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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: missMethyl
Commit: b774345792261c57b843d7871fb0a6dd78674bc0
Author: Jovana Maksimovic <jovana.maksimovic@mcri.edu.au>
Date: 2018-09-25 11:02:31 +1000
Commit message:

 Bumped z version. Updated date.
 
Package: missMethyl
Commit: d300295c219993aca8e62bb532e7026bba4bba14
Author: Jovana Maksimovic <jovana.maksimovic@mcri.edu.au>
Date: 2018-09-25 11:01:41 +1000
Commit message:

 Added missing arguments to \usage statements. Removed missing \links from \item descriptions.
 
Package: missMethyl
Commit: b9a14987d43d018eaae4665bdd76ec9583c78ed8
Author: Jovana Maksimovic <jovana.maksimovic@mcri.edu.au>
Date: 2018-09-25 11:00:07 +1000
Commit message:

 Removed unnecessary "require" calls.
 
Package: gdsfmt
Commit: 3295673fbffd8b34f437a29fe075ce2c3662c2c8
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2018-09-24 16:17:51 -0700
Commit message:

 optimization in 2-bit array decoding
 
Package: prot2D
Commit: 5455c7c01b2a4743c9a086ea93617abfb4e87663
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2018-09-24 12:18:06 -0400
Commit message:

 Package deprecation
 
Package: GeneSelector
Commit: 415ae8e5607e22c1a7c760f567b6e75755b4eb49
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2018-09-24 12:17:08 -0400
Commit message:

 Package deprecation
 
Package: ampliQueso
Commit: a6321698de3e2629139080706b4493ba8e994e3a
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2018-09-24 12:15:07 -0400
Commit message:

 Package Deprecation
 
Package: pbcmc
Commit: 0302d00c9d310bedd55505c623e8ecc231c02931
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2018-09-24 12:11:50 -0400
Commit message:

 Package deprecation
 
Package: cytofkit
Commit: d13a480ee036cbff9b8913f99dfb666182e1b225
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2018-09-24 12:08:52 -0400
Commit message:

 Package deprecation
 
Package: paxtoolsr
Commit: e9707b24a4b2f709743fc337c2d2e68b28aa01bc
Author: cannin <cannin@gmail.com>
Date: 2018-09-20 05:34:14 -0400
Commit message:

 Fixed import issue
 
Package: paxtoolsr
Commit: f500f63dfd685e2542ed008b227cd177389b71f1
Author: cannin <cannin@gmail.com>
Date: 2018-09-20 05:03:03 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
 
Package: paxtoolsr
Commit: f507eba641653ab07f298e229ae1d78348c327b6
Author: cannin <cannin@gmail.com>
Date: 2018-09-20 04:51:31 -0400
Commit message:

 Updated .Rbuildignore
Replaced data.table with readr
Removed incomplete functions
Added examples
Added importFrom statements
Updated reading for PCV10; with an attempt to be backwards compatible
Updated getPcDatabasesNames for recent file name changes
Added additional headers to deal with PC API issues: XML vs JSON return
Switched to query parameter for PC API calls with httr rather than URL creation
Removed skip_on_bioc since now in testthat
Expanded pcFormats
Expanded checkInputFile with additional checks
Updated pathways.txt.gz example file
 
Package: paxtoolsr
Commit: 66cfd3829e75280303d855098c244582a1b299ea
Author: cannin <cannin@gmail.com>
Date: 2018-08-27 13:37:55 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	.Rbuildignore
#	.gitignore
#	DESCRIPTION
#	NAMESPACE
#	R/addAttributeList.R
#	R/checkInputFile.R
#	R/checkOutputFile.R
#	R/convertSifToSpia.R
#	R/convertSifnxIds.R
#	R/convertToDF.R
#	R/convertToDT.R
#	R/convertToPathwayList.R
#	R/downloadFile.R
#	R/downloadPc.R
#	R/downloadPc2.R
#	R/downloadSignedPC.R
#	R/extractIds.R
#	R/fetch.R
#	R/filterSif.R
#	R/fromPsimi.R
#	R/getCacheFiles.R
#	R/getErrorMessage.R
#	R/getNeighbors.R
#	R/getPc.R
#	R/getPcRequest.R
#	R/getPcUrl.R
#	R/getShortestPathSif.R
#	R/getSifInteractionCategories.R
#	R/graphPc.R
#	R/integrateBiopax.R
#	R/loadSifInIgraph.R
#	R/mapValues.R
#	R/mergeBiopax.R
#	R/paxtoolsr.R
#	R/pcDirections.R
#	R/pcFormats.R
#	R/pcGraphQueries.R
#	R/processPcRequest.R
#	R/readBiopax.R
#	R/readGmt.R
#	R/readSbgn.R
#	R/readSif.R
#	R/readSifnx.R
#	R/searchListOfVectors.R
#	R/searchPc.R
#	R/splitSifnxByPathway.R
#	R/summarize.R
#	R/summarizeSif.R
#	R/toGSEA.R
#	R/toLevel3.R
#	R/toSBGN.R
#	R/toSif.R
#	R/toSifnx.R
#	R/topPathways.R
#	R/traverse.R
#	R/validate.R
#	README.md
#	inst/extdata/REACT_12034-3.owl
#	inst/extdata/test_edgelist.txt
#	inst/extdata/test_gsea.gmt
#	inst/extdata/test_sbgn.xml
#	inst/extdata/test_sifnx.txt
#	inst/extdata/test_sifnx2.txt
#	inst/extdata/test_sifnx_250.txt
#	inst/extdata/test_sifnx_sm.txt
#	inst/java/paxtools-4.3.1.jar
#	inst/paxtoolsNotes.txt
#	java/README.md
#	man/addAttributeList.Rd
#	man/convertSifToSpia.Rd
#	man/convertSifnxIds.Rd
#	man/convertToDF.Rd
#	man/convertToDT.Rd
#	man/downloadFile.Rd
#	man/downloadPc2.Rd
#	man/downloadSignedPC.Rd
#	man/extractIds.Rd
#	man/filterSif.Rd
#	man/getCacheFiles.Rd
#	man/getErrorMessage.Rd
#	man/getPc.Rd
#	man/getPcUrl.Rd
#	man/getShortestPathSif.Rd
#	man/getSifInteractionCategories.Rd
#	man/loadSifInIgraph.Rd
#	man/mapValues.Rd
#	man/processPcRequest.Rd
#	man/readBiopax.Rd
#	man/readGmt.Rd
#	man/readSbgn.Rd
#	man/readSif.Rd
#	man/readSifnx.Rd
#	man/searchListOfVectors.Rd
#	man/skip_on_bioc.Rd
#	man/splitSifnxByPathway.Rd
#	man/summarizeSif.Rd
#	man/toGSEA.Rd
#	man/toSifnx.Rd
#	man/topPathways.Rd
#	paxtoolsr.Rproj
#	tests/testthat.R
#	tests/testthat/test_pathwayCommons.R
#	vignettes/using_paxtoolsr.Rmd
 
Package: paxtoolsr
Commit: 4d0b9d5e837260fa38bfd8f789cc783439024570
Author: cannin <cannin@gmail.com>
Date: 2018-08-09 21:27:54 -0400
Commit message:

 Merge branch 'master' of https://github.com/cannin/paxtoolsr
 
Package: paxtoolsr
Commit: 025b78d5433fd4deede353cbb25060830422978d
Author: cannin <cannin@gmail.com>
Date: 2018-07-23 16:02:55 -0400
Commit message:

 URL encode user inputs to traverse
 
Package: paxtoolsr
Commit: 742bbecebcf0171c1bef2337c242ee2d72e51fa5
Author: cannin <cannin@gmail.com>
Date: 2018-07-23 15:33:39 -0400
Commit message:

 Moved results creation for large files so that the code can find nodes
 
Package: paxtoolsr
Commit: 39c9a05effd99295c59e7e7d04b5141ea1abf504
Author: cannin <cannin@gmail.com>
Date: 2018-01-11 17:13:44 -0500
Commit message:

 Added sub-pathway names to readPcPathwaysInfo
Renamed pathways.txt.gz
Changed documentation to force version information in downloadPc2
 
Package: paxtoolsr
Commit: ef557494ba213fe9dd3a5f94d15f534730cc23b4
Author: cannin <cannin@gmail.com>
Date: 2018-01-11 13:52:27 -0500
Commit message:

 Added convertToDataFrameWithListOfVectors (opposite also included)
Removed default version in downloadPc2 (current no longer works)
Deleted idMapping since it was removed (also from vignette)
Added readSifnxSmall for small SIFNX
 
Package: paxtoolsr
Commit: 35594975e9b73e02fbc7574dea3a85291d21209a
Author: cannin <cannin@gmail.com>
Date: 2017-03-24 17:57:36 -0400
Commit message:

 toCytoscape added
 
Package: paxtoolsr
Commit: 194a6bfc205ae2588ad4c47579d54a1ded030fd8
Author: cannin <cannin@gmail.com>
Date: 2017-03-16 08:52:27 -0400
Commit message:

 Merge branch 'master' of https://github.com/cannin/paxtoolsr
 
Package: paxtoolsr
Commit: f036a557c99adb44c3e042e9931c1c01db04a999
Author: cannin <cannin@gmail.com>
Date: 2017-03-16 08:52:13 -0400
Commit message:

 Minor
 
Package: paxtoolsr
Commit: 62aab501b4a1168d5388f2839b6d7149391682bd
Author: cannin <cannin@gmail.com>
Date: 2017-02-22 11:22:03 -0500
Commit message:

 Added readCombinedSifnxFile
 
Package: paxtoolsr
Commit: f99d95cc2824359e252c1be486331756d9ccc241
Author: Augustin Luna <cannin@gmail.com>
Date: 2016-12-10 19:30:53 -0500
Commit message:

 Update .travis.yml 
Package: paxtoolsr
Commit: 01b24fe967cae605ffe02f2c69977b4b91f63262
Author: cannin <cannin@gmail.com>
Date: 2016-11-17 14:38:19 -0600
Commit message:

 Updated Travis CI
 
Package: paxtoolsr
Commit: 2f46dab6e0db25cbea60e2bec755468f702e4c33
Author: cannin <cannin@gmail.com>
Date: 2016-11-17 14:23:03 -0600
Commit message:

 Updated Travis CI
 
Package: paxtoolsr
Commit: 793911c4f6b0f91108e5b243f865d800b85f562b
Author: cannin <cannin@gmail.com>
Date: 2016-11-17 14:20:35 -0600
Commit message:

 Updated Travis CI
 
Package: paxtoolsr
Commit: e38e6851a8729de49945b403a207c55acbfc6237
Author: cannin <cannin@gmail.com>
Date: 2016-11-17 13:34:02 -0600
Commit message:

 Fixed bug in reading 1 entry GMT files
Minor documentation fixes
 
Package: paxtoolsr
Commit: 5597e45220fbec96261b6811aa08b0474ac14f71
Author: cannin <cannin@gmail.com>
Date: 2016-11-15 19:10:23 -0600
Commit message:

 Added additional commands
Added hack for downloadSignedPc since GitHub does not support LAST-MODIFIED
Added additional parameter to filterSif
 
Package: paxtoolsr
Commit: 29bca8da1946da65e688c81b18cb988ef3427de5
Author: cannin <cannin@gmail.com>
Date: 2016-11-10 08:41:13 -0500
Commit message:

 Added parameter to toSifnx
Fixed bugs that repeats pathway names in splitSifnxByPathway and loads unnecessary packages
Added function to split SIF into GMT
 
Package: paxtoolsr
Commit: 03dbc5d72860319d7dcd725c794c5304625f7906
Author: cannin <cannin@gmail.com>
Date: 2016-11-04 12:42:28 -0400
Commit message:

 Merge branch 'master' of https://github.com/cannin/paxtoolsr

* 'master' of https://github.com/cannin/paxtoolsr:
  Update README.md
  Update README.md
 
Package: paxtoolsr
Commit: 4ae3a16e1643a9e4a617dad011f399a4936a627a
Author: cannin <cannin@gmail.com>
Date: 2016-11-04 12:41:03 -0400
Commit message:

 Changed default behavor of filterSif ids to only include IDs asked for
 
Package: paxtoolsr
Commit: 8ffde067e7b2f96cad3559f0386de07ecd918ddc
Author: Augustin Luna <cannin@gmail.com>
Date: 2016-10-29 14:38:43 -0400
Commit message:

 Update README.md 
Package: paxtoolsr
Commit: 850c868d80aaf8b0229c8c410fcd69896682f73e
Author: Augustin Luna <cannin@gmail.com>
Date: 2016-10-29 14:36:20 -0400
Commit message:

 Update README.md 
Package: paxtoolsr
Commit: 30b4f9f9daae38293e4002d2f9dc52cd6c921589
Author: cannin <cannin@gmail.com>
Date: 2016-10-18 13:58:01 -0400
Commit message:

 Fixed bug in readPcPathwaysInfo()
 
Package: paxtoolsr
Commit: 31e9d54a3b19557a230d770ddc9387583f201594
Author: cannin <cannin@gmail.com>
Date: 2016-09-08 16:53:48 -0400
Commit message:

 Added argument passing to read* functions in getPc
Fixed bug with empty genesets in readGmt
Merge multiple pathway info tables into one
 
Package: paxtoolsr
Commit: 08d4ec5a08f10caa5c53f02b21af1141e4792fec
Author: cannin <cannin@gmail.com>
Date: 2016-09-02 11:07:45 -0400
Commit message:

 Updated documentation
Fixed variable name bug
 
Package: paxtoolsr
Commit: 516844be5894a02d9d2a1303b320169c1121f211
Author: cannin <cannin@gmail.com>
Date: 2016-09-02 10:38:44 -0400
Commit message:

 Added feature to pass additional parameters to read* functions
 
Package: paxtoolsr
Commit: 8ce06853077e71f0eca0d825304136728adbb2ce
Author: cannin <cannin@gmail.com>
Date: 2016-09-02 10:15:24 -0400
Commit message:

 Merge branch 'master' of https://github.com/cannin/paxtoolsr

* 'master' of https://github.com/cannin/paxtoolsr:
  Added getPcDatabaseNames Added more options to filterSif Updated SignedPC URL Added default option to toGSEA Updated how URLs are generated in topPathways

# Conflicts:
#	DESCRIPTION
#	R/filterSif.R
#	man/filterSif.Rd
 
Package: paxtoolsr
Commit: 23eb4c73c5fc77e2524e96de75c3ebd13e4b16d0
Author: cannin <cannin@gmail.com>
Date: 2016-08-26 12:44:59 -0700
Commit message:

 Added convertIds
Fixed issue with mediatorIds in filterSif
Added removePrefix and returnDetailed to readGmt
Added function to read PC pathway information
 
Package: paxtoolsr
Commit: 41e8656b77fd5923a0c47314c7402f44813a50fd
Author: cannin <cannin@gmail.com>
Date: 2016-08-26 12:44:59 -0700
Commit message:

 Added getPcDatabaseNames
Added more options to filterSif
Updated SignedPC URL
Added default option to toGSEA
Updated how URLs are generated in topPathways
 
Package: paxtoolsr
Commit: 141b7f7b04616bb70cd9eede3bfd4f9676e9feaf
Author: cannin <cannin@gmail.com>
Date: 2016-05-20 08:08:35 -0400
Commit message:

 Added tests
Added checks for file existence on read* functions
Added error checks and verbose flag to getShortestPathSif
 
Package: paxtoolsr
Commit: acf87479d10aa61b7e9a57fd4f179fddf14b16b7
Author: Augustin Luna <cannin@gmail.com>
Date: 2016-05-12 10:38:45 -0400
Commit message:

 Update README.md 
Package: paxtoolsr
Commit: 6b7cdf7338464dab44ca910abf400626a3ad7c1a
Author: Augustin Luna <cannin@gmail.com>
Date: 2016-05-12 10:38:02 -0400
Commit message:

 Update README.md 
Package: paxtoolsr
Commit: a45ebd229651b05613be8dd27d54d01dc4267fd9
Author: cannin <cannin@gmail.com>
Date: 2016-05-12 10:30:41 -0400
Commit message:

 Updated version and test
 
Package: paxtoolsr
Commit: 35dea0705bf1a6cd1253f7a44a9820904205b077
Author: Augustin Luna <cannin@gmail.com>
Date: 2016-05-12 09:58:06 -0400
Commit message:

 Update README.md 
Package: paxtoolsr
Commit: 33ece64e2b58c3020bb49e78297eeab30f6c0605
Author: cannin <cannin@gmail.com>
Date: 2016-05-09 17:33:13 -0400
Commit message:

 Moved tests to tests/testthat
Minor documentation changes
 
Package: paxtoolsr
Commit: f9d28b71a03b4f12a87bc415466e2a36b14042e3
Author: cannin <cannin@gmail.com>
Date: 2016-05-07 17:24:56 -0400
Commit message:

 Fixed bug to use make use of archives for all downloads
 
Package: paxtoolsr
Commit: a0ebd3c10a888d6700a9ba8121e0490307a0c9de
Author: cannin <cannin@gmail.com>
Date: 2016-04-26 17:01:45 -0400
Commit message:

 Updated documentation
 
Package: paxtoolsr
Commit: f1a59f5de82291baefc38b2716ac37cc36c8becf
Author: cannin <cannin@gmail.com>
Date: 2016-04-26 15:52:01 -0400
Commit message:

 Minor
 
Package: paxtoolsr
Commit: ae749f6dd97350373e6d6a9bee9295644851d8af
Author: cannin <cannin@gmail.com>
Date: 2016-04-21 14:11:03 -0400
Commit message:

 Fixed bug with filterSif edgelist
 
Package: paxtoolsr
Commit: e28292ba3344c672e18ae0212e61d57120693e68
Author: cannin <cannin@gmail.com>
Date: 2016-04-21 13:54:48 -0400
Commit message:

 Fixed issue in filterSif only looking in one direction for edgelist
 
Package: paxtoolsr
Commit: 2d76802f4b994b24ccbd62317bac49d52dcdb7fd
Author: cannin <cannin@gmail.com>
Date: 2016-04-20 13:51:52 -0400
Commit message:

 Added the ability to filter by edgelist
Added getShortestPathSif
Added parameter for getting directed igraph network
 
Package: paxtoolsr
Commit: 12043d8a0873e9a6ff6d6345f3f98b8a65542162
Author: cannin <cannin@gmail.com>
Date: 2016-03-29 11:57:44 -0400
Commit message:

 Fixed bug to add in MEDIATOR_IDS column in convertToDT
Fixed test
 
Package: paxtoolsr
Commit: 6ccebc119d2c18fdf6170117bdc334e9e643fd29
Author: cannin <cannin@gmail.com>
Date: 2016-03-29 11:21:00 -0400
Commit message:

 Fixed bug in graphPc call
 
Package: paxtoolsr
Commit: 50c918cbcf0ef6aeef404eb1a9a903fba2450e84
Author: cannin <cannin@gmail.com>
Date: 2016-03-29 10:58:59 -0400
Commit message:

 Expanded convertToDT
Added additional filtering mechanisms to filterSif
Expanded loadSifInIgraph
Added addAttributeList
Added getShortestPathSif
Added small sinful example
 
Package: paxtoolsr
Commit: 72b3d0cba9af7339209aa0d3999208526d58f27b
Author: cannin <cannin@gmail.com>
Date: 2016-03-06 16:39:26 -0500
Commit message:

 Changed DESCRIPTION
 
Package: paxtoolsr
Commit: 8f0931269d958cc72a7d4a56a02e84058e6a5cf8
Author: cannin <cannin@gmail.com>
Date: 2016-03-04 11:34:55 -0500
Commit message:

 Added README with location of paxtools Java sources
Added description of cache folder
 
Package: paxtoolsr
Commit: f708b78f43ef99f9d905cb41cc5e68479140a5d1
Author: Augustin Luna <cannin@gmail.com>
Date: 2016-02-29 14:07:35 -0500
Commit message:

 Update README.md 
Package: paxtoolsr
Commit: 80404326bfa9979b7c9dad7858cd26af549f90c2
Author: cannin <cannin@gmail.com>
Date: 2016-02-25 07:21:07 -0500
Commit message:

 Revert
 
Package: paxtoolsr
Commit: be4339e5890d4297874daf5ad7bcda407bbdacbe
Author: cannin <cannin@gmail.com>
Date: 2016-02-25 07:11:14 -0500
Commit message:

 Minor
 
Package: paxtoolsr
Commit: 973a7227e46777e127194bb5273b7cfa9baa45f1
Author: cannin <cannin@gmail.com>
Date: 2016-02-25 06:59:43 -0500
Commit message:

 Updated .travis.yml
 
Package: paxtoolsr
Commit: f8fb995ab71a952936763d889a85746c1b10627f
Author: cannin <cannin@gmail.com>
Date: 2016-02-25 06:50:49 -0500
Commit message:

 Changed .Rbuildignore
 
Package: paxtoolsr
Commit: 1bfe3a67732c7733d0a4aa096e092fa428ff8c4c
Author: cannin <cannin@gmail.com>
Date: 2016-02-24 21:14:04 -0500
Commit message:

 Added codecov badge
 
Package: paxtoolsr
Commit: 37c473f075d6d28a8a455a9f9375d3bb265acda6
Author: cannin <cannin@gmail.com>
Date: 2016-02-24 20:51:42 -0500
Commit message:

 Updated .travis.yml
 
Package: paxtoolsr
Commit: bd7a0b7a038985a01aeaaa3067bc61b931dded6c
Author: cannin <cannin@gmail.com>
Date: 2016-02-24 20:47:28 -0500
Commit message:

 Updated README
 
Package: paxtoolsr
Commit: a3caff78acfd00b4e20620168703884c7a04a1e8
Author: cannin <cannin@gmail.com>
Date: 2016-02-24 20:42:53 -0500
Commit message:

 Updated README
 
Package: paxtoolsr
Commit: 1593c9734f282dfc7e4fd186e731e3a7e3b6589b
Author: cannin <cannin@gmail.com>
Date: 2016-02-24 20:36:35 -0500
Commit message:

 Updated README
 
Package: paxtoolsr
Commit: 2ad4150b427fca8b822e0b678dd49be75be27611
Author: cannin <cannin@gmail.com>
Date: 2016-02-24 20:14:23 -0500
Commit message:

 Added .travis.yml
 
Package: paxtoolsr
Commit: a7a218de9be9564d21102e4ce1ee858eea5eec87
Author: cannin <cannin@gmail.com>
Date: 2016-02-24 14:30:19 -0500
Commit message:

 Updated code related to file downloads
 
Package: paxtoolsr
Commit: 414237ab7bd67d3177961f28cc9198ef4e959027
Author: cannin <cannin@gmail.com>
Date: 2016-01-26 15:44:25 -0500
Commit message:

 Changed CITATION
Added verbose flag to download functions
Fixed bug for downloading files outside of cache
Added function for downloading signed PC
 
Package: paxtoolsr
Commit: 89680b19793f90b18a1da406237d57c05324ff45
Author: cannin <cannin@gmail.com>
Date: 2015-12-09 08:30:43 -0500
Commit message:

 Removed old files
 
Package: paxtoolsr
Commit: ba28e0681af45509d19e1b4d1627c7674f435898
Author: cannin <cannin@gmail.com>
Date: 2015-12-09 07:38:55 -0500
Commit message:

 Merge branch 'devel'

* devel: (35 commits)
  Updated DESCRIPTION and documentation
  Hide warnings caused by http progress() Added support for PC2 archives Minor documentation changes
  Fixed bug in searchListOfVectors for queries with one element
  Added graphPc single gene example Fixed multiple datasets in graphPc Switched to using PC_URL system variable
  Changed .gitignore
  Re-did documentation
  Change R dependency Added documentation to skip_on_bioc()
  Comment out entire fromPsimi test
  Commented out fromPsimi test, testthat skip() does not work with Jenkins
  Updated to Paxtools 4.3.1 Added several tests Updated toSifnx and removed fromPsimi due to changes in Paxtools 4.3.1 Changed to* methods to make use of read* methods Switched back to using pathwaycommons.org URL Fixed bug in searchListOfVectors Added new package require checks for parallelized pathway splitter Vignette update
  Added updates to several functions
  Updated DESCRIPTION
  Added convertSifToSpia.R file Updated documentation
  Added helper functions, including: convertSifIds, convertToDT, covertToPathwayList, extractIds, filterSif, getCacheFiles, getSifInteractionCategories, loadSifInIgraph, mapValues, readGmt, searchListOfVectors. Separated several functions from the combined utils.R file Fixed errors in documentation for graphPc and pcGraphQueries
  Split functions
  Commented skipped tests
  Use file.info rather than file.size
  Minor
  Minor
  Minor
  ...

# Conflicts:
#	DESCRIPTION
#	R/pathwayCommons.R
#	R/paxtools.R
#	man/downloadPc.Rd
#	man/getPc.Rd
#	man/graphPc.Rd
#	man/idMapping.Rd
#	man/searchPc.Rd
#	man/topPathways.Rd
#	man/traverse.Rd
 
Package: paxtoolsr
Commit: 0978177882a3e25f5edee5b893f516cbf9147db4
Author: cannin <cannin@gmail.com>
Date: 2015-12-09 07:34:43 -0500
Commit message:

 Updated DESCRIPTION and documentation
 
Package: paxtoolsr
Commit: fd9700ac936cc7d4579ff5ba1feee16e70741555
Author: cannin <cannin@gmail.com>
Date: 2015-12-08 20:00:12 -0500
Commit message:

 Hide warnings caused by http progress()
Added support for PC2 archives
Minor documentation changes
 
Package: paxtoolsr
Commit: dd662d3e1b8952b32162b9df80ac12f28cfde87e
Author: cannin <cannin@gmail.com>
Date: 2015-11-25 14:58:42 -0500
Commit message:

 Fixed bug in searchListOfVectors for queries with one element
 
Package: paxtoolsr
Commit: d4244672076de1db302ce96b218723e2a9c8828a
Author: cannin <cannin@gmail.com>
Date: 2015-11-20 23:20:24 -0500
Commit message:

 Merge branch 'devel' of https://bitbucket.org/cbio_mskcc/paxtoolsr into devel
 
Package: paxtoolsr
Commit: 9e34c5b2fb26977f230daf1cf383b6ffe8c2be4e
Author: cannin <cannin@gmail.com>
Date: 2015-11-20 23:20:14 -0500
Commit message:

 Added graphPc single gene example
Fixed multiple datasets in graphPc
Switched to using PC_URL system variable
 
Package: paxtoolsr
Commit: ec0ea66cc13049b557e876db7e57e23f3fd19759
Author: cannin <cannin@gmail.com>
Date: 2015-10-29 11:21:47 -0400
Commit message:

 Changed .gitignore
 
Package: paxtoolsr
Commit: 0977a9cafc3d7401473f95a59e792e29e1eb721e
Author: cannin <cannin@gmail.com>
Date: 2015-10-01 14:17:16 -0400
Commit message:

 Re-did documentation
 
Package: paxtoolsr
Commit: f988d70821e5bb36a040707648283d38bd1e2a0f
Author: cannin <cannin@gmail.com>
Date: 2015-10-01 14:08:40 -0400
Commit message:

 Change R dependency
Added documentation to skip_on_bioc()
 
Package: paxtoolsr
Commit: 89c7e287b7b5028ffeda8bd05b57d4ed80a3acec
Author: cannin <cannin@gmail.com>
Date: 2015-10-01 12:46:48 -0400
Commit message:

 Comment out entire fromPsimi test
 
Package: paxtoolsr
Commit: c56c2698df772d7e10bb78b7dd50101f5595a880
Author: cannin <cannin@gmail.com>
Date: 2015-10-01 12:34:55 -0400
Commit message:

 Commented out fromPsimi test, testthat skip() does not work with Jenkins
 
Package: paxtoolsr
Commit: 5437e7b02d1e49ba482a4ea739f97f8752072af1
Author: cannin <cannin@gmail.com>
Date: 2015-10-01 12:10:46 -0400
Commit message:

 Updated to Paxtools 4.3.1
Added several tests
Updated toSifnx and removed fromPsimi due to changes in Paxtools 4.3.1
Changed to* methods to make use of read* methods
Switched back to using pathwaycommons.org URL
Fixed bug in searchListOfVectors
Added new package require checks for parallelized pathway splitter
Vignette update
 
Package: paxtoolsr
Commit: 18cd02a7b58867c110bd813d163f04654275baf2
Author: cannin <cannin@gmail.com>
Date: 2015-09-23 15:59:29 -0400
Commit message:

 Added updates to several functions
 
Package: paxtoolsr
Commit: 0b4f153bfd5b3a9b8fdd69295ec4e760f324e85b
Author: cannin <cannin@gmail.com>
Date: 2015-08-28 13:05:56 -0400
Commit message:

 Updated DESCRIPTION
 
Package: paxtoolsr
Commit: ec855aa3044061b1da6aab3e537ace66d6a9e9c3
Author: cannin <cannin@gmail.com>
Date: 2015-08-18 15:36:14 -0400
Commit message:

 Added convertSifToSpia.R file
Updated documentation
 
Package: paxtoolsr
Commit: 7e06f8c4a1d1f6594cea1c02b452d3fb37a49a58
Author: cannin <cannin@gmail.com>
Date: 2015-08-18 15:31:58 -0400
Commit message:

 Added helper functions, including: convertSifIds, convertToDT, covertToPathwayList, extractIds, filterSif, getCacheFiles, getSifInteractionCategories, loadSifInIgraph, mapValues, readGmt, searchListOfVectors.
Separated several functions from the combined utils.R file
Fixed errors in documentation for graphPc and pcGraphQueries
 
Package: paxtoolsr
Commit: 41d7f1f7e76dc09ba91be7687b8cbf10060ebb6b
Author: cannin <cannin@gmail.com>
Date: 2015-08-10 14:28:10 +0000
Commit message:

 README.md edited online with Bitbucket 
Package: paxtoolsr
Commit: f05c47abd8cdaf3c382a99ff64ecb3aff4736a6e
Author: cannin <cannin@gmail.com>
Date: 2015-08-10 14:26:38 +0000
Commit message:

 README.md edited online with Bitbucket 
Package: paxtoolsr
Commit: 5191f38081d42ea582f8cab5a72dd57ec18c554b
Author: cannin <cannin@gmail.com>
Date: 2015-08-10 13:06:15 +0000
Commit message:

 README.md edited online with Bitbucket 
Package: paxtoolsr
Commit: e9241e3678080c6d55a784cd4d9bbe683bb4ea2b
Author: cannin <cannin@gmail.com>
Date: 2015-08-10 13:05:29 +0000
Commit message:

 README.md edited online with Bitbucket 
Package: paxtoolsr
Commit: a8ab7f5e12f77a89684ed09f6f5583dcccefb02b
Author: cannin <cannin@gmail.com>
Date: 2015-08-10 10:55:10 +0000
Commit message:

 README.md edited online with Bitbucket 
Package: paxtoolsr
Commit: 41a346cef6b1ba29f13ddd119072fef08e16fb33
Author: cannin <cannin@gmail.com>
Date: 2015-08-10 10:54:33 +0000
Commit message:

 README.md edited online with Bitbucket 
Package: paxtoolsr
Commit: d16e61ed260fc8c6f69a825005801a6bab03d506
Author: cannin <cannin@gmail.com>
Date: 2015-06-01 21:59:33 -0400
Commit message:

 Split functions
 
Package: paxtoolsr
Commit: b6bd631c69bfdc9d82d17150d5ceabef4326a995
Author: cannin <cannin@gmail.com>
Date: 2015-05-21 17:50:21 -0400
Commit message:

 Commented skipped tests
 
Package: paxtoolsr
Commit: 02598db2b801a33fab8623551ed75268f856ba2c
Author: cannin <cannin@gmail.com>
Date: 2015-05-21 17:46:02 -0400
Commit message:

 Use file.info rather than file.size
 
Package: paxtoolsr
Commit: bea9b7defb06dd8d0eb5464f05692d29800d9064
Author: cannin <cannin@gmail.com>
Date: 2015-05-21 17:41:09 -0400
Commit message:

 Minor
 
Package: paxtoolsr
Commit: 4b2f6365895b136b9d97e16f6950ae29c8d86e59
Author: cannin <cannin@gmail.com>
Date: 2015-05-21 17:39:34 -0400
Commit message:

 Minor
 
Package: paxtoolsr
Commit: 9a61903b21794caa48dfddb48666a1d7365a04cd
Author: cannin <cannin@gmail.com>
Date: 2015-05-21 17:34:50 -0400
Commit message:

 Minor
 
Package: paxtoolsr
Commit: 7d86f6601827db17864f03597ae72cf20337ddcd
Author: cannin <cannin@gmail.com>
Date: 2015-05-21 17:29:56 -0400
Commit message:

 Minor
 
Package: paxtoolsr
Commit: 61ca81d614b2c7f8fa6c7e0437f6566cb89485ca
Author: cannin <cannin@gmail.com>
Date: 2015-05-21 17:26:54 -0400
Commit message:

 Minor
 
Package: paxtoolsr
Commit: 9531b6f8721ed2a261e683bf3e7585213027869a
Author: cannin <cannin@gmail.com>
Date: 2015-05-21 17:22:45 -0400
Commit message:

 Updated documentation
Attempt to make sure file.size() from base can be found
 
Package: paxtoolsr
Commit: 95a2f3ab354b92a1b71c8ca375eeebdd370886a9
Author: cannin <cannin@gmail.com>
Date: 2015-04-16 03:17:34 -0400
Commit message:

 Removed unused argument
 
Package: paxtoolsr
Commit: 98cf79aa3114a8b88a080875b2a25b9afbe0b887
Author: cannin <cannin@gmail.com>
Date: 2015-04-16 03:09:04 -0400
Commit message:

 Changed readSifnx
Added readSifnx tests
 
Package: paxtoolsr
Commit: c6e215fb0d9820b744067007dad900fb9015fa57
Author: cannin <cannin@gmail.com>
Date: 2015-04-15 23:33:04 -0400
Commit message:

 Added skip_on_bioc
Updated documentation
 
Package: paxtoolsr
Commit: ac18c58ffc278cf45c5267c13f3511e2a4dd2a96
Author: cannin <cannin@gmail.com>
Date: 2015-04-15 23:25:27 -0400
Commit message:

 Changed DESCRIPTION
 
Package: paxtoolsr
Commit: edcf526880de7ce8453f286b3490f42d179efd99
Author: cannin <cannin@gmail.com>
Date: 2015-04-15 22:48:46 -0400
Commit message:

 Added colClasses to fread
 
Package: paxtoolsr
Commit: 3ce591f7cfdc403ef8a11b4274737cf9f79b60c5
Author: cannin <cannin@gmail.com>
Date: 2015-04-15 22:45:08 -0400
Commit message:

 Added colClasses to fread
 
Package: paxtoolsr
Commit: 357c0228b7fff55077e950c38242d87e905bb04f
Author: cannin <cannin@gmail.com>
Date: 2015-04-15 22:26:48 -0400
Commit message:

 Major updates
 
Package: paxtoolsr
Commit: 5a468543540a61d1bd2c762aa7c2275985721717
Author: cannin <cannin@gmail.com>
Date: 2015-04-08 23:21:27 -0400
Commit message:

 Minor
 
Package: paxtoolsr
Commit: 55e3a8e0b74a9fcb01ccc73caf3349ebc5d3be89
Author: cannin <cannin@gmail.com>
Date: 2015-04-08 23:20:00 -0400
Commit message:

 Changed fetch example to use package data
 
Package: paxtoolsr
Commit: 5f22ae044508a3de8386c73f336d3a6784486b08
Author: cannin <cannin@gmail.com>
Date: 2015-04-08 23:09:30 -0400
Commit message:

 Added tests
Remove NAs from search data.frame
Added check to not overwrite cache map
Added split SIF by pathway function
 
Package: paxtoolsr
Commit: 620efc864e3cf76a0a0971a72ac90dedf7e297b9
Author: cannin <cannin@gmail.com>
Date: 2015-03-28 19:55:50 -0400
Commit message:

 Added second SIFNX
Added tests
 
Package: paxtoolsr
Commit: 71ddbad15e1ef23a4ff527645d8d888ec6b21205
Author: cannin <cannin@gmail.com>
Date: 2015-03-28 15:25:45 -0400
Commit message:

 Changes from paxtooolsr 1.1.11 Bioconductor changes
 
Package: paxtoolsr
Commit: 51570cc6e709cba32196718fdad8df1a3372403b
Author: cannin <cannin@gmail.com>
Date: 2015-03-28 12:46:17 -0400
Commit message:

 Updated documentation
 
Package: paxtoolsr
Commit: a35f36dcb378511ec38c613fb55f869ffb1069ab
Author: cannin <cannin@gmail.com>
Date: 2015-03-28 10:32:56 -0400
Commit message:

 Updated version
Added examples
Added test stubs
Refactored reading formatted responses
Added utils functions
 
Package: paxtoolsr
Commit: 746426167bbc0d3fc850fb64da2380515d17dd38
Author: cannin <cannin@gmail.com>
Date: 2015-03-27 11:03:29 -0400
Commit message:

 Merge branch 'master' into devel

* master:
  Updated NEWS
  Changed vignette to use quicker examples Changed DESCRIPTION
 
Package: paxtoolsr
Commit: d8f9cb82008bccb0d079df7efd1252ac60bc2075
Author: cannin <cannin@gmail.com>
Date: 2015-03-27 10:56:27 -0400
Commit message:

 Updated NEWS
 
Package: paxtoolsr
Commit: 8b82f805a58d4b3deb3b89ead4aaf1f1a708fbac
Author: cannin <cannin@gmail.com>
Date: 2015-03-27 08:20:09 -0400
Commit message:

 Changed vignette to use quicker examples
Changed DESCRIPTION
 
Package: paxtoolsr
Commit: 7455b17f6f3f4e6c8c4af97201feb6d9ca6f6cdc
Author: cannin <cannin@gmail.com>
Date: 2015-03-27 06:02:29 -0400
Commit message:

 Added new dependencies for reading faster
Added additional functions to simplify dealing with content
Added caching of downloads
 
Package: paxtoolsr
Commit: c6afadaedede6d990fc76a5d364f7bef52c800ab
Author: cannin <cannin@gmail.com>
Date: 2015-03-20 20:45:08 -0400
Commit message:

 Updated documentation
 
Package: paxtoolsr
Commit: 9b7d03aa903d3fdbfa00277558784c76920b1d0d
Author: cannin <cannin@gmail.com>
Date: 2015-03-10 12:25:12 -0400
Commit message:

 Updated NEWS
 
Package: paxtoolsr
Commit: 0aa88d14650144a5a08b12ff48b5629745e9f094
Author: cannin <cannin@gmail.com>
Date: 2015-03-10 12:13:30 -0400
Commit message:

 Removed PC dependent tests for paxtools functions
Added skip_on_bioc()
Updated vignette to use glycolysis pathway that can be converted to gene set
Added fill=TRUE to read.table commands in paxtools.R
 
Package: paxtoolsr
Commit: d9ee8439f0f0e27c6f9ab44b385ee65cd37de0e7
Author: cannin <cannin@gmail.com>
Date: 2015-02-10 14:37:27 -0500
Commit message:

 Changed DESCRIPTION, description section
 
Package: paxtoolsr
Commit: 5fc9de62b6ff201af1c24559a4fd457b57533c55
Author: cannin <cannin@gmail.com>
Date: 2015-02-10 14:24:56 -0500
Commit message:

 Change DESCRIPTION, Description entry
 
Package: paxtoolsr
Commit: 36ea4e0e83cad82abb37c9619bf1c4da07db6f8e
Author: cannin <cannin@gmail.com>
Date: 2015-02-10 13:33:07 -0500
Commit message:

 Changed DESCRIPTION Minor
 
Package: paxtoolsr
Commit: f3baeed20929b63ce40027c6c940a1a2bd2df195
Author: cannin <cannin@gmail.com>
Date: 2015-02-10 13:20:26 -0500
Commit message:

 Updated DESCRIPTION
 
Package: paxtoolsr
Commit: 3fd97a811ce352e67efca9851e98ab3ed472d6b3
Author: cannin <cannin@gmail.com>
Date: 2015-02-10 11:51:53 -0500
Commit message:

 Minor DESCRIPTION change
 
Package: paxtoolsr
Commit: b1ef1c4a0c32ef100fcf9946bf857e9706824ef8
Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-02-10 14:36:15 +0000
Commit message:

 Minor changes

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@99321 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: paxtoolsr
Commit: 3663eedf18d7451c4ca599349cb86ea759db39a0
Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-02-09 20:42:25 +0000
Commit message:

 README.md edited online with Bitbucket

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@99286 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: paxtoolsr
Commit: 8ff6cf1d8936b5d410426ca4aab2fe907fd2a798
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Commit message:

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Package: paxtoolsr
Commit: 8b71ba7aa2b8572856c079141114923b5d544a6f
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Commit message:

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Package: paxtoolsr
Commit: a5f8e374b8710508fb48bd0e31f94ef275199c6c
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Commit message:

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Commit: 1f3f9e49776c21231cf8524ac732fb36cf6655d7
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Commit: 440eae8f5945ed3aef6a7cfa8d886da7011f6f07
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Date: 2015-02-09 08:33:22 +0000
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Date: 2015-02-09 08:21:27 +0000
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 Merge branch 'work'

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Date: 2015-02-09 08:13:24 +0000
Commit message:

 Merge branch 'work'

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Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-02-09 06:56:38 +0000
Commit message:

 Change DESCRIPTION

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Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-02-09 05:33:17 +0000
Commit message:

 Changed NEWS

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Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-02-09 03:13:21 +0000
Commit message:

 Changed DESCRIPTION

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Package: paxtoolsr
Commit: c9dd462446dc561b868608dc426afddcb4604d5f
Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-02-09 02:48:22 +0000
Commit message:

 Added Rstudio files

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Package: paxtoolsr
Commit: 74a40ee006f24f5c8d8873da868d03f1a51096d6
Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-12-15 20:21:22 +0000
Commit message:

 Updated to paxtools 4.3
Added better Java error messages
Added the ability to switch PC versions
Updated to PC version 6

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Package: paxtoolsr
Commit: 0300b64ebe35594033f1f7c3e84d326ef102c54b
Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-11-03 19:33:44 +0000
Commit message:

 Fixed topPathways() bug 
Fixed fetch() example/test
Changed title

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Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-30 15:07:16 +0000
Commit message:

 Added CITATION file

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Package: paxtoolsr
Commit: 3cb7ce618db6ee08e141529706d7ca128216bc13
Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-28 17:00:59 +0000
Commit message:

 Use BiocStyle on vignette

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Package: paxtoolsr
Commit: 737d02441d65e5de225b313090ef0da4ade9c0b0
Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-26 18:27:40 +0000
Commit message:

 Increment version number

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Author: a.luna <a.luna@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-24 15:38:18 +0000
Commit message:

 Transitioned to Pathway Commons Version 5 (PC2 v5)
Changed downloadPc to download from PC2 v5
Changed code to validate Pathway Commons webservice requests 
Added table of contents to vignette 
Added description for traverse() in vignette
Changed R dependency to 3.1.1 to match Bioconductor 3
Added function to download a single file extended SIF, splitSifnx
Added the ability to download GMT in downloadPc
Added function to read GMT files 
Added tests for new functions

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@95980 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: paxtoolsr
Commit: 04ec114b11bd81b72dc361ff68d6b686847a5068
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-13 21:47:41 +0000
Commit message:

 Bumping versions after creating 3.0 release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@95443 bc3139a8-67e5-0310-9ffc-ced21a209358
 
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Commit: eeaa416c08d9ec6bb464612452d5281b30c949bc
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-13 21:38:33 +0000
Commit message:

 Bump package versions prior to creating the 3.0 branch.


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Commit: 4a23bd8f2c1d3f8e23549a305f585b1346daa066
Author: m.carlson <m.carlson@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-03 23:09:29 +0000
Commit message:

 Adds GenomicInteractions/ PSEA/ ALDEx2/ polyester/ MSGFplus/ derfinder/ derfinderPlot/ derfinderHelper/ regionReport/ FEM/ MSGFgui/ IdeoViz/ proBAMr/ ASGSCA/ PAA/ paxtoolsr/ flowcatchR/ to the repos.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@94975 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: recountWorkflow
Commit: 497af6fb8475a2c89bda13d5fd864f88987426d1
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-09-24 11:15:43 -0400
Commit message:

 v1.3.3 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 
Package: recount
Commit: aeae29972856a3332e0edfc100b1f763dd858552
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-09-24 11:11:46 -0400
Commit message:

 v1.7.6 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 
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Commit: 1bf87bcbebfb3a9487970304515cac4e9d606d8a
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-09-24 11:10:16 -0400
Commit message:

 v1.15.5 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 
Package: derfinderPlot
Commit: 23caf30c23273ae6fc313eaa201ddf361a9a3431
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-09-24 11:07:25 -0400
Commit message:

 v1.15.2 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 
Package: derfinderHelper
Commit: 605e767f315227a25cb2f2f9723bbef63ef69231
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-09-24 11:06:30 -0400
Commit message:

 v1.15.2 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 
Package: derfinder
Commit: 3f6e74eb459e4d375080cec5fc3b8f718652a400
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-09-24 11:05:34 -0400
Commit message:

 v1.15.3 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 
Package: IsoformSwitchAnalyzeR
Commit: 8820039615051f6cbc221092098206a2819725db
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2018-09-24 16:24:41 +0200
Commit message:

 Small update to fix 1.3.8 - see NEWS
 
Package: hmdbQuery
Commit: c088cbcd9c94fd1e623cfdbf88ad249e432ad45e
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-09-24 09:54:35 -0400
Commit message:

 improving robustness of HmdbEntry, which failed if underlying XML model is modified; now more predictions are in place, and a failover to returning a list is present
 
Package: hmdbQuery
Commit: c4fa33169f4ebe0f4c36eec24b477605c2525cc4
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-09-24 09:05:17 -0400
Commit message:

 testing version bump
 
Package: hmdbQuery
Commit: 0fe2f0192b29b632f560b97b5486d36d4edb0223
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-09-24 09:02:19 -0400
Commit message:

 setting github in sync with bioc
Merge remote-tracking branch 'upstream/master'
 
Package: hmdbQuery
Commit: 6a6a82d530ac5e52143b1467b566300eca686206
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-09-24 08:49:59 -0400
Commit message:

 Merge pull request #2 from vjcitn/newvincelocal

Newvincelocal 
Package: hmdbQuery
Commit: 1692c02718415f6125a0055e95638b8c8cbb68f3
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-09-24 08:54:18 -0400
Commit message:

 testing merge
 
Package: DAPAR
Commit: 4b407ef76fe2a423a8f6eb675c28a65b112e1137
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-09-24 10:39:10 +0200
Commit message:

 Update for aggregation
 
Package: GenomicScores
Commit: 8ad9e7f45120e6b6291d06baa83539eea5741df1
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-09-24 09:46:26 +0200
Commit message:

 Deprecated classes and methods in BioC 3.7 have now become defunct in BioC 3.8.
 
Package: M3C
Commit: 6f97f16d5be7d1c50d39abb57690fef670e6928f
Author: crj32 <chris.r.john86@gmail.com>
Date: 2018-09-24 08:36:26 +0100
Commit message:

 fixed code for when maxK is high
 
Package: ClassifyR
Commit: 79dc0e3df8ffab2d46810b598f292cc6d75e9d89
Author: Dario Strbenac <dstr7320@uni.sydney.edu.au>
Date: 2018-09-24 17:30:05 +1000
Commit message:

 - ClassifyResult object now store the trained classifiers. They may be reused in a future classification task using the function named previousTrained.
 
Package: GenomicScores
Commit: 613cfe15dbed3089a00c97c80c0fc2fa03da7015
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-09-24 09:12:57 +0200
Commit message:

 Updated citation of the package.
 
Package: Prostar
Commit: 8882dc6f381ef0f1a0a18f595de412bd4c2297a8
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-09-24 08:23:19 +0200
Commit message:

 New code for aggregation
 
Package: Prostar
Commit: 376c84cf803a5be7652e6e3c425cb52b3215349f
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-09-24 08:21:32 +0200
Commit message:

 test
 
Package: Prostar
Commit: 64821f0563b313055afe75fa261f5d9da55eedf6
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-09-24 08:13:38 +0200
Commit message:

 New code for aggregation
 
Package: Prostar
Commit: 378273ef80128b309508dfd0588705ea11265250
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-09-23 19:14:18 +0200
Commit message:

 Update Export file tools
 
Package: Prostar
Commit: a130aef5b7a7ab4ed60f8d85578eb7f8059e81b9
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-31 09:44:14 +0200
Commit message:

 modify usermanual
 
Package: Prostar
Commit: 0b77f184e3e8df97f3df0d9702dec2fd873e0ff0
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-31 09:06:07 +0200
Commit message:

 modify usermanual
 
Package: DAPAR
Commit: f0b1d1c5a020c994acf03ab619a3e48deb378e53
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-09-24 08:08:48 +0200
Commit message:

 New code for aggregation
 
Package: ChIC.data
Commit: 292eabea8662714d10159b5ee9a7be6e01d68a08
Author: carmencita <carmen.livi@ifom.eu>
Date: 2018-09-24 07:49:44 +0200
Commit message:

 adjusting R version and version bump
 
Package: scran
Commit: 4857c1f0d4a5aa7b49221cbc50afabd000b477f1
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-23 19:14:19 +0100
Commit message:

 Continue Win32 debugging efforts on cyclone optimizations.
 
Package: scran
Commit: aec1ef17da5684743b88deffc89df8e127e1bb9c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-23 19:07:46 +0100
Commit message:

 Bumped version, date; updated NEWS.
 
Package: scran
Commit: 471d67bc8473098a92afd8d05c81747c61476e14
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-23 12:52:07 +0100
Commit message:

 Merge branch 'master' of https://github.com/MarioniLab/scran
 
Package: scran
Commit: 0c0d47bb7ed5bc1191d377227ce27330888d637f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-23 12:39:21 +0100
Commit message:

 Updated docs and tests for new 'type=' in buildSNNGraph.
 
Package: scran
Commit: 256091c5bcd7133c5460f36e0aa1dbb6fe71a394
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-23 12:29:23 +0100
Commit message:

 Allow use of number of SNNs directly as the edge weight.
 
Package: scran
Commit: 41ddfebce880b82b31be7573f076fb7d9c9f0513
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-09-22 00:42:28 +0100
Commit message:

 Minor edits to combineMarkers Top explanation. 
Package: edgeR
Commit: e91af831ee5563d61354a406fe315424c4e53694
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2018-09-23 17:25:55 +1000
Commit message:

 * edgeR 3.23.4
- Bug fix to column name returned by decideTestsDGE().
- Improved error messages from DGEList().
- Note added to readBismark2DGE() help page.
- Edit to readBismark2DGE code (not user-visible).
 
Package: BatchQC
Commit: 934877bc5885c28c49e3c1d061f66760dd255a63
Author: mani2012 <mani2012@bu.edu>
Date: 2018-09-22 20:58:49 -0400
Commit message:

 Fixed date
 
Package: BatchQC
Commit: 307430d4a08efc1db77e49a4e95404e597c2e9a7
Author: mani2012 <mani2012@bu.edu>
Date: 2018-09-22 20:04:22 -0400
Commit message:

 Fixed PCA plot tooltips show incorrect values with ComBat and SVA
 
Package: DelayedArray
Commit: 093600ed2da1848747848be6c911094276ae5a85
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-22 12:05:28 -0700
Commit message:

 Add TENxMatrix to list of supported realization backends
 
Package: DelayedArray
Commit: e4e55d01c3da5dd960737996d57fec5aa8e8f8ba
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-22 11:26:29 -0700
Commit message:

 Reduce memory usage when realizing a sparse DelayedArray to disk

On-disk realization of a DelayedArray object that is reported to be sparse
(by is_sparse()) to a "sparsity-optimized" backend (i.e. to a backend with
a memory efficient write_sparse_block() like the TENxMatrix backend imple-
mented in the HDF5Array package) now preserves sparse representation of the
data all the way. More precisely, each block of data is now kept in a sparse
form during the 3 steps that it goes thru: read from seed, realize in
memory, and write to disk.
 
Package: logicFS
Commit: dec7ce3ab4ef09e95acb632e9bbdc69b53475198
Author: holgerschw <holger.schw@gmx.de>
Date: 2018-09-22 14:18:39 +0200
Commit message:

 Corrected DESCRIPTION
 
Package: logicFS
Commit: 59e81da26eb1edd7a0527260b4475d641f229722
Author: holgerschw <holger.schw@gmx.de>
Date: 2018-09-22 14:12:19 +0200
Commit message:

 Updated Description
 
Package: logicFS
Commit: 16d40f2099e1554b1ce31d725a9435a655804bd9
Author: holgerschw <holger.schw@gmx.de>
Date: 2018-09-22 13:48:26 +0200
Commit message:

 Just version update
 
Package: logicFS
Commit: 5b6b979d2e99bebb65ba5a7ab7bc205f930e5941
Author: holgerschw <holger.schw@gmx.de>
Date: 2018-09-18 11:01:03 +0200
Commit message:

 Added survivalFS functions
 
Package: logicFS
Commit: ad511df15853f5dc25175c3c06df727e6c23671d
Author: holgerschw <holger.schw@gmx.de>
Date: 2018-09-13 17:36:12 +0200
Commit message:

 Merge remote-tracking branch 'origin/master'

# Conflicts:
#	DESCRIPTION
 
Package: logicFS
Commit: 44b23e8c216333aa3326934e056d08c6eaefc0fc
Author: holgerschw <holgerschw@users.noreply.github.com>
Date: 2018-09-13 17:19:29 +0200
Commit message:

 Add files via upload 
Package: plyranges
Commit: cbca8917b77e4853df5849ca96417719ccb6fc45
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-09-21 16:32:18 -0700
Commit message:

 version bump; site rebuild
 
Package: DelayedArray
Commit: b8a6103fe81a5df04b57887d44bffcce33d9f43c
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-21 14:53:19 -0700
Commit message:

 Enhance DelayedArray dim() setter

In addition to allowing dropping "ineffective dimensions" (i.e.
dimensions equal to 1) from a DelayedArray object, the dim()
setter now allows adding "ineffective dimensions" to it.
 
Package: iSEE
Commit: 488c2557a9b1ac2a8379a101ea47adebd11771f9
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-21 21:59:15 +0100
Commit message:

 Merge pull request #236 from csoneson/testthat

Test coverage and minor updates. Version 1.1.8 
Package: iSEE
Commit: d0312ed48e2ca50598ec65ceec8042ccd90282a8
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-20 19:02:57 +0100
Commit message:

 attempt to clarify
 
Package: iSEE
Commit: 0946903281877bea07d3b147c3ee009715209d30
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-20 19:00:35 +0100
Commit message:

 typo
 
Package: iSEE
Commit: 8951e8b8b9caf571d185e889256c7b07ef8b0fed
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-20 18:53:05 +0100
Commit message:

 version bump and updated NEWS file
 
Package: iSEE
Commit: 58f666b09dc9512c1b5dc51b980b469032cb3df7
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-20 18:30:55 +0100
Commit message:

 test table links when certain settings are not initialised yet
 
Package: iSEE
Commit: bc97dc88c2e78a08874b413060c875df5c95de09
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-20 18:29:49 +0100
Commit message:

 test annotations in the absence of package
 
Package: iSEE
Commit: 90d39422d8eba9aef46dcde35dfaed08d4a6fb4b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-20 17:40:42 +0100
Commit message:

 .regenerate_unselected_plot independent of session
 
Package: iSEE
Commit: 5fde18fb35550918b3189e7ee10bb3137bbb7337
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2018-09-18 10:46:03 +0200
Commit message:

 fixed annotateEntrez with correct usage of the parameter
 
Package: iSEE
Commit: d763e96f32b9719a8ba29238a380a48f3ba354e4
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-17 12:59:53 +0100
Commit message:

 test if transmitted selection are detected
 
Package: iSEE
Commit: 8975cf73a1ccb87a4918822bbaa0f9d373cb96b3
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-17 12:47:25 +0100
Commit message:

 more tests: brush, lasso, custom, empty colData
 
Package: iSEE
Commit: 232e36853e85cd222183f07b8f4cad640c664be6
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-17 10:51:26 +0100
Commit message:

 complete testing of ECM; move ECM code to appropriate file; move generics definition to new AllGenerics
 
Package: iSEE
Commit: 45327999b7a8d397133a5210bb4ea55defe80083
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-17 10:49:00 +0100
Commit message:

 point out a test that requires a working internet connection
 
Package: iSEE
Commit: e3839777f6b1e8b35cf56c2e1079a9de548b1c4b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-17 08:53:33 +0100
Commit message:

 full coverage of codetrack
 
Package: iSEE
Commit: 00b54476ac5ec807cb18300f8dc061bda7c0ed0e
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-16 23:28:21 +0100
Commit message:

 cover a bit more of codetrack
 
Package: iSEE
Commit: 9fc3ebb08cec9f6fc306d3df901ec36183f20210
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-16 19:33:43 +0100
Commit message:

 fully cover plotting.R
 
Package: iSEE
Commit: 048779ecd014091f8166eeca69ed441a5482401e
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-16 19:33:32 +0100
Commit message:

 typo
 
Package: iSEE
Commit: 89e2ed7fe33bd5df04d53a5847cc70793cf34a27
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-16 16:36:20 +0100
Commit message:

 test heatmap code
 
Package: iSEE
Commit: 8099607d674e611799634af663226f8ad61c539b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-16 16:36:06 +0100
Commit message:

 add ::: to internal function calls in tests
 
Package: iSEE
Commit: 0036e4ca184744ffd2b2b9ddca0766b2a43a415c
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-15 19:43:31 +0100
Commit message:

 bold panel types and add custom panels
 
Package: iSEE
Commit: 51b7f2bcd3c75c73b16fe9f57d302726224617a5
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-09-15 19:03:27 +0100
Commit message:

 updated the README
 
Package: scran
Commit: f1321accdfb5632efec649d38993b46c955e038b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-21 19:18:15 +0100
Commit message:

 Merge branch 'master' of https://github.com/MarioniLab/scran
 
Package: scran
Commit: 26d3196aec80c3e2e0c42d67d5a7a671c73ddc49
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-21 19:18:06 +0100
Commit message:

 Clarified documentation for Top in combineMarkers.
 
Package: TCGAWorkflow
Commit: 93a30ee75be69cf7b53064e0b232f2d98e124a05
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-09-21 14:51:20 -0300
Commit message:

 fix
 
Package: TCGAWorkflow
Commit: e41027f1e8da0f745a46ff77358cb3ae69929def
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-09-21 14:51:09 -0300
Commit message:

 fix
 
Package: TCGAWorkflow
Commit: 33dc813cce7d4ec6e06552ce1b897a9f0ef78315
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-09-21 14:44:01 -0300
Commit message:

 fix merge
 
Package: TCGAWorkflow
Commit: 5378f607e98f6cba5044ba70a928437f56eb7d3c
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-09-20 18:21:01 -0300
Commit message:

 version bump
 
Package: TCGAWorkflow
Commit: 50130bfd4fdc6f93ac018205021ca3b36b5cd663
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-09-20 18:17:18 -0300
Commit message:

 fix clinical
 
Package: TCGAWorkflow
Commit: 0fe2a54438c34c6deaa6a17734dcd526bdd84ca6
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-09-20 18:16:38 -0300
Commit message:

 fix clinical
 
Package: TCGAWorkflow
Commit: 393fc64690eea58da2c1692392ea4d310a059396
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-04-30 07:24:16 -0300
Commit message:

 update fulviu affiliation
 
Package: TCGAWorkflow
Commit: c385b24835005b801ee9b0857109f2f1b7a1e250
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-03-30 21:11:11 -0300
Commit message:

 bug fix
 
Package: DelayedArray
Commit: f880fbd6b411affe32457bc5746022301bd74e78
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-21 10:17:17 -0700
Commit message:

 oops, misplaced parenthesis
 
Package: DelayedArray
Commit: 636a510767466060a89fcad926dff5264bed0e5e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-21 10:12:52 -0700
Commit message:

 Add comment
 
Package: DelayedArray
Commit: 3d643aa1acb2a994ab0115dd9b5ba0b8cfecc472
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-21 10:05:51 -0700
Commit message:

 Small code reorg
 
Package: DelayedArray
Commit: 1aac67c0761d06949d4f012cd8a9a9f14dcf0692
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-21 09:49:16 -0700
Commit message:

 Enhance "aperm" method for DelayedArray objects

In addition to allowing dropping some of the "ineffective dimensions"
(i.e. dimensions equal to 1) from a DelayedArray object, aperm() now
allows adding "ineffective dimensions" to it.
 
Package: ChIC.data
Commit: ad12289bed944ab0aa750fa48db90b5372b50b8f
Author: carmencita <carmen.livi@ifom.eu>
Date: 2018-09-21 18:03:58 +0200
Commit message:

 increment R and version bump
 
Package: ChIC.data
Commit: e2fd503a6a5878db32367cf71d832631b462ffc4
Author: carmencita <carmen.livi@ifom.eu>
Date: 2018-09-21 17:54:59 +0200
Commit message:

 version bump
 
Package: ChIC.data
Commit: 6c6b4d6afd7cc29e25bd87d2d0215e427efd8189
Author: carmencita <carmen.livi@ifom.eu>
Date: 2018-09-21 17:36:08 +0200
Commit message:

 updating RF-models with the models trained without red flagged smples
 
Package: ChIC.data
Commit: 6d3b96277c195c6379a2c9c41a198b20ca53339b
Author: carmencita <carmen.livi@ifom.eu>
Date: 2018-09-21 16:54:39 +0200
Commit message:

 updatin compendium with new dataset (without Red flagged samples)
 
Package: powerTCR
Commit: e99e1199bb438ef0b20eb9c7752d19b3214e88b3
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-21 10:39:53 -0400
Commit message:

 version bump
 
Package: powerTCR
Commit: 33507f4002d980c7dae9a630c74f2c921ace9511
Author: Unknown <hillary.koch01@gmail.com>
Date: 2018-09-20 13:38:13 -0400
Commit message:

 Merge branch 'master' into RELEASE_3_7

 
Package: powerTCR
Commit: 310baf8c0bc5d3a62a0192de68b2f880ce64cd8a
Author: Unknown <hillary.koch01@gmail.com>
Date: 2018-09-20 13:37:45 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master' into RELEASE_3_7

 
Package: powerTCR
Commit: 31d8cd9e5599fbf72d1b0620564747623351b89d
Author: Unknown <hillary.koch01@gmail.com>
Date: 2018-09-17 13:52:39 -0400
Commit message:

 Merge branch 'RELEASE_3_7'

 
Package: powerTCR
Commit: 6c37dff90e9f772de169e8c5bdae4c670340eefb
Author: Unknown <hillary.koch01@gmail.com>
Date: 2018-09-17 13:41:10 -0400
Commit message:

 Merge remote-tracking branch 'origin/master'

 
Package: powerTCR
Commit: 43eff5e5ed8acca3a33471d98331c9a85c04b3c2
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 13:22:36 -0400
Commit message:

 remove .Rproj.user from github
 
Package: powerTCR
Commit: 89f699ce96bd546962a07912639ef56bcbb53394
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:11:44 -0400
Commit message:

 Delete unnamed-chunk-5_af1f59610059ae069f8dc9e8fd46c527.RData 
Package: powerTCR
Commit: cba6415d8a78721e34048ea78523b7960d161121
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:11:38 -0400
Commit message:

 Delete unnamed-chunk-5_af1f59610059ae069f8dc9e8fd46c527.rdx 
Package: powerTCR
Commit: 16ba5849e67609a1d0faa7b874810af383f91bfc
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:11:33 -0400
Commit message:

 Delete unnamed-chunk-3_363953a712b6af1417d17cb350cad5b2.rdx 
Package: powerTCR
Commit: 242c85e771154ccf5e65656cf3cfb56997bc049c
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:11:28 -0400
Commit message:

 Delete unnamed-chunk-3_363953a712b6af1417d17cb350cad5b2.RData 
Package: powerTCR
Commit: 3331cf0d05da23f99274ff486d58621629da91f5
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:11:23 -0400
Commit message:

 Delete __packages 
Package: powerTCR
Commit: bb63389eae9021abf761532b5cfa78a7e411f235
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:11:16 -0400
Commit message:

 Delete unnamed-chunk-10_275b41d00fc7701e5ee962fce70dc95f.rdx 
Package: powerTCR
Commit: 42a950d85b41d0c624270255b3779e666a67ccbe
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:03:20 -0400
Commit message:

 Delete unnamed-chunk-3_363953a712b6af1417d17cb350cad5b2.rdb 
Package: powerTCR
Commit: 688703b86973cc6a72ff6f1251081e248be22eec
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:03:11 -0400
Commit message:

 Delete unnamed-chunk-10_275b41d00fc7701e5ee962fce70dc95f.rdb 
Package: powerTCR
Commit: cec37904671f6fb62ee1afd5e362f3e8e196b997
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:03:01 -0400
Commit message:

 Delete unnamed-chunk-5_af1f59610059ae069f8dc9e8fd46c527.rdb 
Package: powerTCR
Commit: 18e037acbe8a08f6cbaab5f36a292bdc1993e291
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:02:24 -0400
Commit message:

 Delete unnamed-chunk-10_275b41d00fc7701e5ee962fce70dc95f.RData 
Package: powerTCR
Commit: 71a8bd9259a7a5aeb40f63cc9ac14592a2c0b690
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 12:02:09 -0400
Commit message:

 Delete unnamed-chunk-10_bd47a91660517aedb0de4ef3de4c6062.rdb 
Package: powerTCR
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Date: 2018-09-17 11:59:15 -0400
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Package: powerTCR
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Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 11:59:01 -0400
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Author: Hillary Koch <hillary.koch01@gmail.com>
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Date: 2018-09-17 11:56:53 -0400
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Date: 2018-09-17 11:56:40 -0400
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Date: 2018-09-17 11:56:18 -0400
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Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 11:56:11 -0400
Commit message:

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Package: powerTCR
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Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 11:56:04 -0400
Commit message:

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Package: powerTCR
Commit: 91820806061cfd20d6b36880f92fc684082afb73
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 11:55:57 -0400
Commit message:

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Package: powerTCR
Commit: 4264696684316776271de42ffa4bfb2d7f32a581
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 11:55:49 -0400
Commit message:

 Delete powerTCR.tex 
Package: powerTCR
Commit: c4736692e53464b0ac6dda50298d87065db144fb
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-13 09:29:15 -0400
Commit message:

 update get_bootstraps man file to comply with build
 
Package: powerTCR
Commit: 819889bef122a8f72998a5d554e8e9ace432b574
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-13 09:10:01 -0400
Commit message:

 add parallelization imports
 
Package: powerTCR
Commit: 7b190d1a199d9cda2c6885639e70515528248e80
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-13 08:50:46 -0400
Commit message:

 remove superfluous files in vignettes/ to fix build error
 
Package: powerTCR
Commit: 1710f8ec601c2a0de9f81880dc62eb30089bf647
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-10 13:32:57 -0400
Commit message:

 remove vignette cache
 
Package: powerTCR
Commit: e8577c50a4da0b834ef3a998a06abe7370ebe8fa
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-10 13:32:06 -0400
Commit message:

 remove cache from vignette
 
Package: powerTCR
Commit: 084bf6665b42f28e60d5ea39c76fea5dda20839f
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-09 12:57:37 -0400
Commit message:

 version bump
 
Package: powerTCR
Commit: 6448a5ae64e9e55ee75a16e0a0b0040fd40f3dde
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-09 12:56:49 -0400
Commit message:

 version bump
 
Package: powerTCR
Commit: e04588ac315f15a8fc389471fa18c734f296fedc
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-09 12:55:09 -0400
Commit message:

 version bump
 
Package: powerTCR
Commit: 20e1769df25747f1b28f76a2e989fbe7879a7ab4
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-09 12:53:51 -0400
Commit message:

 version bump
 
Package: powerTCR
Commit: 8ce1b7e6de850eacb2d1b7c748ab2b86c5930ae7
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-09 12:53:19 -0400
Commit message:

 version bump
 
Package: powerTCR
Commit: dfec27bc6446ef951cc07604289aa60055f32521
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-09 12:50:41 -0400
Commit message:

 update remotes
 
Package: powerTCR
Commit: 5f11900a9bc20e45c5446d5459a8ce9b27a17524
Author: Unknown <hillary.koch01@gmail.com>
Date: 2018-09-07 20:49:28 -0400
Commit message:

 Merge branch 'master' into RELEASE_3_7

 
Package: ChIPQC
Commit: 2737f7f27c488a42ee525e3ba8cb338db6d15f5b
Author: Thomas Carroll <tc.infomatics@gmail.com>
Date: 2018-09-21 10:38:29 -0400
Commit message:

 fix for unlisting
 
Package: maftools
Commit: 072bdfb76325fadc767b34a917eb322c2c33ab09
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2018-09-21 16:27:22 +0200
Commit message:

 Merge branch 'master' of https://github.com/PoisonAlien/maftools
 
Package: maftools
Commit: 1683b2e8ef4996a015d910255a1ff3079b90792c
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2018-09-21 16:26:11 +0200
Commit message:

 oncogenic pathways
 
Package: maftools
Commit: 48ea6d1119520e38cabaf80ac6dfe430d4101190
Author: Anand Mayakonda <anandmt3@gmail.com>
Date: 2018-09-21 09:57:13 +0200
Commit message:

 Update LICENSE 
Package: FELLA
Commit: 614a5e648cd6c7e89a1dd5917c7a6b898eb88511
Author: Sergi Picart <elpicart@gmail.com>
Date: 2018-09-18 17:02:18 +0200
Commit message:

 Added zebrafish
 
Package: FELLA
Commit: e565a91d753a7631628972307a9d0cf0de5bc28c
Author: SergiPicart <elpicart@gmail.com>
Date: 2018-09-18 09:22:35 +0200
Commit message:

 Added vignette on Mus musculus
 
Package: multiHiCcompare
Commit: e5e33dfd85bddf17278ef2559e33671119172867
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2018-09-21 09:00:33 -0400
Commit message:

 update denependency
 
Package: MSnbase
Commit: b99f4736033809b1dc06d5262787e55c9f05bd5a
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 14:34:57 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/MSnbase into devel
 
Package: MSnbase
Commit: 5a736e1e68a6936b87e21e9b28e9574e172b22c9
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 14:34:51 +0200
Commit message:

 remove docs
 
Package: MSnbase
Commit: 45247cd9841d836b93796e6d129103e30ec7cc2b
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 14:32:28 +0200
Commit message:

 update news with url
 
Package: MSnbase
Commit: 7b9eb89bff42d61fba9cda9aa4d0dea1f5af58ee
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-09-21 13:52:39 +0200
Commit message:

 Fix unit tests (issue #360)
 
Package: MSnbase
Commit: 7478f8b6873f31f7ed05340341a7195174616f19
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 09:35:50 +0200
Commit message:

 new gh devel version
 
Package: logicFS
Commit: e06ba008ea297fb46574486bb54a93ddb69012bd
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-09-21 06:47:37 -0400
Commit message:

 version bump on maintainer request
 
Package: karyoploteR
Commit: 2631dc1f53c35812ac99c2d5f874e182929e0670
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-09-21 12:28:12 +0200
Commit message:

 Fixed a bug with zoom with extra seqlevels

 
Package: DEsingle
Commit: 8b741e5479c35ef54b14ae005d5fe18487f415ec
Author: miaozhun <mz8@foxmail.com>
Date: 2018-09-21 18:01:47 +0800
Commit message:

 Update README.md 
Package: DEsingle
Commit: cde9564782e9effe886329899d0307c501be3176
Author: miaozhun <mz8@foxmail.com>
Date: 2018-09-21 17:53:15 +0800
Commit message:

 Update DEsingle.R 
Package: DEsingle
Commit: 8b9097d0c5822597e318a5d6a70724cc526d9fa0
Author: miaozhun <mz8@foxmail.com>
Date: 2018-09-21 17:38:14 +0800
Commit message:

 Update DESCRIPTION 
Package: DEsingle
Commit: 1493c2934b6f59864f26b1e6fccf46a0b7c3ed58
Author: miaozhun <mz8@foxmail.com>
Date: 2018-09-21 17:36:59 +0800
Commit message:

 Update NEWS 
Package: DEsingle
Commit: 8b4a15dd794a659bb67a7d00d10a76818d043218
Author: miaozhun <mz8@foxmail.com>
Date: 2018-09-21 17:35:04 +0800
Commit message:

 Update DEtype.R 
Package: DEsingle
Commit: 68eccdfb5deb2c00e11477e13f63d7f79be54f8d
Author: miaozhun <mz8@foxmail.com>
Date: 2018-09-21 12:13:49 +0800
Commit message:

 Update DEsingle.R 
Package: scran
Commit: 65cc18e51f9dfcb96998cae28dfca3f8dc641049
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-21 09:40:38 +0100
Commit message:

 Bumped version number, date.
 
Package: scran
Commit: b493fce43ff305a5e41336841532d28a2dc6dfb7
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-21 09:22:17 +0100
Commit message:

 Clarified documentation for design= in pairwiseTTests.
 
Package: scran
Commit: 73522634954facd0c1a1b53fba273e1c60ec5cb4
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-21 09:19:05 +0100
Commit message:

 Reverted cyclone C++ code back to last working version.
 
Package: ChIC
Commit: 46fa20850778a4de47785398ca33249609653892
Author: carmencita <carmen.livi@ifom.eu>
Date: 2018-09-21 10:38:26 +0200
Commit message:

 verion bump
 
Package: ChIC
Commit: dc21d71b9ecf41d0fe84cb58d00b3172e5458bca
Author: carmencita <carmen.livi@ifom.eu>
Date: 2018-09-21 10:37:20 +0200
Commit message:

 updating vignette
 
Package: MSnbase
Commit: 4b63f520c80d698e620e286453f651455511b1ed
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 09:35:13 +0200
Commit message:

 no docs on bioc
 
Package: MSnbase
Commit: 23a56e4d0d2c91f2d5b00fdd57f4d4cf163ded52
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 09:33:36 +0200
Commit message:

 update docs
 
Package: MSnbase
Commit: ad0eeb82f9ee3b00dffb3dcbc4b4f1a9e425380e
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 09:17:44 +0200
Commit message:

 update docs
 
Package: MSnbase
Commit: 957c9d868559d0f8d9d241ed92c57771e1ddcaca
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 09:02:09 +0200
Commit message:

 merge master
 
Package: MSnbase
Commit: 1c2cfc74989db89db90d7833c67e670313b4d2a1
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-21 08:46:48 +0200
Commit message:

 update news
 
Package: MSnbase
Commit: 6c7bdb7ea8e65b87fd12ebd2d00ebedf90e9a3d6
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-09-20 16:04:58 +0200
Commit message:

 Fix wrong MS OBO terms for smoothing and baseline correction

- Fix wrong MS OBO CV terms for data smoothing (MS:1000592) and baseline
  correction (MS:1000593).
 
Package: MSnbase
Commit: f56c62d4d61d9b1a84aa0b1132f64a5b8d9b8b51
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 23:54:05 +0200
Commit message:

 update site with latest version
 
Package: plyranges
Commit: 207364543a48ffe78366e97d067ae8e9e8699147
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-09-20 18:13:15 -0700
Commit message:

 better name
 
Package: plyranges
Commit: 8c4b9d327bdf5da8b1c04b67b4bfa39043fbdc6a
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-09-20 18:01:19 -0700
Commit message:

 missed a few
 
Package: plyranges
Commit: 66dc5bcf6ce9d750dc201c4373288990f3723477
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-09-20 17:47:41 -0700
Commit message:

 updates rlang exports; closes #50
 
Package: plyranges
Commit: b17964871c50a90e4059f75000c3950b2aae4d00
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-09-20 15:54:38 -0700
Commit message:

 vectorise reduce --- should speed up base case
 
Package: plyranges
Commit: f99dac64644577ce72e867c14c38a144b8c7aabd
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-09-20 15:54:17 -0700
Commit message:

 new `n_distinct()` function
 
Package: plyranges
Commit: b56838731bbfafe55f3e7df57fb5bdd9f5866fe8
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-07 14:08:34 -0700
Commit message:

 update stretch per comments in #49
 
Package: plyranges
Commit: bced4ec3da3138b94e17110e322ec658273f96da
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-06 16:17:25 -0700
Commit message:

 rename
 
Package: plyranges
Commit: 15d883f78f8dc40b385a5f9a45b61ece7e13f7f9
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-06 16:12:59 -0700
Commit message:

 rename
 
Package: plyranges
Commit: 65d5f2214ce36ba7c19872b6dab4bdc5d2ecc663
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-06 16:12:22 -0700
Commit message:

 bring back bedtools tutorial
 
Package: plyranges
Commit: b5af20ba051705eb817e4fd954c4231b1dfdb613
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-03 14:59:12 -0700
Commit message:

 ungroup signature fix
 
Package: plyranges
Commit: 3f6cfa18d1a8f5c331cda2542a5de6aa906da1e8
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-03 13:45:49 -0700
Commit message:

 groups/group_vars/ungroup per notes in #32
 
Package: plyranges
Commit: 7af1f1905ceffa38960a6ff0c91941df70127291
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-02 11:30:07 -0700
Commit message:

 update docs
 
Package: plyranges
Commit: 071fa4c8d3b27ee8a64ae2017969dabaef1d9f76
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-02 11:14:16 -0700
Commit message:

 build machine wants stuff
 
Package: plyranges
Commit: fe213b1a2200869a86db467f25fe80546722bc59
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-01 17:03:27 -0700
Commit message:

 update appveyor
 
Package: plyranges
Commit: e02b1c307b4b7d4eedb13bb58fdb1c75ec403ce6
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-01 17:02:55 -0700
Commit message:

 update news
 
Package: plyranges
Commit: 4fbb2862b04fe72906ad1ec6985e8c636db4c5f6
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-01 17:01:58 -0700
Commit message:

 symlink NEWS.md for pkgdown
 
Package: plyranges
Commit: 4bbf67951c44df3ce7d169debcb6470ed8356552
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-01 16:43:33 -0700
Commit message:

 Merge branch 'master' of https://github.com/sa-lee/plyranges
 
Package: plyranges
Commit: ca97653120698859c18de27101a30a88e9d8345c
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2018-08-01 16:43:19 -0700
Commit message:

 fixes #42
 
Package: Rsubread
Commit: a2dfbb2e3b6d0e4bd10777f4de355292bf8fddb9
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-21 11:19:55 +1000
Commit message:

 Change the warning message in subread, subjunc and featureCounts() when the annotation file has format issues.
 
Package: Rsubread
Commit: 254cb6dabcb84b703ea1026eb7ec406794bc77f4
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-21 10:29:09 +1000
Commit message:

 Another warning removed
 
Package: Rsubread
Commit: ed6e7c869ccc199e84ef16699a1c7f2bc0ed936b
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-21 10:26:35 +1000
Commit message:

 Removed many warning messages from gcc 8.1
 
Package: Rsubread
Commit: 31060464e488868dc9e4134ddefa0b4bab651ffd
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-21 10:21:46 +1000
Commit message:

 Changed buffer sizes to remove warnings
 
Package: Rsubread
Commit: eca1cb60c2281ee626f7f9bb6bb8d077dfd9108e
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-21 10:18:30 +1000
Commit message:

 Changed data type in sprintf to remove warnings
 
Package: Rsubread
Commit: 35972603d76ed669fc6a0b1ad8231d85a583ea36
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-21 10:15:14 +1000
Commit message:

 Changed the scalling factor in index-builder to better suite the new index structure
 
Package: runibic
Commit: 13995bb3fa0a168bf70f32872a28fa89b9db3ba7
Author: athril <patryk.orzechowski@gmail.com>
Date: 2018-09-20 16:57:27 -0400
Commit message:

 Updating dev version number
 
Package: runibic
Commit: 9fb6daa1e14a579ddf060aad6487b28576d71669
Author: athril <patryk.orzechowski@gmail.com>
Date: 2018-09-20 16:46:12 -0400
Commit message:

 Updating CITATION
 
Package: runibic
Commit: 924ecc7c22e3792e2e724babe09e8b1b5bf84854
Author: Artur Pańszczyk <a.panszczyk@cad2cad.com>
Date: 2018-05-24 22:42:00 +0200
Commit message:

 Fix for default value of useLegacy parameter
 
Package: TENxBrainData
Commit: abda92514b3d29792ab1636b347ed31479784f26
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-09-20 13:07:46 -0400
Commit message:

 update metadata.csv
 
Package: TENxBrainData
Commit: a81cfea537ed955ae0cf0ccc4eb28b0cb6f65f58
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-09-19 19:35:51 -0400
Commit message:

 Merge branch 'with_20k'

- Thanks to Aaron Lun
- closes #5
 
Package: TENxBrainData
Commit: b178185dca669dbf1c975b9ffad1b4cb4caee545
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-09-19 19:33:49 -0400
Commit message:

 minor clean-up

- whitespace
- use more precise terminology to describe HDF5 & dense matrix
 
Package: TENxBrainData
Commit: 7bf47f98b52769374f9e8e8494bf0596c83d6948
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-08 13:46:48 +0100
Commit message:

 Bumped version number, date, rebuilt NAMESPACE.
 
Package: TENxBrainData
Commit: f237b2a1d5beaad52c155cf0a36e2f444d6e164b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-08 13:45:48 +0100
Commit message:

 Updated docs to describe TENxBrainData20k.
 
Package: TENxBrainData
Commit: 2c436e1553cd3d20e1a3c193a7a91ed8620afc4e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-08 13:45:14 +0100
Commit message:

 Added TENxBrainData20k with generalized SCE creation code.
Roxygenated imports/exports.
 
Package: TENxBrainData
Commit: 5bb586736b001496a96f498bb3f58c80eba933bd
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-08 13:35:24 +0100
Commit message:

 Updated metadata maker to include 20k subset.
 
Package: TENxBrainData
Commit: 6c82b6dd8529446b99b150cfebcd1c4947d7f312
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-08 12:29:19 +0100
Commit message:

 Added make-data code for 20K subset.
Updated make-data.R, avoid use of TENxGenomics class.
 
Package: trackViewer
Commit: eb7dab9a558f29dc111102caa6a43bb35d9a37a3
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2018-09-20 16:20:07 -0400
Commit message:

 update the version number.
 
Package: trackViewer
Commit: f0472366b088ea66fc2fa7d0474ec2eaee52d4c0
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2018-09-20 15:44:51 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/trackViewer
 
Package: trackViewer
Commit: f8711e86f9c345987c8b070b30c952d75c8b8c4e
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2018-09-20 15:43:50 -0400
Commit message:

 fix a issue of circle type in lollipop plot (pdf is different from png version)
 
Package: sesameData
Commit: 61cc61212d66cd0b32d7d19dc65d87a899d62f1c
Author: zwdzwd <zhouwanding@gmail.com>
Date: 2018-09-20 14:52:55 -0400
Commit message:

 version bump 0.99.5
 
Package: multiHiCcompare
Commit: 5d346ff5ea61d18add57bdba9c6a25dc62add102
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2018-09-20 14:39:22 -0400
Commit message:

 edit ignore
 
Package: multiHiCcompare
Commit: 97c92d47a24b5e193e88357819cbb9e9097e2db9
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2018-09-20 12:59:11 -0400
Commit message:

 update dependencies
 
Package: ELMER
Commit: fbf589501eb035138d28d69640041547f54c38a4
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-09-20 15:39:46 -0300
Commit message:

 fix heatmap plot
 
Package: ELMER
Commit: 207f80398996bef2a593e67b9e7c12f3ae10a768
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-20 11:34:34 -0700
Commit message:

 Merge branch 'master' of https://github.com/tiagochst/ELMER
 
Package: ELMER
Commit: 17b72e79b42ad19ead302bbab17272575af352e2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-09-20 11:34:26 -0700
Commit message:

 Fixing the cluster within groups for heatmap
 
Package: BioCor
Commit: 6ef78ffe4dd866844a2d29a967d12545d47531d2
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-20 19:44:55 +0200
Commit message:

 Add a bullet to the news
 
Package: BioCor
Commit: 4a7cb4aa21434395663c59aa53a538e3158c5fee
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 16:57:34 +0200
Commit message:

 Update NEWS
 
Package: BioCor
Commit: 8f9aa6ca4b93b1d182e3e064742838234e0e9256
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 16:52:18 +0200
Commit message:

 Simplify the combineScores* functions
 
Package: BioCor
Commit: 826316c0eaf426bb3cad9a93c860d4fba516bfa9
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 16:15:55 +0200
Commit message:

 Move from NEWS to NEWS.md
 
Package: BioCor
Commit: 633ec0168ce7175edbed9bdfdd2c3411989947ba
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 16:10:09 +0200
Commit message:

 Increment version number 
Package: BioCor
Commit: 288fd3de52c633261c5b52daefeb734b2a572582
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 16:10:00 +0200
Commit message:

 Reduce complexity
 
Package: BioCor
Commit: 23a972eab5c9a79efbc9311abd767200e2166239
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 16:09:34 +0200
Commit message:

 Improve wording
 
Package: BioCor
Commit: 6fb13576e81c5aa7767a7caf41952fc2fd589bc5
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 16:07:55 +0200
Commit message:

 Improve efficiency of code in vignettes
 
Package: BioCor
Commit: 78dd17c75a41a4285b197d80fbf22dbcacbeda36
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 16:07:21 +0200
Commit message:

 Improve the documentation
 
Package: BioCor
Commit: e65bb479aaa7c219ed6c3225aba52d2643541cf8
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 13:41:14 +0200
Commit message:

 First the development badges then the Bioconductor badges
 
Package: BioCor
Commit: 0e991f2f7dfb31483bc3809305822c669d757b63
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 13:37:49 +0200
Commit message:

 Add a section about GeneOverlap
 
Package: BioCor
Commit: dbead3d8f9fe491fd50d948680a3737f648d3059
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 13:15:17 +0200
Commit message:

 Update notifications of appveyor
 
Package: BioCor
Commit: 3ca62e12f2d570f454dcd8a21d2bcf1800721abd
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 13:09:32 +0200
Commit message:

 Update README installation names

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

# Conflicts:
#	DESCRIPTION
#	README.md
 
Package: BioCor
Commit: 8590582eaad75521ab8a22f84e3dfa5e1cbc1205
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 13:01:35 +0200
Commit message:

 Increment version number 
Package: BioCor
Commit: c3014f8ba2a4e39ce9b7d4c750b67f9856bfee94
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 13:01:20 +0200
Commit message:

 Expose my .Rprofile
 
Package: BioCor
Commit: 330dfae2afc2e8e6252003088afe85c8f23b35dd
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 13:00:52 +0200
Commit message:

 Update README with an example
 
Package: BioCor
Commit: 1d5dbcd667d573449769ccbd03a4a4c52eca7d8c
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 12:32:23 +0200
Commit message:

 Normalize the description
 
Package: BioCor
Commit: 8cb9481a8fd49d9c3c645566ade2cfa3dd976114
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 12:26:56 +0200
Commit message:

 Use covrpage for reporting tests
 
Package: BioCor
Commit: f159b1b79053994fc202c7edcd8803bcdebe9735
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 12:26:32 +0200
Commit message:

 Correct spelling mistakes
 
Package: BioCor
Commit: 9b02e4f7550b9a90c538b5d30cd053708026fb40
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 12:25:55 +0200
Commit message:

 Check spelling
 
Package: BioCor
Commit: b1d3df8caf299e949e4f5b34209c431b2130d08e
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 12:25:28 +0200
Commit message:

 Appveyor only on changes
 
Package: BioCor
Commit: 47a0875657b395dfbb2736fa232b5a8c1877d09c
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-09-15 12:25:11 +0200
Commit message:

 Update documentation
 
Package: BioCor
Commit: bb99291b739dc34667163e1f13bdff3fd5a5365c
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-07-16 22:44:41 +0200
Commit message:

 Update also the README for BiocManager
 
Package: BioCor
Commit: 680c33426485361d3e027014fc2416de70855a37
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2018-06-23 09:38:03 +0200
Commit message:

 Merge branch 'master' of github.com:llrs/BioCor
 
Package: BioCor
Commit: 4e34eed9ff45151e7945084408f9e6ad1438b1c9
Author: Lluís <llrs@users.noreply.github.com>
Date: 2018-05-02 17:41:30 +0200
Commit message:

 Remove Maintainer and Author role 
Package: KEGGREST
Commit: 5d4e360d302b87c60c685fde6510fb474e79681f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2018-09-20 13:24:26 -0400
Commit message:

 Update test

  - output column removed
 
Package: maftools
Commit: f6c17e14b64803e1db6fb95c5a0363f32f9de5b5
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2018-09-20 18:40:41 +0200
Commit message:

 version-bump
 
Package: maftools
Commit: 9c563f24be2d6efc27469bf3c0ca87761bac32c4
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2018-09-20 18:39:47 +0200
Commit message:

 drug-gene interactions
 
Package: maftools
Commit: 2bc2512ca24195cec846ca6c60481acbabbeb2b4
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2018-09-10 17:03:02 +0200
Commit message:

 address #186
 
Package: RGMQL
Commit: b4c0357f8972e3556b26a2518463da38857f6c74
Author: Simone <simone@Simones-Mac-Pro.local>
Date: 2018-09-20 17:56:54 +0200
Commit message:

 minor fix
 
Package: Pi
Commit: 647f364deca8e81a10545d6d59ddf7092d6946eb
Author: Hai Fang <hfang.shanghai@gmail.com>
Date: 2018-09-20 16:00:20 +0100
Commit message:

 Update to the version 1.9.3
 
Package: IsoformSwitchAnalyzeR
Commit: 066e556be7466239239c10fca8989f54572611a9
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2018-09-20 15:39:12 +0100
Commit message:

 Update of importCufflinksFiles
 
Package: mQTL.NMR
Commit: 80208e7de5ea4f7ab47f84f706f9ab1cf2c75229
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2018-09-20 10:13:50 -0400
Commit message:

 Package Deprecation
 
Package: dmrseq
Commit: 24372f0112911812871c6066e2c89b40e6fca24a
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-09-20 09:30:10 -0400
Commit message:

 Remove deprecated args from read.bismark
 
Package: limma
Commit: 47ab38859db9f05e2a06feb387908a0dacee247e
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2018-09-20 20:00:07 +1000
Commit message:

 20 Sep 2018: limma 3.37.7

- Reverting the p-value adjustment in cumOverlap() back to the
  original directed Bonferroni method, because it is more powerful
  when the number of Ids contributing to the significant overlap is
  small.
 
Package: limma
Commit: f227828897ad33a2031afa0a2172d51e961deaaf
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2018-09-20 19:05:53 +1000
Commit message:

 20 Sep 2018: limma 3.37.6

- Bug fix for cumOverlap(), which was under-counting overlaps in some
  cases. cumOverlap() now uses Holm's method for p-value adjustment
  and computes an overall p-values by Simes method.
 
Package: consensus
Commit: 23af19c498af7f8502a179ebd60125e5e8e2eb9f
Author: Tim Peters <t.peters@garvan.org.au>
Date: 2018-09-20 17:42:46 +1000
Commit message:

 consensus_0.99.17
 
Package: rhdf5
Commit: 39bd14cc3e87c0c42f99a70307f0def3a1f733db
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-17 14:07:27 +0200
Commit message:

 Complete merge

Merge branch 'master' of github.com:grimbough/rhdf5

# Conflicts:
#	DESCRIPTION
 
Package: rhdf5
Commit: 3b52d94e10992326aff275cc723d5900a765e6c4
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-17 13:56:25 +0200
Commit message:

 Fix test that fails only on Windows
 
Package: rhdf5
Commit: 2dc2ac6b8b50279435ff8231c08a47bf2c782f92
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-17 10:37:14 +0200
Commit message:

 Registration of S3 methods
 
Package: rhdf5
Commit: c317ad05237b638f5df3af46cc89921e7e1ad822
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-05 16:12:15 +0200
Commit message:

 Improved handling of 64bit integers (#24)

- Provides the option to write R-doubles as 64-bit integers in `h5create()` & `h5write()`
- No longer converts short ints and signed 32-bit ints when using `h5read()` and `bit64conversion = "double|bit64` - these stay as native R-integers.
- Fixed bug that would try to use `integer64` when `bit64conversion = "int"`
 
Package: rhdf5
Commit: 7e1cc2a5f0022e20c35744919beb99723cf648fd
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-05 15:26:26 +0200
Commit message:

 Version bump
 
Package: rhdf5
Commit: 479ada65c33878be677215572c23a3e2de9b07b7
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-05 15:24:57 +0200
Commit message:

 Remove print statement
 
Package: rhdf5
Commit: 4cca8f52c1befaf8e360c0a31b6c311d15803447
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-05 15:13:56 +0200
Commit message:

 Swap malloc for R_alloc
 
Package: rhdf5
Commit: 30c6ba2ecdf403fa631c9f30cf379da7a44499d9
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-05 11:21:09 +0200
Commit message:

 Try to improve clarity for handling 64-bit integers
 
Package: rhdf5
Commit: f62cf04641d51fa6d4f0cf9522a47bdb58da4596
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-09-04 14:05:22 +0200
Commit message:

 Merge changes in master branch

Merge branch 'master' into write-64bit

# Conflicts:
#	R/h5write.R
 
Package: rhdf5
Commit: 203d8994d3022a2b2b19495da7df2789ea74247f
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-08-23 13:06:28 +0200
Commit message:

 First tests with writing 64-bit integers
 
Package: Rsubread
Commit: 7903e40094bedbfa7491a4f7258e5ca474910ac3
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-20 15:22:01 +1000
Commit message:

 Fixed the issue of not quiting when the annotation format is wrong
 
Package: GenomicRanges
Commit: 550a4794511968d9b2a65fd269cc329ae94af831
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-19 20:58:20 -0700
Commit message:

 Make [[, as.list(), lapply(), and unlist() fail more graciously
on a GenomicRanges object
 
Package: IRanges
Commit: c41a10186ad06a55597e864979e2f46ccb7100a3
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-19 20:34:20 -0700
Commit message:

 Also make unlist() fail more graciously on an IRanges object
 
Package: scmeth
Commit: 197ff9e29f30f3d0361321b807836a9e5da7b51d
Author: Divyagash <sdivyagash@yahoo.com>
Date: 2018-09-19 22:01:30 -0400
Commit message:

 Changed visualization for methylation distribution visualization
 
Package: Rsubread
Commit: c957a454a34ef598580f0f814906d512d99371d0
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-20 10:41:06 +1000
Commit message:

 Chanegd some return values from align() and subjunc()

Hope to be last commit before copying code to RELEASE_3_7
 
Package: RTCGAToolbox
Commit: 65c1a60cfa3dacbb0f5a92aa50c1b8f7814103b6
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-19 17:51:37 -0400
Commit message:

 Use NA instead of NULL for missing genome builds
 
Package: sesame
Commit: efb18d28e83008de256367c654820890cae4d0fd
Author: zwdzwd <zhouwanding@gmail.com>
Date: 2018-09-19 17:40:03 -0400
Commit message:

 version bump 0.99.7
 
Package: sesame
Commit: 8c27e28046b2056e66b5f37a0059bf21db180ccb
Author: zwdzwd <zhouwanding@gmail.com>
Date: 2018-09-17 17:30:27 -0400
Commit message:

 added phenoage and skin and blood age
 
Package: sesameData
Commit: aae1c0b52c8a2b9a22765520246fad5ee87c85cf
Author: zwdzwd <zhouwanding@gmail.com>
Date: 2018-09-19 16:25:09 -0400
Commit message:

 updated inst/extdata
 
Package: sesameData
Commit: 3e01cf8ad6acafadd5d81708e8886057369891ad
Author: zwdzwd <zhouwanding@gmail.com>
Date: 2018-09-19 16:17:24 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: sesameData
Commit: 0e9a6925633150f78e101596bf3cd440281f48e8
Author: zwdzwd <zhouwanding@gmail.com>
Date: 2018-09-19 16:16:09 -0400
Commit message:

 version bump 0.99.4
 
Package: sesameData
Commit: c2abe649234669c970e8e265fb0f6cca7bbe5dd2
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-09-19 16:14:20 -0400
Commit message:

 update to the new EH snapshot at 2018-09-19
 
Package: chimeraviz
Commit: 19412d1538a9e46012db082b9d0827918850efba
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-09-19 19:51:41 +0200
Commit message:

 Bumpm version
 
Package: chimeraviz
Commit: cd8859365fcffe93ac535a1ac71248b5d06975de
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-09-19 19:51:13 +0200
Commit message:

 Don't import all of data.table
 
Package: simpleSingleCell
Commit: 04db4e054a6f129ac8c41d0f12015be9a8bdab46
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-19 11:56:28 +0100
Commit message:

 Removed intercept for new design= behaviour in findMarkers().
 
Package: scran
Commit: 392e7c640c9be16b21b68c9f3d546f613cbcddfb
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-19 11:59:31 +0100
Commit message:

 Warn against intercept in design=.
 
Package: scran
Commit: fda842e5927c7f7961252eea479b95725e7c7dc7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-19 11:22:31 +0100
Commit message:

 Bumped version number, date.
 
Package: scran
Commit: 26288d2f3ef155a41b66751e6eaf9f448fe7a5ed
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-19 10:55:21 +0100
Commit message:

 Reverted cyclone optimizations to pass CHECK for Win32.
 
Package: scran
Commit: dcf5fba410111ea4be0728f5bd90b026259f8579
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-19 10:28:08 +0100
Commit message:

 Preserve order of groups in pairs= for combineMarkers output.
 
Package: scran
Commit: 82a7f9e1189a3598a46479785913dd842c66b30c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-18 19:49:04 +0100
Commit message:

 Removed unnecessary utility functions.
 
Package: RforProteomics
Commit: f10ce072b710d5191cbb2c3969739ed01a662665
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-19 09:52:15 +0200
Commit message:

 no docs on bioc
 
Package: RforProteomics
Commit: dd5f5e5de732119f3832eaedf1f65d2e2d896f75
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-19 09:51:01 +0200
Commit message:

 update news and pkgdown site
 
Package: RforProteomics
Commit: 61b6ed061c8656218747582b43e0884939440f44
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-19 09:49:48 +0200
Commit message:

 update news
 
Package: RforProteomics
Commit: 089f6d7f05487e7d5d75e200b8d5bda30f0db201
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-19 09:32:55 +0200
Commit message:

 remove old installR4P.R script
 
Package: RforProteomics
Commit: 8d4225fd7141af398fb712d0f262b9eb9ddfa292
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-19 09:32:20 +0200
Commit message:

 fix conflicts
 
Package: RforProteomics
Commit: b61bbbd31d0d17c4d0caf599937f5f6c63ce5809
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-19 09:27:41 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/RforProteomics into devel
 
Package: RforProteomics
Commit: 64f1a206814e184a925835c16d37525d3f31dee6
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-19 09:27:34 +0200
Commit message:

 update docs
 
Package: RforProteomics
Commit: 9a71564bbec1b7a1d13c829b61dfbe8c8adefec6
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-19 09:27:18 +0200
Commit message:

 fix rmd typo
 
Package: RforProteomics
Commit: ddf09f6bcc6c1c4d113f30faea8e9e0b9bf8651e
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-07-24 17:47:41 +0100
Commit message:

 add new vig
 
Package: RforProteomics
Commit: 316cbfdab7e63a974801521bbec9c9e2c7e4a7d8
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-18 15:23:10 +0000
Commit message:

 add mention of biocpkgs::contribs in footnote - see https://github.com/lgatto/biocpkgs/issues/2
 
Package: MSstatsQC
Commit: 0a0010b483f9302294c95097cf7a828eae71c275
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-18 22:33:47 +0300
Commit message:

 evaluated CP chunk
 
Package: MSstatsQC
Commit: 7748a955965d5a47e0f36ce60d09ce9a479809fb
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-18 22:26:54 +0300
Commit message:

 version number fixed
 
Package: MSstatsQC
Commit: 01dfefca2cb973ba8623bd134b5b09a6882ee4b9
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-18 22:18:44 +0300
Commit message:

 vignette update
 
Package: MSstatsQC
Commit: bc052cad0ca802178f3008ec4b6b3b4a905f75da
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-18 15:01:51 +0300
Commit message:

 Vignette update
 
Package: MSstatsQC
Commit: a0e84bc441c853f31225b3fc615724ff70eb2537
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-18 12:12:29 +0300
Commit message:

 2.0 update
 
Package: MSstatsQC
Commit: 3a3660842150ce7ad3560fad1c26d7ce624e444f
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-17 15:13:53 +0300
Commit message:

 vignette fixed
 
Package: MSstatsQC
Commit: e5b2ce162cc52043056c1bf4ea205d8465470cfc
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-17 14:48:09 +0300
Commit message:

 new datasets added
 
Package: MSstatsQC
Commit: 020369e6eb67ec76d3dd6cb9b512bf915c28053a
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-17 14:42:49 +0300
Commit message:

 MissingDataMap included
 
Package: MSstatsQC
Commit: 42651303725995e87c4b481f22b9f4e58a65da07
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-14 15:07:17 +0300
Commit message:

 missing data treatment added
 
Package: MSstatsQC
Commit: 3f170f06c638e1c64ec3ebcedcdfb9961079ee9f
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-09-14 15:02:19 +0300
Commit message:

 missing value treatment added
 
Package: MSstatsQC
Commit: 00383274d6bdd6a14f4ba647be14d1d2b19e5ff6
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-03-19 16:42:40 +0200
Commit message:

 version bump
 
Package: MSstatsQC
Commit: 480330062cb5dbce6184d57c608ee480718e5bf1
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2018-03-19 16:34:52 +0200
Commit message:

 v 1.1.4 vignette fix
 
Package: simpleSingleCell
Commit: 17eedcc9a4b3709f2e7cc6b4a78d65cf99a2d6d3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-18 19:23:47 +0100
Commit message:

 Updated comments for overlapExprs.
 
Package: simpleSingleCell
Commit: 12fde3f2716136b26407babd0f86a83a331ecba6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-18 19:21:45 +0100
Commit message:

 Updated cluster checks for new findMarkers output.
 
Package: RGMQL
Commit: b448373f498ff9e79229a445a8a6650cabbeeb63
Author: Simone <simone@Simones-Mac-Pro.local>
Date: 2018-09-18 18:01:08 +0200
Commit message:

 Fixed conflicts in version change
 
Package: RGMQL
Commit: 7cf7d93591a1e83c7c830c52b08b7d06f70712fb
Author: Simone <simone@Simones-Mac-Pro.local>
Date: 2018-09-18 18:00:05 +0200
Commit message:

 Fixed conflicts in version change
 
Package: RGMQL
Commit: 9a5a50869d870a6c55cb4fdcad40002abfc549e8
Author: Simone <simone@Simones-Mac-Pro.local>
Date: 2018-09-16 09:24:18 +0200
Commit message:

 change descr
 

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