importing 1 sample
Package: tximport
Commit: b76361114ea12436d40e55e364364b5b381df024
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2015-12-06 15:59:07 +0000
Commit message:

 Update README.md
Package: tximport
Commit: a6b55298b1b8b717164266bb1a760d4a0aef0cd1
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2015-12-06 15:58:37 +0000
Commit message:

 Update README.md
Package: tximport
Commit: dc7c0a811f6991bcdea5ba2d2cfc92e0053ed65f
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-04 13:04:04 -0500
Commit message:

 update docs
Package: tximport
Commit: f457550c72c4f26d45054457323c921edb22d252
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-04 12:24:47 -0500
Commit message:

 update to new deseq2 and include limma-voom
Package: tximport
Commit: a95d536d67c3cd532eaf0da1901033d85435cf6c
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-04 11:44:41 -0500
Commit message:

 fix
Package: tximport
Commit: 3d537eb0bf05b96583e59212136e2b22ab462242
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-04 11:39:14 -0500
Commit message:

 countsFromAbundance in list output for all output types
Package: tximport
Commit: d89b0bb9408c1d0ebf746bab79b7c553b3a6a68c
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-04 09:48:18 -0500
Commit message:

 add info on creation
Package: tximport
Commit: 336b92d55c8e9165cfd14f52da6aae6aca164063
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-03 14:18:17 -0500
Commit message:

 update with edgeR, DESeq2 examples
Package: tximport
Commit: 458c3465b9604e4bcba94c16c8783840c9d897b1
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-03 13:34:50 -0500
Commit message:

 Merge branch 'master' of github.com:mikelove/tximport
Package: tximport
Commit: 64ec22370e98529352323e74dd86412666483130
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-03 13:34:48 -0500
Commit message:

 adding example
Package: tximport
Commit: 34d36161f9ce8ae96c54d4b49f0b9d8b85250ffe
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-03 09:04:34 -0500
Commit message:

 version bump
Package: tximport
Commit: 0d41b821e8d96b2055462f0ce5c9b11f601f07c4
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-03 09:04:20 -0500
Commit message:

 fix bug when gene2tx not factor
Package: tximport
Commit: 6bdae6b7d4ae2c688157f7b4216468a71530a842
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-02 09:49:42 -0500
Commit message:

 gitignore
Package: tximport
Commit: 6874e79fc0b332d0a1ccd6a4d7b133901a48d1ae
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-02 09:49:14 -0500
Commit message:

 run vignette
Package: tximport
Commit: 2962a9db15214f6a5bb8b514ec77b8c0d24d1a04
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-02 09:45:21 -0500
Commit message:

 version bump
Package: tximport
Commit: 85c842cb881be97e3c7b19f79a14db22441284e5
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-02 09:43:42 -0500
Commit message:

 update from Charlottes notes
Package: tximport
Commit: f726b8ee9abc8ecf5cb8912cf6a795b556226d4d
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-01 13:36:57 -0500
Commit message:

 update
Package: tximport
Commit: 419bc0ffbd617d7c181698ebd98d74a88451ee9a
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-01 13:17:23 -0500
Commit message:

 spell fix
Package: tximport
Commit: 3e486811eec9aa3ac12920ef4c1d196a4795cc86
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-01 10:37:12 -0500
Commit message:

 update
Package: tximport
Commit: aa0e0b74868f451eb595e99f2f9d1761ff2a7f3e
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-01 10:36:05 -0500
Commit message:

 update
Package: tximport
Commit: 5604efc53f9007de03ae6e5535130af6242d23df
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-01 10:31:42 -0500
Commit message:

 update
Package: tximport
Commit: 7a8ee05e0540230dbadd7658b30a34c2c8a48c24
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2015-12-01 10:30:37 -0500
Commit message:

 Delete LICENSE
Package: tximport
Commit: 783b86d7ad89adfb11b1bf96408e8c880dcf5eff
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-01 10:29:59 -0500
Commit message:

 update
Package: tximport
Commit: 862c1518f7033a6941cf1a2a89ee5e94d462cfdd
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-12-01 10:12:11 -0500
Commit message:

 update
Package: tximport
Commit: fa5ea6543972322991f910a9a1dc5a2f50243adf
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-30 17:15:09 -0500
Commit message:

 small stuff
Package: tximport
Commit: 807aae989e009fee46854040afdb154526cfcef5
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-30 10:15:37 -0500
Commit message:

 adding preset software types
Package: tximport
Commit: 5e00ac67f99a8a1d1446677a3ec923c0297f6ab6
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-29 17:07:04 -0500
Commit message:

 update
Package: tximport
Commit: 2c192afbbd0ed26ba472df790d14965308da6703
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-29 16:06:07 -0500
Commit message:

 todos
Package: tximport
Commit: 9823ea83092e2f05ecdd97f9a20c6d94529c80ee
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-29 09:40:10 -0500
Commit message:

 counts from abundance
Package: tximport
Commit: 2f5c8d8a81bb1fe9cef89e0e57e2c3f12f809bfc
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-29 09:26:28 -0500
Commit message:

 use message not cat
Package: tximport
Commit: 53d565bbfb503ad9bd8b9452a22a307c7061feb9
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-29 09:22:00 -0500
Commit message:

 update
Package: tximport
Commit: 5b69ddcd75abd5c090e20ff57b7f0c917a9ae4db
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-28 13:40:20 -0500
Commit message:

 moving around
Package: tximport
Commit: 68be2b475cc559b6c5e7531186a6b655c16fb88d
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-27 16:31:45 -0500
Commit message:

 version num
Package: tximport
Commit: 57376bfd730493ede94f18d8ca162fbe8de838e7
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-27 16:31:00 -0500
Commit message:

 make pkg
Package: tximport
Commit: d448619eec4a7af20182dba8f96aebc03d8363f3
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-25 16:11:54 -0500
Commit message:

 replace NaN with mean of other samples
Package: tximport
Commit: 232b29d0b6c090c2b423808259217dbe6f936f8c
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-25 11:49:06 -0500
Commit message:

 tweak
Package: tximport
Commit: ef300223489a664babe4710648f506bf94387ee6
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-25 11:47:59 -0500
Commit message:

 use Mark's code instead of by()
Package: tximport
Commit: 02e289fbcfd7a6ec630bba847f4428d104308415
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-25 10:07:36 -0500
Commit message:

 use matrices
Package: tximport
Commit: 32ac3c2df4a536a04a9f1393f61dfe5bfd87a584
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-23 15:10:30 -0500
Commit message:

 update
Package: tximport
Commit: 16f92f99e0b0cac4d9d9f9ffe534c47b3cdc66a4
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-23 10:49:50 -0500
Commit message:

 update
Package: tximport
Commit: 70e2ae144dc93674a8b6a14dc227a7140683d636
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-23 10:39:48 -0500
Commit message:

 update
Package: tximport
Commit: a48f8dc2dc2766893ab81edeacce3b71f73ee5e7
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-22 15:25:13 -0500
Commit message:

 point about averaging for missing data
Package: tximport
Commit: 7da8ff562fb7e342fddab71677d0579fc583c752
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-22 11:25:12 -0500
Commit message:

 also summarize counts
Package: tximport
Commit: da1c2e503b05160a8ae8a0f4d41c9e5e4e325d72
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-22 11:10:35 -0500
Commit message:

 update code to use 'by'
Package: tximport
Commit: 10b4f2fc81a0deec7bb9b3084b3d0b4b2cd1504f
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-20 10:57:48 -0500
Commit message:

 update
Package: tximport
Commit: 5d186b3f671d1a8c0f19b99eddca38b16441c72d
Author: Mike Love <michaelisaiahlove@gmail.com>
Date: 2015-11-19 12:17:41 -0500
Commit message:

 faster using tapply
Package: tximport
Commit: 3014f7f897b99ea238cde8f7e92f9e6f1407b795
Author: mikelove <mikelove1@gmail.com>
Date: 2015-11-18 10:03:26 -0500
Commit message:

 update
Package: tximport
Commit: ec598d7789b50b68435fda1d13ec095ef3d88460
Author: mikelove <mikelove1@gmail.com>
Date: 2015-11-18 08:52:12 -0500
Commit message:

 update
Package: tximport
Commit: 09746493bdfef155a0a1741d5dd3f2a087df5cef
Author: mikelove <mikelove1@gmail.com>
Date: 2015-11-18 08:31:35 -0500
Commit message:

 update
Package: tximport
Commit: 1766ddc7f16e100e2f1e0bba0860c13a28c6e5ae
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2015-11-18 08:13:13 -0500
Commit message:

 Initial commit
Package: GenomicRanges
Commit: a925fe841c6fcde04cbef8bfae6cb4d6405fa59f
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-20 16:16:42 -0700
Commit message:

 Resync GenomicRanges validity method with IRanges 2.19.4
Package: IRanges
Commit: 3e4ac3f6060eb791901604dec4bb1bd692654913
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-20 16:04:04 -0700
Commit message:

 IPos objects now exist in 2 flavors: UnstitchedIPos and StitchedIPos

IPos is now a virtual class with 2 concrete subclasses: UnstitchedIPos
and StitchedIPos. In an UnstitchedIPos instance the positions are stored
as an integer vector. In a StitchedIPos instance, like with old IPos
instances, the positions are stored as an IRanges object where each range
represents a run of consecutive positions. See ?IPos for more information.

Old serialized IPos instances will need to be converted to StitchedIPos
instances with updateObject() (not ready yet).
Package: Rsubread
Commit: 8327574a5753aa5f1d035e84698a0706ba278081
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-05-21 08:59:09 +1000
Commit message:

 Fixed a bug of basename.
Package: CEMiTool
Commit: e7e57ef5adf1851863461a1a13e02cbab2c3acc7
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-05-20 19:56:24 -0300
Commit message:

 Updating package; bugfix on plot_gsea; version bump
Package: CEMiTool
Commit: 2d8209cd65c3d1ea22a981eb25983546c01bb7fb
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-05-16 22:59:52 +0000
Commit message:

 Version bump
Package: CEMiTool
Commit: b9d1c561d611ffc4306d46abedead3aaca43efc5
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-05-16 22:55:47 +0000
Commit message:

 O problema no GSEA plot se dava pelos limites na escala que a gente aplicava ao tamanho dos pontos para deixar os mais enriquecidos maiores;
no caso, estávamos colocando o tamanho dos pontos entre 0 e 30, o que fazia com que os menor ponto de todos não aparecesse
no gráfico (tamanho 0). Na maior parte das vezes isso não é um problema porque é um módulo com classes não-significativamente
enriquecida, e o valor de NES era setado para zero (pelo p-val). Só que no caso encontrado, a tabela de NES não tem módulos não-significativos,
então o módulo M1, que tem o menor valor de NES estava sendo removido. A solução foi mudar o comando scale_size para 'scale_size(range=c(0,30), limits=c(0, NA)) +'
Package: CEMiTool
Commit: df876e1a70af397a26b9e165db82e69f62ce35eb
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-03-15 15:25:35 -0300
Commit message:

 Version bump
Package: CEMiTool
Commit: 5d46c22be353b7cd558e713450b1329e7c61757e
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-03-14 14:45:57 -0300
Commit message:

 Bugfix: find_modules wasn't passing parameters to get_adj correctly
Package: CEMiTool
Commit: cb023c8a813fa4205e929005cfc002ee94a735fe
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-03-07 17:25:29 -0300
Commit message:

 Bugfix: mod_gene_num problem in error handling
Package: CEMiTool
Commit: 477b4aa187e1881a2c33bdfee263019bf6c2cd65
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-03-07 16:51:33 -0300
Commit message:

 Add number of genes in modules in mod_activity; add mod_gene_num function
Package: CEMiTool
Commit: da0614c0335236a967d8ffe6ccd2ab56114758ad
Author: Thiago D. C. Hirata <thiagodch@users.noreply.github.com>
Date: 2019-03-01 13:51:14 -0300
Commit message:

 line 724 added is.null(names(analyses))

Will change the names in mod_stats for GSE names in figures
Package: CEMiTool
Commit: 0cf5032d7e393346f44713e18079f0087c46dbcc
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-01-29 13:39:14 -0200
Commit message:

 Adding parameter 'plot_diagnostics' to cemitool()
Package: CEMiTool
Commit: 3d696b7c27d1885f031a53937ed5488263495f48
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-01-17 17:55:42 -0200
Commit message:

 Fixing bug in report.Rmd
Package: CEMiTool
Commit: 7de43376e767d29e291413433b5a977a2f19515d
Author: pedrostrusso <pedrostrusso@gmail.com>
Date: 2019-01-14 17:43:22 -0200
Commit message:

 Updating filter paradigm
Package: piano
Commit: d52d9084b92bf2719cdb3a0279b4ea7823c5aeba
Author: varemo <leifvaremo+git@gmail.com>
Date: 2019-05-20 23:26:18 +0200
Commit message:

 Update NEWS
Package: piano
Commit: 5c36f1477698157c5ca73b4ce678558b872c7049
Author: varemo <leifvaremo+git@gmail.com>
Date: 2019-05-20 23:02:02 +0200
Commit message:

 bump version
Package: piano
Commit: b62c36738b5c482af6c72b8eb7bef613f9970417
Author: varemo <leifvaremo+git@gmail.com>
Date: 2019-05-20 23:01:21 +0200
Commit message:

 Fix error message handling in network plot in Shiny app
Package: piano
Commit: b715d62af2449e23bb62eaf2978d5437d422bcfc
Author: varemo <leifvaremo+git@gmail.com>
Date: 2019-05-20 23:00:34 +0200
Commit message:

 Remove an old debugging print statement
Package: infercnv
Commit: 214c2201e175ec4898c4604fbfe68f7255fe5eaa
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-20 15:49:40 -0400
Commit message:

 Version bump to 1.1.1
Package: infercnv
Commit: f61c75b4d4acc6fb2195a141b995fbf34b0adb4d
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-20 15:22:30 -0400
Commit message:

 Updated NEWS file for devel changes.
Package: infercnv
Commit: 4f63b1ae11579cf0eafab640c1dcb8fad7000713
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-20 15:22:15 -0400
Commit message:

 Updated NEWS file for changes to go into current release.
Package: infercnv
Commit: 4149e40ad477ad0b705700bfa55857767ba121b2
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-16 17:53:06 -0400
Commit message:

 Merge branch 'experimental' into devel
Package: infercnv
Commit: c1e1fcd766e2d492975b9401612524f78c8d29b6
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-16 17:30:02 -0400
Commit message:

 Fix sampling when upsampling from 1 cell in a group producing NAs.
Added script with tests for sampling methods.
Package: infercnv
Commit: 68532dd4208287561741ae5837c0dd4feef36e6e
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-14 18:20:19 -0400
Commit message:

 Added documentation for new sampling method and method to plot each group on a different plot.
Updated provided infercnv_obj rda in data to have clustering information for references so new example can run.
Fixed incomplete argument name warning in matrix().
Generated roxygen doc.
Package: infercnv
Commit: e716b22c759db5178d70c93446c3d04ccb8689d8
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-14 17:27:23 -0400
Commit message:

 Typo in CLI.
Package: infercnv
Commit: 2d1962f83740a1dc2f0d7deb0f4ac78bc7fe1ec0
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-14 17:24:04 -0400
Commit message:

 Updated doc for run() after adding output_format parameter.
Package: infercnv
Commit: 053bc246a6a7fb2f954d2329a6da1f6affdf594d
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-14 17:13:21 -0400
Commit message:

 Added flag to plot_cnv() for output_format and linked it to all calls.
Added output_format option in CLI script.
Package: infercnv
Commit: bb435738ad8b3a57a2e52370362f9397d9b7f7cc
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-14 15:19:58 -0400
Commit message:

 Made NA value for output_format be taken into account properly when running plot_cnv() so that only text outputs are generated and not the figure itself.
Package: infercnv
Commit: 1fd5aabb6fc8b054bd0b962e7d2b7cc68f92978a
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-14 15:18:03 -0400
Commit message:

 Added arguments to plot_per_group to be able to save RDS objects generated, write text outputs, only output text and not plot itself.
Package: infercnv
Commit: cafa5b7a99634252ffd1417dd9c01cc78f1da8c4
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-14 11:36:17 -0400
Commit message:

 Added check that annotation name of cells can be used for file name when doing 1 plot per group.
Package: infercnv
Commit: f427eaeab3be59fe27b82b2f26c7179c16f3fa5b
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-13 17:53:40 -0400
Commit message:

 Added method that takes as input an infercnv object and plots each annotation group on a separate plot, automatically settings bounds and center for all of them based on the full data. Adjusted sampling method to allow above_m to be set without every_n to combine with this new method.
Package: infercnv
Commit: 33ffd8dafb8c66b15cefac55b35d235a5369402d
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-13 15:09:49 -0400
Commit message:

 Fix weird character that got inserted by error.
Package: infercnv
Commit: 3db63887e93520052d7069fe0ec30a49cbc479de
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-13 15:09:33 -0400
Commit message:

 Fix use of sampled indices.
Fixed non updated labels when upsampling to less than twice the total size of a group.
Changed the way leaves are pruned from hclust/dendrogram when downsampling to make it way faster (~10 minutes to 2 seconds on trees with 2k+ labels to prune).
Added some logging information to sampling method.
Package: infercnv
Commit: ac33c978a361b2bcb43c579447e6192a6bc85bdb
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-10 16:37:35 -0400
Commit message:

 Updated sampling method to support upsampling of clusters that only have 1 cell in them (and hence no hclust object stored).
Package: infercnv
Commit: 3eeaca66ab5e93b6851227fd9e4b7539b33a8fc6
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-10 13:48:36 -0400
Commit message:

 Fixes when there is only 1 reference group with 1 cell in it (due to heatmap plotting requiring at least a 2x2 matrix).
Package: infercnv
Commit: efe0d41e2fce43225de758444d133a7b118fc0a3
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-10 13:14:55 -0400
Commit message:

 Fix when running plot_cnv() with 1 reference group and no clustering of references.
Package: infercnv
Commit: 20c392bd827431ac1bc7a051488c5b009b6f043f
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-10 12:23:02 -0400
Commit message:

 Fixes to allow sampling to work in cases where only 1 cell will get sampled (very large every_n and small above_m for example).
Fix indices in @tumor_subclusters$subclusters for cases where only 1 cell is a presnet in a cluster and so no hclust can be stored, so subclusters indices are relied on.
Package: infercnv
Commit: bca9a80f0579427bfda4aa403d6f156e544d5450
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-10 12:20:46 -0400
Commit message:

 Fix the cell label when plotting groups with a single cell in them.
Package: infercnv
Commit: 3297d2b752163eed9926b822bb8bc529696af9ac
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-09 17:02:59 -0400
Commit message:

 Tweak to where clustering is done when analysis_mode!="sample" so that it is done after centering of data, improving quality.
Package: infercnv
Commit: db5ffe85c2f5d4ab61b36d95c4bc9313dffa3df3
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-09 15:26:38 -0400
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: infercnv
Commit: 83d2bcf8ed8ac0e7bc3022836b49a85a04734c3b
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-09 15:26:19 -0400
Commit message:

 Multiple changes in method to sample infercnv_obj:
Fix data not being transfered when observations were not being sampled.
Added support for a set of arguments every_n and above_m to sample 1 cell every_n cells in clusters that have at least above_m cells within. Will preserve at least 1 cell from every subcluster, even if the every_n step is bigger than some subcluster and would skip over them entirely.
Fix new naming of cells when upsampling so that plot_cnv() can properly rely on labels for ordering.
Package: infercnv
Commit: e17acddee47e1c2dc8ad03fd05eaf429fd8c1135
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-09 15:22:10 -0400
Commit message:

 Fix issues to defining (sub)clusters when an annotation group only has 1 cell.
Extend plot_cnv() support for cases where an annotation group only has one cell and hence no hclust defined.
Fix sorting in plot_cnv() when clustering references when annotation and cells are not sorted in the same order.
Package: infercnv
Commit: 12209e5fcb6a7a23d98a2f7a09a4d992ee11b045
Author: M. Brown <35315693+brownmp@users.noreply.github.com>
Date: 2019-05-08 11:55:51 -0400
Commit message:

 Merge pull request #145 from brownmp/devel

Added ability to reassign CNV states, plot before and after normal pr…
Package: infercnv
Commit: dec701bc114cc37ba1ae272bca8154bcfe5cc14b
Author: M. Brown <35315693+brownmp@users.noreply.github.com>
Date: 2019-05-07 12:00:29 -0400
Commit message:

 Updated mcmc_obj data, add arguments to inferCNVBayesNet, updated documentation
Package: infercnv
Commit: f7174627a6fc8d4fb6a79c17b1f66a1b6b5c5ae9
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-06 17:48:21 -0400
Commit message:

 Fix ordering of cells and color bars on heatmap and text outputs when cells are not sorted in the same order in the input matrix and the annotation file, with certain combinations of settings.
Package: infercnv
Commit: 9382627600c3024483f14686a8e5205c23ee7ded
Author: M. Brown <35315693+brownmp@users.noreply.github.com>
Date: 2019-05-06 16:03:00 -0400
Commit message:

 Added ability to reassign CNV states, plot before and after normal probabilities, no_plot prevents plotting Bayes network probabilities.

Add option to reassign HMM identified CNV states based on probability of each state. Plot the normal probabilities before and after filtering. The flag "no_plot" now prevents plotting Bayes network probabilities.
Package: infercnv
Commit: 72c36bac699979bf8b2d710d51ce188de6e2c608
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-03 17:35:03 -0400
Commit message:

 Added method to sample the data in an infercnv object to a set number of cells per annotation. Can be applied to references/observations only or both. Works with both up and down sampling and preserves clustering.
Package: infercnv
Commit: e80ae2b893468b50735e51b4543611c4507927bd
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2019-05-01 16:06:30 -0400
Commit message:

 Added gc() calls before calling plot_cnv() as it requires a large vector for some internal calls.
Added option setting to CLI "preferRaster" that should improve plotting performence.
Package: celda
Commit: e041eff5909b8b6631a33b64cca4512699d8d5f0
Author: 87875172 <314100793@qq.com>
Date: 2019-05-20 15:40:03 -0400
Commit message:

 add MCDT
Package: celda
Commit: 35734959b715cf5d775081b2a1823713795c91b4
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-05-19 16:53:20 -0400
Commit message:

 Merge pull request #177 from zhewa/master

Add MCDT
Package: celda
Commit: db583918d3d0b494d6098b0187180d955ef5b9e9
Author: zhewa <zhe@bu.edu>
Date: 2019-05-19 16:52:05 -0400
Commit message:

 Merge branch 'MCDT' of https://github.com/campbio/celda
Package: celda
Commit: f4aebf8a9986c2e371f1ed6ee743a7c54e83f2bb
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-05-19 16:51:48 -0400
Commit message:

 Merge pull request #176 from zhewa/MCDT

Mcdt
Package: celda
Commit: 1ea02356ac345e9ab0816f958d90713d3bfc0059
Author: zhewa <zhe@bu.edu>
Date: 2019-05-19 16:51:12 -0400
Commit message:

 session info
Package: celda
Commit: 9d6813c310e2df9c458455f4e77c1396e4582816
Author: zhewa <zhe@bu.edu>
Date: 2019-05-19 16:09:58 -0400
Commit message:

 pROC::coords
Package: celda
Commit: 4aff1478f2c09eb11cbc8b0d93a4b1f94e73a0f6
Author: zhewa <zhe@bu.edu>
Date: 2019-05-19 15:28:00 -0400
Commit message:

 fix package imports and lints
Package: celda
Commit: 74e52bd50123843256bda76e0c2d71093240f438
Author: zhewa <zhe@bu.edu>
Date: 2019-05-18 20:03:25 -0400
Commit message:

 update package imports in DESCRIPTION
Package: celda
Commit: 3e70598c944445db02166f43c14487f767ee880f
Author: zhewa <zhe@bu.edu>
Date: 2019-05-18 20:01:21 -0400
Commit message:

 Merge branch 'MCDT' of github.com:ericreed/celda into MCDT
Package: celda
Commit: 1dec030960537e46701bdba05117fe4387c85ee4
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-05-14 12:11:04 -0400
Commit message:

 Merge pull request #168 from zhewa/MCDT

Mcdt
Package: celda
Commit: 547c38d71d18f9e5f3e475b688c4571d420975dd
Author: 87875172 <314100793@qq.com>
Date: 2019-05-14 12:05:22 -0400
Commit message:

 Merge branch 'master' of https://github.com/campbio/celda into MCDT
Package: celda
Commit: 5a75fdd5c2e97990b87486a08bda4488bd9956dd
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-05-10 14:34:51 -0400
Commit message:

 Merge pull request #163 from zhewa/MCDT

Mcdt
Package: celda
Commit: 2a53cc7313064d037b7ca80cbf3f9a0e4d44e6d1
Author: zhewa <zhe@bu.edu>
Date: 2019-05-10 14:34:07 -0400
Commit message:

 Merge branch 'master' of https://github.com/campbio/celda into MCDT
Package: celda
Commit: 3dc266625e9690eba9c383aca6b770cda130a683
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-10 13:38:53 -0400
Commit message:

 Updating manual pages
Package: celda
Commit: ad84bf46d8c0b91bb1f3216295e36bdbe131e7b7
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-10 13:34:43 -0400
Commit message:

 Fixed some tab errors
Package: celda
Commit: a01885f6170728d7268aab9d380a660cc0ed907e
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-10 13:26:46 -0400
Commit message:

 Added vignette for multiclass decision trees
Package: celda
Commit: e3dc649d151d64454b423f0880b638b55962ff3f
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-10 11:29:58 -0400
Commit message:

 Fixed comments in example
Package: celda
Commit: 4478849d800c1ed8cc334f90e0f012d90377269f
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-10 11:22:58 -0400
Commit message:

 Changes a message
Package: celda
Commit: 9e0fa7ebd42c8b7873363f7ac26cf6edf25758ef
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-10 11:15:37 -0400
Commit message:

 Added decision tree functions and their documentation
Package: celda
Commit: 4609d7d162cb3c4f691c90c7ce679814f3ee0b99
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-10 11:11:31 -0400
Commit message:

 Merge branch 'master' into MCDT
Package: celda
Commit: 9651e64b4511ccdcb0781cac186a900f510c6e2e
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-04-28 22:20:05 -0400
Commit message:

 Merge pull request #148 from zhewa/MCDT

Mcdt
Package: celda
Commit: 5d5c7333c63b09e0618a9f1243c6c9ab314c4f19
Author: zhewa <zhe@bu.edu>
Date: 2019-04-28 22:16:57 -0400
Commit message:

 Merge branch 'master' of github.com:zhewa/celda into MCDT
Package: celda
Commit: 07eabd90aba3c4e898fa22b5da24b5088e9cda1b
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-04-26 13:39:07 -0400
Commit message:

 Merge pull request #144 from zhewa/MCDT

Mcdt
Package: celda
Commit: 217618d7763201fbed13cc3659df3fa8e2d361c4
Author: 87875172 <314100793@qq.com>
Date: 2019-04-26 13:38:19 -0400
Commit message:

 Merge branch 'devel' of github.com:zhewa/celda into MCDT
Package: celda
Commit: 9f72229634e1f9940f98d5ac8fd1e65f689f8905
Author: 87875172 <314100793@qq.com>
Date: 2019-04-26 13:19:54 -0400
Commit message:

 Merge branch 'devel' of github.com:zhewa/celda into MCDT
Package: celda
Commit: dc5446818683e6ee4df9074366ef950e84b147c9
Author: 87875172 <314100793@qq.com>
Date: 2019-04-26 12:50:46 -0400
Commit message:

 Merge branch 'master' of https://github.com/campbio/celda into MCDT
Package: celda
Commit: 9d6a7787f851cd21ae7b75033f3587b04c8ef2b6
Author: Zhe Wang <314100793@qq.com>
Date: 2019-04-23 11:26:59 -0400
Commit message:

 Merge pull request #128 from zhewa/MCDT

Mcdt
Package: sevenbridges
Commit: b52ddf564ed5cebadf34cdc6bc69e638409bb741
Author: Nan Xiao <road2stat@gmail.com>
Date: 2019-05-20 15:20:15 -0400
Commit message:

 v1.15.1
Package: MultiAssayExperiment
Commit: 282e87b87e987973557913c6a644a20ee94a4129
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-05-20 13:09:57 -0400
Commit message:

 bump version after cherry-pick bug fix and other commits
Package: MultiAssayExperiment
Commit: 7c6f9413003d598735fea7124e7871f4571bcda3
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-05-20 13:03:16 -0400
Commit message:

 remove Rproj
Package: MultiAssayExperiment
Commit: eb57d050f79459dad1d6ff4c550319726b07509a
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-05-20 13:02:12 -0400
Commit message:

 update docs
Package: MultiAssayExperiment
Commit: 26f4655f68e5a08ffd1e444148a21052958f152e
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-05-20 13:00:11 -0400
Commit message:

 bug fix in merge helper
Package: ATACseqQC
Commit: ddb1a583e04af584e4c30009286eae0df99afd82
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2019-05-20 12:48:33 -0400
Commit message:

 Fix the bug if the bam file contail mix of single ends and paired ends.
Package: AnnotationHubData
Commit: 9464d7e03f60ac09925fb5281c52fec4573df4bb
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-05-20 12:38:04 -0400
Commit message:

 Update NonStandardOrgDb recipe

  - will try and rerun resources that have failed.
  - if all aws empty or all avaialble assumes rerun of all resources
  - new helper function that should be used to determine if resources failed and main function shoud be rerun
Package: ExperimentHubData
Commit: f44ca74eea55f5320b6c08cc6ff216bd2c0f66f7
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-05-20 12:36:14 -0400
Commit message:

 Update CheatSheet for running core functions
Package: tximeta
Commit: aa7a05e9d3ab052d209230cb8369c4471a24739e
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-05-20 11:51:05 -0400
Commit message:

 introducing txp range hashing
Package: tximport
Commit: 225953efef09f2a925c99242034abfa4d933a0f7
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-05-20 09:39:38 -0400
Commit message:

 add cpm code
Package: AUCell
Commit: 967d05371ebaca2263a9a89a41be667860afc58f
Author: s-aibar <s-aibar@example.com>
Date: 2019-05-20 11:36:13 +0200
Commit message:

 Added function cbind()
Package: IsoCorrectoR
Commit: 7ba62f9bad09c0577173458543b8de541cda0ea7
Author: Christian Kohler <christian.kohler@ur.de>
Date: 2019-05-20 10:03:10 +0200
Commit message:

 update citation / references
Package: IsoCorrectoR
Commit: a6814f3a21b6ed972d484fbda29f7ff8cf45acba
Author: Christian Kohler <christian.kohler@ur.de>
Date: 2019-05-20 10:02:31 +0200
Commit message:

 update DESCRIPTION
Package: IsoCorrectoR
Commit: d0d27bf74bab04ba792ed8c4a3c450c042720fd9
Author: Christian Kohler <christian.kohler@ur.de>
Date: 2019-05-20 10:00:51 +0200
Commit message:

 update DESCRIPTION
Package: Rsubread
Commit: 6d4cb710d79e6fbb45d672df1f0fc1cefbf71f28
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-05-20 16:20:52 +1000
Commit message:

 See CHANGELOG for 1.35.3 version
Package: treeio
Commit: 4345c9c353624a47a73289419e6aff7964f8c8fd
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-05-20 14:11:55 +0800
Commit message:

 redefined root method by using ape::root.phylo for compatibility
Package: universalmotif
Commit: c0652017be3c41066cbd47f9eeebffcefc4ac888
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 23:28:46 -0400
Commit message:

 new comparison metrics, recalculated dbscores
Package: Cardinal
Commit: 2bfae6f7db55c4db4be83fb1f24e9841c7df3a1b
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-19 21:54:08 -0400
Commit message:

 v2.3.11 faster spatialFastmap and clustering; new dissimilarity metrics
Package: Cardinal
Commit: e996812fbe1fc051cfd972edacc68bc02a356421
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-19 17:52:27 -0400
Commit message:

 fix error on lims=NULL when printing facet plots
Package: Cardinal
Commit: aae88c9511d4a89bdab4d27d1f551e84640daacb
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-19 17:35:01 -0400
Commit message:

 rearrange some things
Package: Cardinal
Commit: 83e394dc0a0911cd95804e00561ed7a248212acc
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-19 04:47:25 -0400
Commit message:

 faster spatialShrunkenCentroids
Package: Cardinal
Commit: 9cfdf3528971039d75b4e8c1ae08b2d7a1229852
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-19 01:57:16 -0400
Commit message:

 added docs for new dissimilarity metrics
Package: Cardinal
Commit: 728050d644dd12d6bba2ba12d6826a4defbdcb6a
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-19 01:29:21 -0400
Commit message:

 bugfix spatialKMeans centers calculation
Package: Cardinal
Commit: ac1305a92f9ce1e444e21953816c38aab709fbb1
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-19 00:52:21 -0400
Commit message:

 add average and correlation spatial distances for FastMap
Package: Cardinal
Commit: 6fd0864d7ba58d6bf528bb1cda3c6d60c859c0dc
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-18 22:47:00 -0400
Commit message:

 faster spatialFastmap
Package: matter
Commit: e828261456ad95368ffbf79bab3ca3dba70b4400
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-19 20:24:35 -0400
Commit message:

 fix nobs() with na.rm=TRUE in stream_stat
Package: universalmotif
Commit: 2dc7e59fbadbff2a7e7f6b1a05fe79b310f691c0
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 19:16:01 -0400
Commit message:

 new compare_columns() util
Package: universalmotif
Commit: 010eadc5d5d0d1a7a70f638621709302e95b2218
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 16:45:45 -0400
Commit message:

 remove ci
Package: universalmotif
Commit: 1b85fd5dc592c76843a96f3c869125c1431dbb26
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 16:41:27 -0400
Commit message:

 clean badges
Package: universalmotif
Commit: 06596113e61722a7f224773d69be575623220dbd
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 16:38:49 -0400
Commit message:

 another attempt at .travis.yml
Package: amplican
Commit: 121dacc1eef91c8136b1dccdaa7eadb073c9897d
Author: JokingHero <kornellabun@gmail.com>
Date: 2019-05-20 00:11:03 +0200
Commit message:

 standarize output from the regular plots, now it will constantly output grob
Package: universalmotif
Commit: 867a76b8be1de8da4edac513417773f53f4223ea
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:55:22 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 132577b4e5210d238575c28f3942ecf87209279d
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:35:07 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 336f93775c259813a8c405129e1728a67f7482f0
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:34:17 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 5d4e254ed89c22b7063a63090434834a313b619c
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:24:11 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: b69865cdd92f23d13562f4c22be739a38ad79651
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:19:57 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 1606abf8143389e04cbe5cf3e9a538ee7795bae6
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:13:20 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: d1e4c9816cadcb851ba0c8f46e02a2ca209fd43e
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:12:01 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: da0bd8366574bb001b6ba62a471cb7c0c0ff4f58
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:06:15 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 5198bbbdb55ae1c93231fb7611feeabb6d8e0e0f
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 15:04:52 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 773b889ce9737251e0cd8a2d7628b8b90d915c0f
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:56:51 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: fd2d5b81087885b765fbd1e835fd453eb17b3d68
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:46:27 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 575ec838c438f8096985bcb78a5da1dd67bbfbff
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:39:23 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 8308409bd329f4c69cc00137bfe507341ee9bb6b
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:30:24 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: d1119d6cec232851d9e131039369a370da457d96
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:26:08 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 51ceb6d15b91a222b165aed1d545085e2f79fa37
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:25:27 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 4faaa4d183285f70900606966db09bf625c60fff
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:25:13 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 9a8eb768ead0264b27ba0ae78e01624da70b1b5b
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:20:20 -0400
Commit message:

 .travis.yml changes
Package: universalmotif
Commit: 0dc643e0917538c649bfb1ece9a20864edc2eabe
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 14:19:48 -0400
Commit message:

 new get_bkg() implementation with RcppThread, changes to .travis.yml
Package: universalmotif
Commit: 1c1c039b66382a8e33ea2e10038fc2efc37b0cd1
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-19 11:18:43 -0400
Commit message:

 new ALLR comparison metric, reworked make_DBscores() + database scores
Package: VariantAnnotation
Commit: 78422da86fd47d44bd2673373fc303f9cf75f824
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-05-19 09:55:35 -0400
Commit message:

 Merge branch 'RELEASE_3_9'

- bug fix, scanVcf,connection-method
- closes issue #29
Package: VariantAnnotation
Commit: fb1ab00872570afb280522c4663e347dafc07a9e
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-05-19 09:52:56 -0400
Commit message:

 version bump
Package: VariantAnnotation
Commit: e2109f22ccd9f1023ce3e833f18fb1fa4521083e
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-05-19 09:51:05 -0400
Commit message:

 misc cleanup

- import GENETIC_CODE from Biostrings
- resolve rtracklayer:::checkArgFormat
- whitespace
Package: VariantAnnotation
Commit: b223d1c61629b58a6a0a2e50342d542b523df26c
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-05-19 09:48:48 -0400
Commit message:

 fix scanVcf,connection-method, support for n= argument

- closes issue #29
Package: VariantAnnotation
Commit: b21d9c1e802d4058e9a5df55afb965872846973e
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-05-15 03:45:21 -0400
Commit message:

 update ?readVcf

- use VcfFile and indexVcf rather TabixFile and indexTabix
Package: simpleSingleCell
Commit: 34e9051683feae120b9cf80f5a2617e4c702c071
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-05-18 22:43:40 -0700
Commit message:

 Bumped version, date.
Package: simpleSingleCell
Commit: b6f4cf1a4cb440e8367c3f4f1fae8d990ae780ab
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-05-18 22:29:08 -0700
Commit message:

 Use published Lawlor count matrix from GEO directly.
Updates to exploit richer Lawlor metadata.
Package: simpleSingleCell
Commit: 419b3d12bd9db43c3894ea8aae854d9dbcf0e901
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-05-17 22:02:16 -0700
Commit message:

 Fixed vignette entry for the miscellaneous analyses.
Package: simpleSingleCell
Commit: 96afdbaf9f3c4c8306c66ce156fd5aed1ffb3adf
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-05-17 21:24:02 -0700
Commit message:

 Minor wording edit for removal of per.gene=.
Package: tximeta
Commit: 270a489a06e4bd96f26c86cfb9b54de46a76530f
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-05-18 17:39:40 -0400
Commit message:

 update to gencode 30/M21, ensembl 96
Package: GSEABenchmarkeR
Commit: 33541bf9967948a9c5fd45b98aa5809c59bd30e3
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2019-05-18 16:29:01 -0400
Commit message:

 runEA: accept user-def methods
Package: cbaf
Commit: 5b96584e73b5f53ce8effd45389a073178640059
Author: armanshahrisa <shahrisa.arman@hotmail.com>
Date: 2019-05-19 00:21:25 +0430
Commit message:

 - availableData() is now more accurate but slower!

- Message function seperates output for different functions in console.
Package: Cardinal
Commit: 727cb4a964b43e7dda207218c9586dd76fb71ba6
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-18 15:49:11 -0400
Commit message:

 v2.3.10 spatialDGMM speed improvements; optim -> optimize
Package: Cardinal
Commit: bcba8a44510cb9a8176de47f1c6edd3f29db4c29
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-18 15:17:00 -0400
Commit message:

 spatialDGMM uses faster C_spatialFilter
Package: Cardinal
Commit: c5128fa6751e954a1b00cd453a8f0619804f23e0
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-18 03:58:34 -0400
Commit message:

 added C_spatialFilter; optim -> optimize
Package: mAPKL
Commit: a3b44453e312ee2171908ea1c09aa7c54acf8011
Author: asakellariou <argisake@gmail.com>
Date: 2019-05-18 21:39:44 +0300
Commit message:

 Fixed conflicts in version change
Package: mAPKL
Commit: 6b4d90fb7062217bb436473e72e1f4203beec01f
Author: asakellariou <argisake@gmail.com>
Date: 2019-05-10 23:11:21 +0300
Commit message:

 updated files
Package: mAPKL
Commit: 6885d4760968bb6ee9a589ba0dee3a225364b53a
Author: asakellariou <argisake@gmail.com>
Date: 2019-05-09 22:02:53 +0300
Commit message:

 Add files via upload
Package: mAPKL
Commit: c7c9471d8d6a44f6a8f2a15d23b2d8951e84c108
Author: asakellariou <argisake@gmail.com>
Date: 2019-05-09 22:01:49 +0300
Commit message:

 Add files via upload
Package: mAPKL
Commit: 1cd2bc375154983575d24c3aee1b26fb228d4556
Author: asakellariou <argisake@gmail.com>
Date: 2019-05-09 21:41:29 +0300
Commit message:

 Add files via upload
Package: mAPKL
Commit: f4013e3638cbd9ea887686b9b04f633c348cf343
Author: asakellariou <argisake@gmail.com>
Date: 2019-05-09 21:04:29 +0300
Commit message:

 Final updated versions
Package: mAPKL
Commit: b094abb503b233b01a3f062530ea41e9f7ae189e
Author: asakellariou <argisake@gmail.com>
Date: 2019-05-05 18:28:36 +0300
Commit message:

 More changes
Package: mAPKL
Commit: a3fc5929083e10ec2d6fe93f1c67cb43bd757d75
Author: asakellariou <argisake@gmail.com>
Date: 2019-05-05 18:25:40 +0300
Commit message:

 The changes
Package: DropletUtils
Commit: 5fcd06450b4fdcb4a46655ca7ed6b790d0f83779
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-05-17 21:33:35 -0700
Commit message:

 Test workaround in absence of deep all.equal for HDF5Array.
Package: DropletUtils
Commit: 5a4c1c9276ba95dbbd9850dec0a270240d25b8a9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-05-12 12:22:45 -0700
Commit message:

 More structured DESCRIPTION.
Package: universalmotif
Commit: 0bc52599e65049bff5540943b7080a93404f5e6b
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-17 23:56:48 -0400
Commit message:

 some cleaning
Package: universalmotif
Commit: 21ecae34aa2a12d4033ca8c49506a2c4f596ab1d
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-17 22:54:05 -0400
Commit message:

 fixed missing bkg errors
Package: universalmotif
Commit: 9c3750722c0291f08bc247ef103cc75a03548250
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-17 21:51:33 -0400
Commit message:

 reworked c++ utilities, fixed a couple param arg checking bugs
Package: Cardinal
Commit: 6205ddaeefdfa9bfe88ad24047a12bcb30d3c73e
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-17 17:14:53 -0400
Commit message:

 minor Cardinal.history() and logger changes
Package: Pigengene
Commit: 2499d0b46aac3f746f9dc9187d1190ed92aae1e8
Author: mshort7 <mshort7@gmail.com>
Date: 2019-05-17 15:49:59 -0500
Commit message:

 combine.networks documentation
Package: Rcpi
Commit: a279d50d75c1086752ff7525b5b09084cc8dd9a4
Author: Nan Xiao <road2stat@gmail.com>
Date: 2019-05-17 15:55:15 -0400
Commit message:

 v1.21.1 release
Package: celda
Commit: 7824f5c44e3531ee6e4832e9633807f597c8c6dc
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-05-17 15:49:01 -0400
Commit message:

 Merge pull request #173 from zhewa/master

master
Package: celda
Commit: ffc979b2748f5abd7aedd7a30f82aed0d40fe6b3
Author: 87875172 <314100793@qq.com>
Date: 2019-05-16 16:02:42 -0400
Commit message:

 Merge branch 'master' of https://github.com/campbio/celda
Package: celda
Commit: e49e0a41abcee30819c8876b9035d3466c5141d1
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-05-14 12:06:55 -0400
Commit message:

 Update README.md
Package: celda
Commit: 1da8dd9a1cbfa4a62ab0a3b257965af97afe380f
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-05-14 12:02:30 -0400
Commit message:

 Merge pull request #165 from zhewa/master

Master: subset rows and columns before row scaling fix #164
Package: universalmotif
Commit: 9c8eebc94e629effafe731eb127a2110337e1b70
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-17 14:58:31 -0400
Commit message:

 all uses of motif_simil_helper.cpp code has been replaced with compare_motifs_helper.cpp
Package: universalmotif
Commit: c1c4c3e19a39c33a5bdce61a79841610bb9d8693
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-16 15:49:07 -0400
Commit message:

 hopefully done with new merge_motifs()
Package: universalmotif
Commit: 2202d9660c8089182f2fb8fce88a5268e4a390f1
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-16 15:18:04 -0400
Commit message:

 fixed up merge_motifs()
Package: universalmotif
Commit: fb3e0f2375428e8e6d06bc2edb277ea760862827
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-15 22:30:52 -0400
Commit message:

 new merge_motifs() internals
Package: universalmotif
Commit: 56a5912de0757fc9964137a9275b0b61eb01d55e
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-15 15:10:20 -0400
Commit message:

 forgot to export make_DBscores()
Package: universalmotif
Commit: 3e1d408f06113a956281d642a0b2e2c32574c5ee
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-15 15:07:55 -0400
Commit message:

 fix spelling mistakes, add old make_DBscores()
Package: universalmotif
Commit: 6c0e7054988aa8aec6c42bd3aab7d7e5b4411e4a
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-05-15 14:40:16 -0400
Commit message:

 changes to make_DBscores()
Package: mzR
Commit: 219af40910fe044e21f937dd2f8e5a6df3f614ce
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2019-05-17 16:29:43 +0200
Commit message:

 Bump dependency, version, add NEWS item. Closes #190
Package: mzR
Commit: 9740d701087bdd1277b269baf0d608fc9a8b9e0c
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2019-05-17 13:27:37 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/mzR
Package: mzR
Commit: 879e905bec9db313517303c2de81e414ded41d42
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2019-05-17 13:27:05 +0200
Commit message:

 Merge branch 'fix/issue190'
Package: mzR
Commit: 1423cb408de623c0cc89e3e9d95d22b67f879232
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2019-04-01 23:31:20 +0200
Commit message:

 Backporting the minmax stuff from boost-1.67.0
Package: mzR
Commit: d9ea53110b65246e20a0fae4c6446a15901a6801
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2019-04-01 23:09:09 +0200
Commit message:

 Backporting the fix boostorg/range/commit/adcb071dc6b06e69aa4ddcc080d23695a5da378f
Package: PepsNMR
Commit: 154126e0199ae5e8d4c2ab503752da7dd830cf9e
Author: ManonMartin <manon.martin@uclouvain.be>
Date: 2019-05-17 15:29:32 +0200
Commit message:

 bump in version for debugging
Package: PepsNMR
Commit: f99e48cc815b1305c3a4bb9aeb38727619480e9d
Author: ManonMartin <manon.martin@uclouvain.be>
Date: 2019-05-17 15:24:37 +0200
Commit message:

 (Future) Bug fix: ggplot issue with annotate()
Package: scMerge
Commit: 4547b42892906505aabcbffeeac36b19f569c286
Author: kevinwang09 <kevin.wang@sydney.edu.au>
Date: 2019-05-17 12:29:32 +1000
Commit message:

 delete Rplots.pdf in testthat

Merge remote-tracking branch 'upstream/master'

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
Package: scMerge
Commit: 02f4ea5516b54ea84fa4775f8dc4ab503439f805
Author: kevinwang09 <kevin.wang@sydney.edu.au>
Date: 2019-05-17 12:27:17 +1000
Commit message:

 version bump after Nitesh upd branch
Package: scMerge
Commit: 72a25d15bf129f91e3a67a0834c1aaa679f3da08
Author: kevinwang09 <kevin.wang@sydney.edu.au>
Date: 2019-05-14 10:59:07 +1000
Commit message:

 switch travis install to travis script
Package: scMerge
Commit: 2a4512ccbc93a3fbd9c9d043adfd45fc3cd23a9b
Author: kevinwang09 <kevin.wang@sydney.edu.au>
Date: 2019-05-14 10:29:47 +1000
Commit message:

 customise travis build Bioc3.9
Package: scMerge
Commit: 3d0bbc97bfa510e66e4f4047c7e055bde913abae
Author: kevinwang09 <kevin.wang@sydney.edu.au>
Date: 2019-05-07 11:46:31 +1000
Commit message:

 edit .travis.yml
Package: BEclear
Commit: 4db6dce6fa2d9b0453075b7c19b5f51d0d1e05c3
Author: David Rasp <David.J.Rasp@gmail.com>
Date: 2019-05-17 13:40:20 +0200
Commit message:

 closes #14
Package: biomaRt
Commit: 70aa3862d6a2a807b084a1c7df567dd431b49580
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-05-17 11:25:30 +0200
Commit message:

 Address bug where a progress bar `bp` could be defined outside the call to getBM().
Package: cbaf
Commit: d3ff13f0a45d3aada241cca39ddfb4c4741bb54e
Author: armanshahrisa <shahrisa.arman@hotmail.com>
Date: 2019-05-17 15:47:19 +0430
Commit message:

 - Optimizations
- Errors less frequently stop functions.
Package: karyoploteR
Commit: 1f6dba8ad05be0a603e047b057175a6a65eb14dc
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-05-17 12:19:19 +0200
Commit message:

 version bump
Package: karyoploteR
Commit: 70acd865af73a04c0e678bd16f90a2b1d6460507
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-05-17 12:19:09 +0200
Commit message:

 moved coverage to granges to regioneR::toGRanges
Package: edgeR
Commit: 890ef732d2c41c83f7b6e3872ddef1bc44c60bd1
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-05-17 19:33:57 +1000
Commit message:

 Correcting approx() in dispBinTrend.R to use ties=mean because x might not be pre-ordered.
Package: limma
Commit: ee273682ca99f8bc436a420cb17f585e98e4cc17
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-05-17 19:22:25 +1000
Commit message:

 17 May 2019: limma 3.41.2

- The approxfun() call in vooma() now sets
  `ties=list("ordered",mean)`. This doesn't change the output but
  is slightly faster and avoids a warning message in R >= 3.6.0.

- limma now depends on R >= 3.6.0 because of the use of a list value
  for the `ties` argument of approxfun().

- The approx() call in fitFDistRobustly() now uses `ties=mean`
  instead of `ties=list("ordered",mean)` because the `x` argument is
  not generally pre-ordered.
Package: Cardinal
Commit: 7125cf05de2a15eea1d8a0c23a307954471ca73b
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-17 04:50:15 -0400
Commit message:

 v2.3.9 clean up generics
Package: QuasR
Commit: d250419a1b61b52a8ad10048a44c68fea0887e4a
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2019-05-17 10:08:49 +0200
Commit message:

 Merge pull request #16 from fmicompbio/rhisat2link

Rhisat2link
Package: QuasR
Commit: c3001ada6cfede2806e6db6140de77b4ab82dc4e
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-05-17 09:53:15 +0200
Commit message:

 update version
Package: QuasR
Commit: c050e8d71c0cfdcf31224d0b5d5866a781764d8b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-05-17 09:35:20 +0200
Commit message:

 Change Rbowtie link to Rbowtie-package
Package: QuasR
Commit: 8a6a0dbe38a059c5ae4f444bb86a2c90d32c1b2a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-05-17 09:26:51 +0200
Commit message:

 Fix link to Rhisat2-package in qAlign.Rd
Package: karyoploteR
Commit: 187fbb50a2bc154f535ae15b79c9812cbbc47642
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-05-17 09:34:31 +0200
Commit message:

 Version bump
Package: karyoploteR
Commit: 53e7c762e4dbcb20950648f1b7bf1dc9dfcaad3c
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-05-17 09:34:04 +0200
Commit message:

 Added the actual coverage to the object returned by kpPlotCoverage
Package: karyoploteR
Commit: 81a1915d16253a692f832ed9331ef6bf5080cfd6
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-05-07 12:13:50 +0200
Commit message:

 Added an explicit package (regioneR) to a function
Package: Rhisat2
Commit: ec9bc33001462f3a5a980388d123eab54b664eef
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-05-16 20:23:27 +0200
Commit message:

 Fix NAMESPACE
Package: Rhisat2
Commit: 802090911449da0257547c5bfb93f25ad9944898
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-05-16 20:07:08 +0200
Commit message:

 Add man page for Rhisat2-package
Package: Cardinal
Commit: 947d5f475a5d06f03d73e6ce3097a0b653b12e01
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-17 03:18:27 -0400
Commit message:

 removed unused options()
Package: regioneR
Commit: 6e638212a2fa98ecec48e6e27625182f8f6c63b1
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-05-17 09:08:12 +0200
Commit message:

 Version bump
Package: regioneR
Commit: bb30996e784d43f1fe30a62d689765b7af5ded26
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-05-17 09:02:38 +0200
Commit message:

 Improved error message in toGRanges
Package: Cardinal
Commit: 583ad2d73c50c844609fd9b1483965ad623f9a10
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-17 03:00:14 -0400
Commit message:

 clean up generics; removed unused setters
Package: Cardinal
Commit: 2fc11915ed356892435860132b7397f2280501f0
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-17 01:24:04 -0400
Commit message:

 updates to logger
Package: scran
Commit: 2c1c886275fbcf1555e199acb4986e1bebe7f4b1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-05-16 19:37:32 -0700
Commit message:

 Removed remaining instances of per.gene=.
Package: SingscoreAMLMutations
Commit: ae4cfd7786a61928c5efc9e28048af8c352ae062
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-05-17 14:10:41 +1000
Commit message:

 updated link to original mutation dataset
Package: SingscoreAMLMutations
Commit: 7aa2feff2bc3ce18ba3270cedbfa1f45aea41e26
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-05-17 13:22:55 +1000
Commit message:

 copy edits from F1000
Package: Cardinal
Commit: d53f864097d86236b82f96c3c84828a1619977c9
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-16 21:55:08 -0400
Commit message:

 v2.3.8 more plot() and image() methods
Package: Cardinal
Commit: 96dfc914da2030c2620a9809911aeee7df58c795
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-16 21:28:49 -0400
Commit message:

 updated stats vignette
Package: Cardinal
Commit: 71162eceefa57f8d12af853d9f219e371f4a7556
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-16 20:55:52 -0400
Commit message:

 added docs for new plotting methods; add jitter option to boxplots
Package: Cardinal
Commit: 2d083ff20a41294f5a7650ddcbe41793b649ac63
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2019-05-16 20:19:41 -0400
Commit message:

 added image() methods for MeansTest and SegmentationTest
Package: TCGAbiolinks
Commit: 4b9d1075d0cf2c3625f50d26de2e7255611b6ab7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 22:33:57 -0300
Commit message:

 adding missing man
Package: TCGAbiolinks
Commit: fb2f42c916a0e5924af72af884c1d6cbc5b96895
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-16 18:53:43 -0400
Commit message:

 PCBC_stemSig description

PCBC_stemSig description
Package: TCGAbiolinks
Commit: f0afd572e0a9666aec4d93004eb526ab5b7c597c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 19:27:33 -0300
Commit message:

 removing example
Package: ELMER
Commit: e202bc6d86096f7b57daa5b15af03681b49d33a6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 17:11:40 -0500
Commit message:

 Fixing man
Package: TCGAbiolinks
Commit: 583b018b8021f0b64ed5e227740746d5de57e154
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 19:13:12 -0300
Commit message:

 conclude merge
Package: TCGAbiolinks
Commit: eed4bbd674aff521a556aca45634cc21aa84fee8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 17:02:09 -0500
Commit message:

 Add files via upload

Reducing sizes
Package: TCGAbiolinks
Commit: ccc1553215edf897a95353c06dc08aac0056d735
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 12:12:48 -0500
Commit message:

 Add files via upload
Package: TCGAbiolinks
Commit: 3771333821380bf74f0ff521841163e86468c89b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 12:12:14 -0500
Commit message:

 Delete case2_Heatmap.png
Package: TCGAbiolinks
Commit: ce3ddd67b47a916fb53f06fec00e497e6161b2e4
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 12:11:58 -0500
Commit message:

 Update casestudy.Rmd
Package: TCGAbiolinks
Commit: cbeb104f5b8300636c34f4b509e3fba07e056c19
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 12:08:20 -0500
Commit message:

 Update DESCRIPTION
Package: TCGAbiolinks
Commit: 21bed90c189536c04de5ae9e24ac4635b1de77bf
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 12:07:48 -0500
Commit message:

 Update casestudy.Rmd
Package: TCGAbiolinks
Commit: 23b06e74a14ccbfe72656de68d9261f65ccf90a0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 12:06:26 -0500
Commit message:

 Delete elmer2.png
Package: TCGAbiolinks
Commit: 801eddc7f4395b55fda02efe671b113f8e688d2a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 12:06:09 -0500
Commit message:

 Add files via upload
Package: TCGAbiolinks
Commit: 3f8926a539b3a1ef064a5f0a31f9b3acdcb2d79e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-16 12:04:47 -0500
Commit message:

 Update bibliography.bib

Reduzing size of the package
Package: TCGAbiolinks
Commit: 2790d5a2ed23f7c177133d495fa82b36e206a2d8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-15 17:32:11 -0500
Commit message:

 update man


Former-commit-id: 9dd5abc3a04c79e88942c1e961997c4f16e6e9e9
Former-commit-id: cf423144622ba2e49bf04cd6212ebde54aae9975
Package: TCGAbiolinks
Commit: 5748a7873800a2b8542649c290fdd0b881ab0c7e
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-13 17:55:51 -0400
Commit message:

 TCGAanalyze_Stemness annotation (subtype or sample type)

TCGAanalyze_Stemness annotation (subtype or sample type)


Former-commit-id: df019c76b6ec06ecf68a80caab67d3cce554fe94
Former-commit-id: e030fce202b2d604236909fd12a0730c070d3004
Package: TCGAbiolinks
Commit: 21db2b096cd7075de33a4dd5b36b1eeb27dc2e2d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-13 16:26:33 -0500
Commit message:

 Bug fix


Former-commit-id: a1af52a9aafc9943ec1d97ba3fb57c7cab314e3a
Former-commit-id: 1ce707fb4f1932d1b72bc3a7b258c491c44784f6
Package: TCGAbiolinks
Commit: 42c1bf6f54ccfe4c10c2c6a6e8bc1f10a1087ee1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-08 15:11:30 -0300
Commit message:

 TCGA colDataprepare considering samples with no information


Former-commit-id: ecf6f7f2136310b4fcb3c0e790fb45c8de357677
Former-commit-id: bd6406554ef2803218ee5ff59c282b26a5d4ade2
Package: TCGAbiolinks
Commit: 4585f09a98cd19c82331daaf662ae259cddb1c92
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-08 15:06:37 -0300
Commit message:

 TCGA colDataprepare considering samples with no information


Former-commit-id: b69151b1e334cc08ff11b3fc847b5b03e0054ca5
Former-commit-id: d9160bc86771494a92307f75598d32f61a47f749
Package: TCGAbiolinks
Commit: b410f0f9dd578c297cbc2e7ff4375cbde30f712b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-08 14:53:00 -0300
Commit message:

 TCGA colDataprepare considering samples with no information


Former-commit-id: fd6212faa72e119544cabd3791c8a970ba9a2eb4
Former-commit-id: 1ed4c4d0a0f9b5f462797588cd270cbc3035c2de
Package: TCGAbiolinks
Commit: c5cfba26603ceabb6b2d75e283706355b8ff815f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-08 14:53:54 -0300
Commit message:

 version bump


Former-commit-id: 02139b5c74dab129b0b2313c87bb00c16d73e87c
Former-commit-id: ff5f2b14e03eea6dff232458c8522a8d64bb36fa
Package: TCGAbiolinks
Commit: acea7dafacfb9ae9ecbff6753d18752739bb71fa
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-08 14:49:11 -0300
Commit message:

 version bump


Former-commit-id: 0ef7ddec8498c613e7b4d3ef0c23447150b4023e
Former-commit-id: 109f9367b372e6627b1389bf548d1720d7b1117d
Package: TCGAbiolinks
Commit: aa66ed7b8ffbe9bfdceb0f48b49cd957edc45403
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-05-08 14:48:24 -0300
Commit message:

 Merge remote-tracking branch 'upstream/master'


Former-commit-id: 621553859d86f156527b0294a1171b0d7cccb6df
Former-commit-id: f8db919a9cfb14801a4871954f1a1e291f02176a
Package: TCGAbiolinks
Commit: e7d7a00b89a719ea4389386fc6c495d6b8be4672
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-06 13:21:14 -0400
Commit message:

 TCGAanalyze_Stemness part 2

TCGAanalyze_Stemness part 2


Former-commit-id: 6d2625e00ac71b152e315c1bb5445cbf8536437b
Former-commit-id: 53234202ebe5acf646c5fa325eb7ee6fd6364d05
Package: TCGAbiolinks
Commit: d64df43edb0bf573c02f797f659818e61119ada9
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-06 12:15:52 -0400
Commit message:

 TCGAanalyze_Stemness with PCBC

TCGAanalyze_Stemness with PCBC


Former-commit-id: d17e6f95cfac16a9c140436d0c29c7a791da2b93
Former-commit-id: 8536412a6c9b530439c66a29e36e01f4b979d7f3
Package: TCGAbiolinks
Commit: df755277a369ca4bb281eed702d14804712cbc89
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-06 11:44:38 -0400
Commit message:

 Description update

Description update


Former-commit-id: f69082aac5782156b7aafe7d682377f6fa8f1179
Former-commit-id: f663dd025dcac7600e86ccd7a5f8b6db09bb5134
Package: TCGAbiolinks
Commit: 7740a71af5f15b6b545c316a1d0612feac709785
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-05-02 12:12:54 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_9    branch


Former-commit-id: 348812ace319f54e18f3ebf1abe09dd978394d36
Former-commit-id: 65f76b7c6b120a1b2724cdcf47450a2af1f4e35a
Package: TCGAbiolinks
Commit: 5ebdaf227b44841ceb35308c95de874bc277c3ce
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-05-02 11:53:56 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of            RELEASE_3_9 branch


Former-commit-id: e873767ceedbebc0397a91c186a571698358c8d3
Former-commit-id: e1eb75d83d892eb78289ed20234b27176752f35f
Package: TCGAbiolinks
Commit: 7f083272c094bd56b2fd0b17bce54334ed1cc4a9
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-29 09:55:36 -0300
Commit message:

 Update appveyor.yml

Former-commit-id: 44d6355bba8fce5efa968d5141a5ad97698f813a
Former-commit-id: 997bd897855319193dab381f9dbeae52e81538e4
Package: TCGAbiolinks
Commit: cac252fbc09c72f5d7e8168ee5db1a4cd496c07c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-29 09:45:59 -0300
Commit message:

 Update README.md

Former-commit-id: e36987bcab395a376bcb18dd7652c10aa86d7c6d
Former-commit-id: f5bdb5184a6fa7227ca3b0c7309b39870733b11d
Package: TCGAbiolinks
Commit: c954a35b787d1a421a289e4474983b7813a6cd03
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-29 09:38:29 -0300
Commit message:

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


Former-commit-id: 3d3b337b28606b6e7c4c155e589370583567f951
Former-commit-id: 667e0f8283acacdfe1e3f544d5c5ce2081b7be45
Package: TCGAbiolinks
Commit: 11dad5c2ab3b80611772ef37e0fe5484a36a84ac
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-24 11:05:03 -0300
Commit message:

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


Former-commit-id: 96563fb0dc0f9a513f3c13aa6b72abdcdcef1e17
Former-commit-id: 8593db8ccf3dd8002086011b250542b56fc90865
Package: TCGAbiolinks
Commit: f23810c5211837b33e2e77f6f6356ccf6c1d62d8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-24 11:05:03 -0300
Commit message:

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


Former-commit-id: 11dad5c2ab3b80611772ef37e0fe5484a36a84ac [formerly 8593db8ccf3dd8002086011b250542b56fc90865] [formerly 96563fb0dc0f9a513f3c13aa6b72abdcdcef1e17]
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Package: TCGAbiolinks
Commit: c4d917fb184b50bd2ddccc9091ab0242824d74b2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-24 10:55:53 -0300
Commit message:

 Version bump


Former-commit-id: dbd89ea2ec02bd7d5dad0f04a421b744adaa6bad
Package: TCGAbiolinks
Commit: 186de69e49ec11b22eddf17770314a733638f545
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-24 10:55:53 -0300
Commit message:

 Version bump


Former-commit-id: c4d917fb184b50bd2ddccc9091ab0242824d74b2 [formerly dbd89ea2ec02bd7d5dad0f04a421b744adaa6bad]
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Former-commit-id: 1a5cfc99df62122187347cb00991e0f9e9bad409
Package: TCGAbiolinks
Commit: 5eb516ee94e86557dc043e54688ae5c7719c2a03
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-24 10:55:30 -0300
Commit message:

 Fixing GISTIC samples labels


Former-commit-id: 6381c5f7378120a04abaebaaf177181e8a8aba03
Package: TCGAbiolinks
Commit: 252404340c783b4f3b224c34951f2841a93eea05
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-24 10:55:30 -0300
Commit message:

 Fixing GISTIC samples labels


Former-commit-id: 5eb516ee94e86557dc043e54688ae5c7719c2a03 [formerly 6381c5f7378120a04abaebaaf177181e8a8aba03]
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Former-commit-id: fe0dd1f8046e20aff2bae95555b94cc599714160
Package: TCGAbiolinks
Commit: f829ace526fa7f88e89613141fdad626d6c440d8
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-18 11:09:39 -0300
Commit message:

 fix merge


Former-commit-id: c29f188dc8e533ff268cdd14859129b96b384e3b
Former-commit-id: f076bb5b54b1b356495ef21d060d9171dc62c5f7
Package: TCGAbiolinks
Commit: 24e34c75c723c9a44e95853c1a024d8a1adf53d5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-18 11:09:39 -0300
Commit message:

 fix merge


Former-commit-id: f829ace526fa7f88e89613141fdad626d6c440d8 [formerly f076bb5b54b1b356495ef21d060d9171dc62c5f7] [formerly c29f188dc8e533ff268cdd14859129b96b384e3b]
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Package: TCGAbiolinks
Commit: d06dc64269b7dadbe342ea9e4819435b2a4fb68a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-18 11:09:14 -0300
Commit message:

 Updating R appveyor


Former-commit-id: b31f7c421b0089f31759a975968b0138c2a08141
Package: TCGAbiolinks
Commit: 3e866a0318dc3a67918c4c733d3baf995de483e0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-18 11:09:14 -0300
Commit message:

 Updating R appveyor


Former-commit-id: d06dc64269b7dadbe342ea9e4819435b2a4fb68a [formerly b31f7c421b0089f31759a975968b0138c2a08141]
Former-commit-id: 64cb03318935c884ad5ab86fe2076fb6e2e6d452
Former-commit-id: 4ce3e93c082e8a147b7e6452b3c95b38ccf3ee53
Package: TCGAbiolinks
Commit: 2bd2486a2e11aef0d775c87881f7c160122b8dce
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-18 11:02:58 -0300
Commit message:

 Removing warning


Former-commit-id: 4182098fe99a89b2a06a74a1399878475ad5c637
Package: TCGAbiolinks
Commit: 04cf678b2c0a07efec950206154e83c3bdf9a421
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-18 11:02:58 -0300
Commit message:

 Removing warning


Former-commit-id: 2bd2486a2e11aef0d775c87881f7c160122b8dce [formerly 4182098fe99a89b2a06a74a1399878475ad5c637]
Former-commit-id: 50823d983103d118891e106b8ea19de493b3a6c4
Former-commit-id: bee1b8e80427b5bf9a1ace8ca657828f40a4f352
Package: TCGAbiolinks
Commit: cf983f5d46dfdb158b398399e9d1f81b72fc70c3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-08 13:00:05 -0300
Commit message:

 typo fix


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Package: TCGAbiolinks
Commit: 09b4ebf3aef2bb403bd7fbd258b767776f00229c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-08 13:00:05 -0300
Commit message:

 typo fix


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Commit: 9b026def325def2ba935d93decc6af4b02fca06a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-08 13:00:05 -0300
Commit message:

 typo fix


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Commit: 9aaad6beb678f75b96b9f24e70afbc9599fbb947
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-08 12:37:36 -0300
Commit message:

 improving ensembl access


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Commit: 955807445ec3704d2eb5b8101f7eccf1f8a70549
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-08 12:37:36 -0300
Commit message:

 improving ensembl access


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Commit: c83131974b82031841208a98dc5d5f16d6750cc2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-04-08 12:37:36 -0300
Commit message:

 improving ensembl access


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Commit: 1e830648a045315d2635f19ec0e3e8baf0cb929d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:09:58 -0300
Commit message:

 version bump


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Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:09:58 -0300
Commit message:

 version bump


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Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:09:58 -0300
Commit message:

 version bump


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Commit: 50c9d452b96d7334ac7e1118b02b351efaf88014
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:08:18 -0300
Commit message:

 Preparing multiple GISTIC files #304


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Commit: 5f342f722ad58e085179cf7359278c141a3ca17c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:08:18 -0300
Commit message:

 Preparing multiple GISTIC files #304


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Commit: de4ee782e25139fc0fdbc0115a988e8747aecb24
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:08:18 -0300
Commit message:

 Preparing multiple GISTIC files #304


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Commit: af52021a41c7ae03347ba931640242cfeabf0a3b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 10:56:15 -0300
Commit message:

 Changing from patinet ID to  sample ID #304


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Package: TCGAbiolinks
Commit: 90c035b68a16e2ffbb498fc33f6c872a1cba8373
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 10:56:15 -0300
Commit message:

 Changing from patinet ID to  sample ID #304


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Commit: 642548cbad802d604e547858b2b330c53b6b95bb
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 10:56:15 -0300
Commit message:

 Changing from patinet ID to  sample ID #304


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Commit: 13f0bd8ffb5c7efaaa5a2b426cea21964ed02363
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:16:50 -0300
Commit message:

 Improving error handling


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Commit: 9d0403d44273e5f41e99862985fa74fb4a848c0e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:16:50 -0300
Commit message:

 Improving error handling


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Commit: c72e6eba0425c55d8db766bb4dba2e3f4a732def
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:16:50 -0300
Commit message:

 Improving error handling


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Commit: ec60b5c758334e6c5c51d190d15405f35108e2bf
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:12:37 -0300
Commit message:

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


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Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:12:37 -0300
Commit message:

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


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Commit: 48ac34b8eb5f9823cf622c5e984dca0653799746
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:12:37 -0300
Commit message:

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


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Commit: de52e2909465d9345b0f98d617889cb8a14d10a7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:12:16 -0300
Commit message:

 Improving output


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Package: TCGAbiolinks
Commit: 4f43de1aa4928c3e22f5c27abfa6f42ecf7e6de1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:12:16 -0300
Commit message:

 Improving output


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Commit: f5a105a91f6506e9ae0ae0e2756e1d5ab5837f75
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 14:12:16 -0300
Commit message:

 Improving output


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Commit: 66c2220a3938ae221026c2a8bc6e3e16772bd0ee
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 13:25:44 -0300
Commit message:

 Merge pull request #300 from reese3928/master

typos

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Commit: e596b8baeda94345144896c9e755d43800d283e7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 13:25:44 -0300
Commit message:

 Merge pull request #300 from reese3928/master

typos

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Commit: a63999f29e79dc86cb0e1cfbad7459ab5ded6762
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-18 13:25:44 -0300
Commit message:

 Merge pull request #300 from reese3928/master

typos

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Commit: d98a2737b053b0f1af796e3ca642ff916de2be04
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2019-03-15 12:39:12 -0400
Commit message:

 typos


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Commit: 2ddcd590efcdf5922f64c22e2b8b0903d5d9bb41
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2019-03-15 12:39:12 -0400
Commit message:

 typos


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Commit: 06f25681e38fd12fe4c070567cb2fb4041dc55af
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2019-03-15 12:39:12 -0400
Commit message:

 typos


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Commit: 4432277b6a3888a030f20740ed564407917cfd2d
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-05 13:48:37 -0300
Commit message:

 Fix second query if first is not able to access GDC


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Commit: 0e139a4129eab31dea66c8e757179898d997bf23
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-05 13:48:37 -0300
Commit message:

 Fix second query if first is not able to access GDC


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Package: TCGAbiolinks
Commit: dc25e5f41892d2690dddbf0ac9635f5d5eedcfd4
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-05 13:48:37 -0300
Commit message:

 Fix second query if first is not able to access GDC


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Commit: bd6dcd1e07943370ff6e0ff134d72146da8ac0d4
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-04 11:56:49 -0300
Commit message:

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


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Commit: a796903a2eac2f29d0b6b3aab98ce179f80c7b2e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-04 11:56:49 -0300
Commit message:

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


Former-commit-id: bd6dcd1e07943370ff6e0ff134d72146da8ac0d4 [formerly 8183a3e12454177351253b41a87eb6415a53f0a2] [formerly 6d2b78e257f1a107b80d703a70630797ac72cc7a]
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Package: TCGAbiolinks
Commit: cc07f1910e3192e848fb1966dd27a9282dd7597a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-04 11:56:49 -0300
Commit message:

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


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Commit: 8b1c783f15f30ca521873cc7566a0e43c6b05452
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-28 10:36:29 -0600
Commit message:

 Add miRNA example


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Commit: cd05c5289aef6be40207a059bebedf3e58de1645
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-28 10:36:29 -0600
Commit message:

 Add miRNA example


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Commit: 2143ad522102eed30fca76156064aab4c547f842
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-28 10:36:29 -0600
Commit message:

 Add miRNA example


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Commit: b932a185d6bd186fa77d1af43a60f9af1bfd1e62
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:45:08 -0600
Commit message:

 Removing masking from matrix DNA methylation to SE


Former-commit-id: 0cd9d4321c927b6386333ade82b2ce3f7ab76cbd
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Commit: 5bc0e2dca4a582c8a5e0da71a455380d3067b5e0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:45:08 -0600
Commit message:

 Removing masking from matrix DNA methylation to SE


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Commit: 1f359ddbfaefed268611bc92e3f09905c663feee
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:45:08 -0600
Commit message:

 Removing masking from matrix DNA methylation to SE


Former-commit-id: 5bc0e2dca4a582c8a5e0da71a455380d3067b5e0 [formerly 407f1e906141ddbab19706113210c1e5a3bf6af2] [formerly 66cbfe3d46b48d8bd6e8f189b558a6bcd15770d9] [formerly b932a185d6bd186fa77d1af43a60f9af1bfd1e62 [formerly 7cc4cf642d23c736b22c0efab054ef225f1fb509] [formerly 0cd9d4321c927b6386333ade82b2ce3f7ab76cbd]]
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Commit: 7e3c6f42f1d99d51296be4c18a8c87aa157c5db2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:18:57 -0600
Commit message:

 Adding IDAT prepare to vignette


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Commit: 732b1054808df128c88727dd50948778f9d8705b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:18:57 -0600
Commit message:

 Adding IDAT prepare to vignette


Former-commit-id: 7e3c6f42f1d99d51296be4c18a8c87aa157c5db2 [formerly 32503253a0d663b7f9333d33eb504c8a9a8f96a8] [formerly b98e37b1729971e11349a9e6fb907f34e60049a2]
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Commit: 2bd16c84767b2bf44ee25004b70d54b0a3e9d8a0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:18:57 -0600
Commit message:

 Adding IDAT prepare to vignette


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Commit: 951a354229b5e833cb5cfa45883f937662bd62c3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:08:19 -0600
Commit message:

 Removing note


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Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:08:19 -0600
Commit message:

 Removing note


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Commit: 1b74412668eee3dca8a818bd4f6ae9936044100a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:08:19 -0600
Commit message:

 Removing note


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Commit: 379c1031d63c1503da7ebb76477f6c6e9accdb5c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:36:45 -0600
Commit message:

 fixing appveyor


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Commit: b6b616f9c847ea8a0109ebdc28630694737580cd
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:36:45 -0600
Commit message:

 fixing appveyor


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Commit: 4cfa867f19e34eec473089dde383326317738f8b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:36:45 -0600
Commit message:

 fixing appveyor


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Commit: f56c342109d8bb1448c3d3972fbf118706857d14
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:34:16 -0600
Commit message:

 bug fix


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Commit: 7d2bf0c465a881e54517fbb17b1ad565f76f9cb2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:34:16 -0600
Commit message:

 bug fix


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Commit: b533982c07150e328554d9d8ed63ff187fc1611c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:34:16 -0600
Commit message:

 bug fix


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Commit: e6d931b1a465edcb7949ff912dc2959463409e0f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:16:29 -0600
Commit message:

 Fix Description


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Commit: 95e993eb58da59c5d081edfd558da265225d549c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:16:29 -0600
Commit message:

 Fix Description


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Commit: 7d362c89552f061886112b01e32382863cc2e344
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:16:29 -0600
Commit message:

 Fix Description


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Commit: 2c8167a268086a3a3227765f7fc156cbbaece8a5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:13:50 -0600
Commit message:

 updating aapveyor and namespace


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Commit: bbe8823ece9619b0a8c491605978d123228d41eb
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:13:50 -0600
Commit message:

 updating aapveyor and namespace


Former-commit-id: 2c8167a268086a3a3227765f7fc156cbbaece8a5 [formerly d6ad88008458df53310e00793e966ca2f5868005] [formerly f82a2f1dd260507e4bc7127598dc696775da012b]
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Commit: 01d1071ddde68dd03e74c6c96c6d69bf4d779b86
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:13:50 -0600
Commit message:

 updating aapveyor and namespace


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Commit: 84cdc04c9d319b2890a7bff0c562476815b65bf5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:36 -0600
Commit message:

 Version bump


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Commit: 052b015cdb31cfed9098fdc7dc910f40e83640a0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:36 -0600
Commit message:

 Version bump


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Commit: 0f5ad9864f7c3a10dc62d63195954f7e4368580a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:36 -0600
Commit message:

 Version bump


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Package: TCGAbiolinks
Commit: a12cd79229767c4bde9a96f0aae86effba86ae40
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:08 -0600
Commit message:

 Update internal function for idat function


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Package: TCGAbiolinks
Commit: fc33c111537ac225d764252458619c54cc78f3e1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:08 -0600
Commit message:

 Update internal function for idat function


Former-commit-id: a12cd79229767c4bde9a96f0aae86effba86ae40 [formerly 8c8d5e37a2466d259a9e1cad6ac0e542a3f542fe] [formerly 87e1384b529f652c647846882b60e90a36554e89]
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Commit: ba7aaa52b7ec3971576c08f55643e481f0e2187e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:08 -0600
Commit message:

 Update internal function for idat function


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Commit: 030d3b47d3cc65673943ff71ea31acb17d077133
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:06:35 -0600
Commit message:

 Adding IDAT pprepare using sesame


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Package: TCGAbiolinks
Commit: 2ab55abf90c69e789fd49d895ce3160bee14cc2c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:06:35 -0600
Commit message:

 Adding IDAT pprepare using sesame


Former-commit-id: 030d3b47d3cc65673943ff71ea31acb17d077133 [formerly 642caa9ad6953edeab8fe59a3e2ca48974f6eef0] [formerly 76e1110adb46f67f58e287c28f6caf924f03cbb5]
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Commit: b98523ec0258e864883726d59901f0006eadd099
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:06:35 -0600
Commit message:

 Adding IDAT pprepare using sesame


Former-commit-id: 2ab55abf90c69e789fd49d895ce3160bee14cc2c [formerly 38bcc8a718fab015b1d8a1718d0de6753e38159d] [formerly f73c4ec55a332da0af1540c7d839126daba417ba] [formerly 030d3b47d3cc65673943ff71ea31acb17d077133 [formerly 642caa9ad6953edeab8fe59a3e2ca48974f6eef0] [formerly 76e1110adb46f67f58e287c28f6caf924f03cbb5]]
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Commit: a47002cf71a05213788ceb17a845925c908f18a4
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 12:15:40 -0600
Commit message:

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


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Package: TCGAbiolinks
Commit: 2a858a289b5b66059f3a1545c3ac17e15c90ac25
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 12:15:40 -0600
Commit message:

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


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Commit: 103ad521628f42791e4464d357b616982c320f00
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 12:15:40 -0600
Commit message:

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


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Commit: 1e635c2f139c52695c54057b8798bda44d744e50
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 12:15:13 -0600
Commit message:

 Improving hg19 access


Former-commit-id: 8d684ae93c7377a966b7f328e2346931ca331041
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Commit: 84e4204a47ce877f8f149ab499d4e908225c00da
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 12:15:13 -0600
Commit message:

 Improving hg19 access


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Commit: da8ff8a6dc5a4fe9543f71693d7532eb661848b0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 12:15:13 -0600
Commit message:

 Improving hg19 access


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Package: TCGAbiolinks
Commit: 6228a11f7fac15a2ff73d7bdd5df8f0417788cdf
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-02-04 12:53:00 -0500
Commit message:

 fix in TCGAanalyze_Preprocessing

fix in TCGAanalyze_Preprocessing


Former-commit-id: 85c3f3e63dcc4ac542958f84d61074443dca0f99
Former-commit-id: 8c4fb98f4d782e1163ab65e8fa3eace9ca8e4423
Package: TCGAbiolinks
Commit: 327eeeebc7368e89dd4ef8f3a2bc7734c4869585
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-02-04 12:53:00 -0500
Commit message:

 fix in TCGAanalyze_Preprocessing

fix in TCGAanalyze_Preprocessing


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Commit: 62f67feee6327734312e16676b858c861575ad98
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-02-04 12:53:00 -0500
Commit message:

 fix in TCGAanalyze_Preprocessing

fix in TCGAanalyze_Preprocessing


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Commit: c2a309a057c3c0ef585db71441f3d3b6bf2d7b7b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 11:02:27 -0600
Commit message:

 Change host for hg19 fix #292


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Package: TCGAbiolinks
Commit: 68a4d11389e3707f4d6b5d6118a88cbc736f5a73
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 11:02:27 -0600
Commit message:

 Change host for hg19 fix #292


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Commit: c25901eca992913097a59551b839ab854955f840
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-04 11:02:27 -0600
Commit message:

 Change host for hg19 fix #292


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Commit: e3384635b07c2c0414f2979affb8b6bea5976907
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-24 17:16:03 -0600
Commit message:

 Bug fix in gistic preparing


Former-commit-id: 8c5449958ad2e1cd300daa033d57d1267e7c9d6d
Former-commit-id: 1edcade4a53ad8297dd9c46a83fe097bd254b11d
Package: TCGAbiolinks
Commit: 374d20a8bce1503b46d3c2b2fe475c33380c6fdd
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-24 17:16:03 -0600
Commit message:

 Bug fix in gistic preparing


Former-commit-id: e3384635b07c2c0414f2979affb8b6bea5976907 [formerly 1edcade4a53ad8297dd9c46a83fe097bd254b11d] [formerly 8c5449958ad2e1cd300daa033d57d1267e7c9d6d]
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Commit: 1a436333fc67cdeec15b4ce3da08d0c5b6dc9806
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-24 17:16:03 -0600
Commit message:

 Bug fix in gistic preparing


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Commit: dc25b49c3db4b02612d1a86ca9ae503b0b0abb1a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-21 11:50:10 -0600
Commit message:

 Reduce query size by adding experimental strategy as a URL filter


Former-commit-id: ddd63c9b2a68eb2eb308a6c7528cb6bfa0119a07
Former-commit-id: adee31b050f5014279c8f58ff2d2329f78a23677
Package: TCGAbiolinks
Commit: 721981916a6c0817c7b55f177cefb4266c62a351
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-21 11:50:10 -0600
Commit message:

 Reduce query size by adding experimental strategy as a URL filter


Former-commit-id: dc25b49c3db4b02612d1a86ca9ae503b0b0abb1a [formerly adee31b050f5014279c8f58ff2d2329f78a23677] [formerly ddd63c9b2a68eb2eb308a6c7528cb6bfa0119a07]
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Commit: 262a2c29ceef317526d90ef806cf67c26f980a9b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-21 11:50:10 -0600
Commit message:

 Reduce query size by adding experimental strategy as a URL filter


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Package: TCGAbiolinks
Commit: 88b2d9d7d020cbff1f411176bc0267529648c395
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 21:09:22 -0600
Commit message:

 Fix description


Former-commit-id: 57e7b0d0383ec4453878c578e4f621ae2f205abe
Former-commit-id: e9895f6c07443718461c26cf47e69017e71742a7

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