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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: 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
 
Package: RGMQL
Commit: 0783f5bb82df3fd3635f00c4dc559ec1d28e12bd
Author: Simone <simone@Simones-Mac-Pro.local>
Date: 2018-09-16 09:19:24 +0200
Commit message:

 minor fix
 
Package: RGMQL
Commit: 10164259c52ddb2d235be3230e9b0eeaf849330e
Author: Simone <simone@MBP-di-Simone.homenet.telecomitalia.it>
Date: 2018-08-23 20:06:30 +0200
Commit message:

 fixed url
 
Package: HiCcompare
Commit: 77d2b90bdd4498595e5e2cf82b1590250ff135a8
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2018-09-17 20:31:56 -0400
Commit message:

 Match the number of workers and requested processors
 
Package: scran
Commit: afa5f6ca721790c0ade9d479e2026999067576f9
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 13:30:47 +0100
Commit message:

 Further clean-ups to NEWS.
 
Package: scran
Commit: 3101c5b0550383de5fd057d9efa4fa3e50bd64d8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 13:11:28 +0100
Commit message:

 Updated NEWS.
 
Package: scran
Commit: 2d52f8dac836d77b4da475b16cce079181be6197
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 13:09:46 +0100
Commit message:

 Documentation cleanups, mostly for 'seealso' sections.
 
Package: scran
Commit: aba1c564243c856fd8bdf4ccf942337015479c3a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 13:06:11 +0100
Commit message:

 Fixed overlapExprs argument documentation.
 
Package: scran
Commit: 702c4b0f18ddca539254bd6a0e3d647328e6bc41
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 11:46:49 +0100
Commit message:

 Bumped version number, date.
 
Package: scran
Commit: 8bc46494e0d2cf4605651fbb1d18a1b29f62906d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 11:29:54 +0100
Commit message:

 Avoid improper sorting of NAs in Simes C++ code.
 
Package: scran
Commit: fe71effbd274c54ed7c533dd314c47b79a78d3a6
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 09:28:08 +0100
Commit message:

 Updated combineMarkers docs.
 
Package: scran
Commit: 2a9cf540bd9d80c1625220084453576d2eb6f2af
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 09:27:50 +0100
Commit message:

 Migrated overlap explanation to pairwiseWilcox docs.
 
Package: scran
Commit: 08a219292ff7a8eb03dfe7f09fedfa2fec7d08cf
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-09-18 09:27:14 +0100
Commit message:

 Renamed 'effect' to 'overlap' for Wilcoxon tests.
 
Package: scran
Commit: 0692526eca81e425e6d882c0f84110d2da5d6b7e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 23:36:23 +0100
Commit message:

 Rebuilt NAMESPACE.
 
Package: scran
Commit: 282e680b13790f570aa9cc868acbd3fb1433146c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 23:36:13 +0100
Commit message:

 Stripped back overlapExprs documentation and tests.
 
Package: scran
Commit: e0872d5521770b9b75f7dee4ab41a746678f28ad
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 23:25:22 +0100
Commit message:

 Refactored overlapExprs to use other functions.
 
Package: scran
Commit: d2b6c126e166ccf5ea139b235dfb6d3b994a314e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 23:18:48 +0100
Commit message:

 Removed SnowParam tests, as these are slow.
 
Package: scran
Commit: 7b33c909065661aa153d630be9a6da18fa0b6ad1
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 23:16:52 +0100
Commit message:

 Fixed pairwiseWilcox tests for asymmetry in one-sided p-values.
Removed unnecessary design-based tests.
 
Package: scran
Commit: 72ecfc39ed620ec7b622c27c54e79a80006e60be
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 23:15:59 +0100
Commit message:

 Switched to approximate Wilcoxon for scalability.
 
Package: scran
Commit: 01a16a6d5b5d3ceb1b4f30b1e71e622bc85a7e52
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 23:15:11 +0100
Commit message:

 Reworked overlapExprs() C++ code for better tie handling.
 
Package: scran
Commit: 16aed82c00709b9748ec56c84ee2258963f884b2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 20:33:18 +0100
Commit message:

 Cleaned up pairwiseTTests docs.
 
Package: scran
Commit: 46f735deb477d12ff7685577c51f80aa7b388cb0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 20:33:03 +0100
Commit message:

 Updated pairwiseTTests for generalized utility call.
 
Package: scran
Commit: dda396c5bfe6544d327fa1397773a2b925e65337
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 16:49:13 +0100
Commit message:

 Migrated testing utilities out of pairwiseTTests.
 
Package: scran
Commit: 76d51dff76f595d406b3f5cc085d5e5d4c6e5f22
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 16:45:53 +0100
Commit message:

 Added a separate suite of tests for pairwiseWilcox.
 
Package: scran
Commit: 0a60c6b0f2004a8cd35e7c05d4b708d426a1f156
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 16:34:11 +0100
Commit message:

 Documented pairwiseWilcox.
 
Package: scran
Commit: ca20d2b2f6037c68b574d3308d472660b3d49fac
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 16:33:55 +0100
Commit message:

 Greatly simplified overlap_exprs C++ code.
 
Package: scran
Commit: 0cdc5e70f70fbcde9e4d9a3e6a655d08dd104d28
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 16:31:31 +0100
Commit message:

 Added dedicated pairwise Wilcoxon testing function.
 
Package: limma
Commit: 48ee8226edcc2fb184ff21603e25db08f05d8d21
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2018-09-18 18:03:38 +1000
Commit message:

 18 Sep 2018: limma 3.37.5

- The colors "blue", "red" and "yellow" used by coolmap() changed to
  "blue2", "red2" and "yellow2" when used in a color panel with white.
 
Package: ClassifyR
Commit: f89c9574edecf940c5297a2cd8aae30d11be98fb
Author: Dario Strbenac <dstr7320@uni.sydney.edu.au>
Date: 2018-09-18 17:05:12 +1000
Commit message:

 - Folding cross-validation schemes now use stratified random sampling to allocate samples to folds, so that every fold contains an almost identical proportion of classes to the entire data set.
 
Package: missMethyl
Commit: f66ed57bf215102474051af7ee1500497c37ce34
Author: Jovana Maksimovic <jovana.maksimovic@mcri.edu.au>
Date: 2018-09-18 16:51:01 +1000
Commit message:

 Updated package to use latest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 EPIC annotation by default. Bumped z version. Updated NEWS.
 
Package: missMethyl
Commit: 71291a4ea082b951b963136e07527eba7e71de85
Author: Jovana Maksimovic <jovana.maksimovic@mcri.edu.au>
Date: 2018-09-18 16:43:25 +1000
Commit message:

 Updated manual entries for getMappedEntrezIDs, gometh and gsameth to explain new optional argument for passing in the array annotation.
 
Package: missMethyl
Commit: 391c364afb089a3516d5423e532f28917b16fa6d
Author: Jovana Maksimovic <jovana.maksimovic@mcri.edu.au>
Date: 2018-09-18 16:41:50 +1000
Commit message:

 Replaced .flattenAnn function with .getFlatAnnotation to speed up execution by optionally passing the array annotation in as an argument. Modified getMappedEntrezIDs, gometh and gsameth functions to reflect this change.
 
Package: QuaternaryProd
Commit: 54b2bf624ee12569b3775b2cf616467080f4c85e
Author: kolonel <carlfakhry@gmail.com>
Date: 2018-09-18 01:05:13 -0500
Commit message:

 added UTF-8 encoding for roxygen2 and changed example for RunCRE_HSAStringDB
 
Package: Rsubread
Commit: 6bbf0be416093f2bb37e6730a97a73967d68a4b7
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-09-18 13:01:42 +1000
Commit message:

 See DESCRIPTION (1.31.12)

The last commit (I hope) before updating the RELEASE_3_7 branch.
 
Package: GENESIS
Commit: d68f9fc6b847d4fc358c543223552540599c671f
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-09-17 10:09:27 -0700
Commit message:

 reorder phenotypes to match cov.mat in null model

Since the covariance matrix may be block diagonal, we should not
reorder it. Instead, reorder the data frame to match cov.mat.
fitNullModel for AnnotatedDataFrame now calls the data.frame
method, and createDesignMatrix is a function, not a method, that
operates on a data.frame only. This makes it easier to deal with
all sample.id operations in one place. The sample.id argument no
longer specifies the order of samples, only which ones to include.
 
Package: GENESIS
Commit: f3db7705fd6dbf71d7a4ca3eb4a6a5e1c61769ea
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-09-14 10:01:55 -0700
Commit message:

 removed unit test for deprecated function
 
Package: GateFinder
Commit: 5011904797a7a3889a4e8fba81a9afcaeccb692f
Author: tculos <tonyculos@gmail.com>
Date: 2018-09-17 14:34:55 -0700
Commit message:

 corrected vignette to proper target population to be consistent with plot example
 
Package: RTCGAToolbox
Commit: 5c690c6a20e5ccd439571ce8a78cc67bc746db56
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-17 18:44:23 -0400
Commit message:

 remove extra dependencies
 
Package: RTCGAToolbox
Commit: dac5217d93da74a75809371d2751a278ac11e453
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-17 18:01:56 -0400
Commit message:

 use DelayedArray when returning methylation
 
Package: TFBSTools
Commit: 90341176efe71e550062c6bfc5a55d18944210a7
Author: Ge Tan <gtan@me.com>
Date: 2018-09-17 23:09:33 +0200
Commit message:

 version 1.19.3

assign sequence name when not available in runMEME.
 
Package: BiocOncoTK
Commit: 28a125f4147168855e8e3cb5dc2b2db50f259860
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-09-17 14:38:52 -0400
Commit message:

 introduce new data and code for actual MSIsensor scores provided by M Bailey
 
Package: multiHiCcompare
Commit: 1bbad2ca2751a49321ac44a50824581615dcc16e
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2018-09-17 14:31:19 -0400
Commit message:

 update documentation
 
Package: multiHiCcompare
Commit: 320ea9735cedcf9e3f7a89b669760e9980be51a6
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2018-09-17 13:51:21 -0400
Commit message:

 merge
 
Package: multiHiCcompare
Commit: 920280a4c5991d59f11c0a6d306de2509e08b34b
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2018-09-17 13:45:45 -0400
Commit message:

 round cpm and fc in topdirs
 
Package: multiHiCcompare
Commit: 7104d67b68ee97984ba5fc1c63f43fbdda78b959
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2018-09-14 12:39:46 -0400
Commit message:

 Some important piece not committed due to merging conflict
 
Package: multiHiCcompare
Commit: f0c6ad8d64faf100963693ccd4b7c2b94882b308
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2018-09-14 12:39:15 -0400
Commit message:

 Resolving conflicts in my modification of help

Merge branch 'master' of https://github.com/dozmorovlab/multHiCcompare

# Conflicts:
#	R/manhattan.R
#	R/topDirs.R
 
Package: multiHiCcompare
Commit: 7114a8a72689d2160ca98fd438f260ac954b8085
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2018-09-14 11:23:35 -0400
Commit message:

 Adjust help
 
Package: multiHiCcompare
Commit: c05cc91e376fe454b64e40d7e7fa1ee0366cdf3d
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2018-09-14 11:13:16 -0400
Commit message:

 Adjust help
 
Package: plotGrouper
Commit: a9e076524789979a4a44b140aa805cd933a8d3bf
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-17 10:22:08 -0700
Commit message:

 Version bump
 
Package: plotGrouper
Commit: 1a1e235873a6b566ee715f8e4eff456fed2cfc00
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-17 10:21:45 -0700
Commit message:

 Add buffer to edges of report during save
 
Package: plotGrouper
Commit: bffebbe8fe660fa4b10385693833e12d1bf6ad24
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-17 10:16:43 -0700
Commit message:

 update README
 
Package: plotGrouper
Commit: 6ff8b7f40a9d8e737bfa44b95b3f7d593eac138f
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-17 10:15:14 -0700
Commit message:

 update README
 
Package: plotGrouper
Commit: d9668ad9d5d184854d2c67b9a5c32e53cdc4df74
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-16 17:33:54 -0700
Commit message:

 Update README
 
Package: powerTCR
Commit: 95f47907f89ff707b22cf5d778a19232c5fc10d3
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 13:18:55 -0400
Commit message:

 removed cache from vignette
 
Package: scran
Commit: 24119bed101f93eb1e24ca42a0ff3733f920243e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 13:26:23 +0100
Commit message:

 Added BPPARAM option to findMarkers.
 
Package: scran
Commit: fd81a76dd7effb648df35daa9dd67924527efee6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 12:58:25 +0100
Commit message:

 Bumped version, date.
 
Package: scran
Commit: 74ae5dc7cda82552d293749736c41204ec1217e3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 12:50:47 +0100
Commit message:

 More conservative termination in cyclone() to overcome numerical imprecision.
 
Package: scran
Commit: a0a84e13ea7970dba8262adb62f1c4e6fe7e7b6c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 12:49:34 +0100
Commit message:

 Minor fixes to pairwise-T tests.
 
Package: scran
Commit: 0ef9970a24f1a69f2f39177534411ead805daa60
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 12:46:53 +0100
Commit message:

 Added option for coefficient return for internal LM fitter.
 
Package: scran
Commit: 8241c6a4ebb86791a508ab8d31d154d408575405
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 12:46:15 +0100
Commit message:

 Tested parallelization, correct factor behaviour in pairwise-T.
 
Package: scran
Commit: d9e733c6769caf11f5cbce81056c2cfb0521b6fe
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-17 12:44:32 +0100
Commit message:

 Added support for parallelization in pairwiseTTests.
 
Package: bsseq
Commit: fb28afa2e6681460d8828f557412a710ba64695a
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:47:23 +1000
Commit message:

 Version bump

 
Package: bsseq
Commit: 5114a8088fd320b8d1df6d1b46dd8a3200f9aa13
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:17:52 +1000
Commit message:

 Merge refactor branch into master

 
Package: bsseq
Commit: 3d8da200727b97efef127be9d018fab92c4be371
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:08:44 +1000
Commit message:

 Fix vignette

 
Package: bsseq
Commit: 29c575d8461cabbbff28ee5823b985d204a1fbd6
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:08:34 +1000
Commit message:

 Tweak and update unit tests

 
Package: bsseq
Commit: b8c41a989e83abf7394b0533148c0c0102d6501c
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:08:03 +1000
Commit message:

 Update DESCRIPTION

 
Package: bsseq
Commit: ccc329654b80bbbe53794b3f4e91118aefe698d8
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:07:48 +1000
Commit message:

 Tweak collapseBSseq()

 
Package: bsseq
Commit: 5469cca5a2fc104f0937c4b62dcdd2446566eb50
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:07:27 +1000
Commit message:

 Simplify BSseq() and BSseq validity method, refactor strandCollapse()

 
Package: bsseq
Commit: f8b9f93cd916baebfc789209af909d73aa94fad3
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:05:59 +1000
Commit message:

 Add TODO

 
Package: bsseq
Commit: a6a3f7f2832efc476f60a3e91d61063795a4b235
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:03:43 +1000
Commit message:

 Update docs

 
Package: bsseq
Commit: 57cc26c6968fbdf2de8e4a014e8997e15162bc2e
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:02:52 +1000
Commit message:

 Rename findCytosines as findLoci and document

 
Package: bsseq
Commit: d70eb2f29fb35c1a88d034b5b9fbb74c29619b3b
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-04 06:03:52 +1000
Commit message:

 Re-design collapseBSseq()

- Arguments to collapseBSseq() are changed
- Support parallelisation
- Internally, use DelayedMatrixStats::colsum() 
Package: bsseq
Commit: 296c9077509486c92660a5fc648bbc0243c158b2
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-21 13:47:21 +1000
Commit message:

 Regenerate NAMESPACE

 
Package: bsseq
Commit: 65e163c3dacce307a88ba21401a91b7ed1aba876
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-07-20 14:31:21 +1000
Commit message:

 Updates for recent changes

 
Package: bsseq
Commit: 3ee5357f74371bf4a23d4e3ac14ee827c1c45a56
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-07-20 14:30:21 +1000
Commit message:

 Modify BSmooth()

- Automatic selection of appropriate BACKEND and better control over HDF5 options (when applicable)
- Tweak unit tests
 
Package: bsseq
Commit: 045886b5becdd05dac055b3f103940484186e2c7
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-07-20 14:28:37 +1000
Commit message:

 Modify read.bismark()

- Pass colData rather than sampleNames
- Better control over HDF5 file and its location
- Save BSseq object if HDF5-backed
- Tweak unit tests 
Package: bsseq
Commit: f2908a047ac4ddbc6caa5f7d1dacf762a87737f8
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-07-10 14:39:30 +1000
Commit message:

 Remove deprecated arguments

Kasper wants these removed without deprecation/defunct cycle 
Package: bsseq
Commit: 673019b83c08574ea6f79038a650229b0278f831
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-07-04 09:36:07 -0400
Commit message:

 Remove temporary file on exit

 
Package: bsseq
Commit: 0656078974325effacdaabeaba68bc5c07bfe704
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-07-04 09:24:07 -0400
Commit message:

 Explicitly gunzip to tempfile()

Avoids error 'gzip: stdout: No space left on device' (https://github.com/Rdatatable/data.table/issues/717#issuecomment-226038307) 
Package: bsseq
Commit: 868a6f2da324a0d500a80091b2d60701a810990f
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-07-03 22:41:15 -0400
Commit message:

 Remove readr dependency

Found that `readr::read_tsv()` was painfully slow for large gzipped Bismark files (e.g., mCH loci). 
Instead, now use:
- If file is gzipped and `gzip` is available at the command line, then use `data.table::fread()`.
- If file is gzipped and `gzip` is **not** available at the command line, then use `utils::read.table()`.
- If file is not gzipped (plain text) use `data.table::fread()`. 
 
There are still some kinks to work out and tradeoffs to explore. 
Package: bsseq
Commit: 627e0331cb9f8d36516d87487c2035b2053139fc
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-29 10:30:47 -0400
Commit message:

 colGrid() and rowGrid() moved to DelayedMatrixStats as of v1.3.4

 
Package: bsseq
Commit: 6a11fba23502452809fc0b228ba9a80786ae4c6d
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-28 19:34:03 -0400
Commit message:

 Add TODOs

 
Package: bsseq
Commit: 1debd55731f9087ed8f52d5494d6a08c25a3b9de
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-28 19:33:16 -0400
Commit message:

 Don't import stats::qnorm

Need to use the S4 generic `qrnom()` from DelayedArray. It's default method is `stats::qrnom()`, so it does the right thing. 
Package: bsseq
Commit: 2420db830a94135d1b6cff59ae125c71dd7273a7
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-28 12:27:46 -0400
Commit message:

 Don't import stats::plogis

Need to use the S4 generic `plogis()` from DelayedArray. It's default method is `stats::plogis()`, so it does the right thing. 
Package: bsseq
Commit: 463d05ef9bb20e47a6f96460fcf26576c35a28f0
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-28 12:12:40 -0400
Commit message:

 extract_block() was replaced with read_block() in DelayedArray 0.7.15

 
Package: bsseq
Commit: fc52a8dbc3f5fedb11d58c400806f87ac1b00393
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-28 12:03:26 -0400
Commit message:

 write_block_to_sink() was replaced with write_block() in DelayedArray 0.7.15

 
Package: bsseq
Commit: 6f7e079fdeb856d9aeffc20904d7a13d86a45a5d
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-20 12:20:05 -0400
Commit message:

 Update TODOs

 
Package: bsseq
Commit: 90182086c88fdbc942217ebb797bfc25e4839cb0
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-20 12:19:24 -0400
Commit message:

 Speed up .collapseMatrixLike() and, in turn, BSseq()

- Addressed #71, thanks @scottgigante
- Removes undocumented behaviour of BSseq() sorting the output. In previous versions, this was done via `reduce(gr)`; see https://github.com/hansenlab/bsseq/blob/RELEASE_3_7/R/BSseq_class.R#L176-L223. In the refactor branch I had changed it to use order(gr). Now, it is completely removed. 
Package: bsseq
Commit: 0c791a3b5b6cc626c6a013e2735573931f573982
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-18 16:14:02 -0400
Commit message:

 Add strand argument to findCytosines
 
Package: bsseq
Commit: d4d338c2723b2b45ced8b715361b5edc34d5ecab
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-18 09:27:53 -0400
Commit message:

 Add TODO

 
Package: bsseq
Commit: ca5bb6e84b91979c59be00a8882365ed648d2c4c
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-14 20:48:26 -0400
Commit message:

 Passing R CMD check locally without errors

- There are still warnings and notes
- And still more stuff to re-factor 
Package: bsseq
Commit: 61dabc442177e84c5d55a22f8856180463ec4bd1
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-14 16:43:20 -0400
Commit message:

 Tweak DESCRIPTION and NAMESPACE

- HDF5Array and beachmat in Imports rather than Suggests 
Package: bsseq
Commit: 1823d04b5a05f63a73a7baeab7df9690d4289f01
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-14 15:39:15 -0400
Commit message:

 Quieten R CMD check

 
Package: bsseq
Commit: 6075570da5fec6823d4ac419802a90fdc5c1563e
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-14 13:48:18 -0400
Commit message:

 Complete switch from RUnit to testthat

 
Package: bsseq
Commit: 597d6250b8ef8e9488c2297f665422a13b92e1ae
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-14 10:54:19 -0400
Commit message:

 Fix bug in BSmooth()

Accidentally deleted some still-required code in 9392512c7b4229e5a58258544d454d3edf1e58ba 
Package: bsseq
Commit: d4c7a86cbcfba04a9ac77507407b27e0d1d746ab
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-14 10:45:45 -0400
Commit message:

 Migrate read.bismark() unit tests to testthat

 
Package: bsseq
Commit: 0efa6ec869d1e2dd434286df4c61950f6aa2fd32
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-14 10:34:33 -0400
Commit message:

 Update TODOs

 
Package: bsseq
Commit: 9392512c7b4229e5a58258544d454d3edf1e58ba
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-14 10:31:16 -0400
Commit message:

 Remove BPREDO from BSmooth()

- This was not fully/properly implemented and in this state was dangerous. E.g., you can accidentally clobber an existing BSseq object (see https://support.bioconductor.org/p/109374/#109459).
- I'll make it a long-term goal to support this functionality 
Package: bsseq
Commit: e6cb9673898862ee4dbd94bf06baefb4c3b27679
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-13 22:05:45 -0400
Commit message:

 Add some TODOs and NOTEs
 
Package: bsseq
Commit: 5aa8515c5acaa9c6fa477077d4d6b0252dbaa53e
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-13 10:17:09 -0400
Commit message:

 Improve `findCytosines()`

- Make generic with methods for _BSgenome_ and _DNAStringSet_ (e.g., a FASTA file imported with `rtracklayer::import()`) 
Package: bsseq
Commit: 876631066e730720727e93c6a6dd5c3b8dc29ee4
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-12 20:25:21 -0400
Commit message:

 Add TODOs

 
Package: bsseq
Commit: 168df69aa26666d885a7985a0c58bda7e262b8b4
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-12 20:25:08 -0400
Commit message:

 Tweak findOverlaps() in read.bismark()

 
Package: bsseq
Commit: acd3fb4ecd7a3ca6c9358b51a5918710e8969a0b
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-12 15:58:27 -0400
Commit message:

 Update read.bismark() documentation
 
Package: bsseq
Commit: 015577264536a35623644c23d671571ef830dd6c
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-12 15:56:44 -0400
Commit message:

 Formatting
 
Package: bsseq
Commit: 52279d5f26139b36c006b15132a331953631dfd2
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-11 10:12:03 -0400
Commit message:

 Fix bug in `combine()` that merged adjacent loci

- Cannot use `union()` as that calls `reduce()` with `min.gapwidth = 1L`, which leads to adjacent (unstranded) loci being combined into a locus with width == 2.
- Re-ran `inst/scripts/get_BS.chr22.R` to update the included data, `BS.chr22` 
Package: bsseq
Commit: e4c7e203843fdb3ed22c2becc4a5ff7516a48ba7
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-11 09:44:25 -0400
Commit message:

 Tweak

 
Package: bsseq
Commit: 4fb2eaeb445019aee49f48ed6349858e53b7fec9
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-11 09:44:13 -0400
Commit message:

 Add `BACKEND` and `...` arguments to `BSmooth()`

- The user can now set the name of the HDF5 file via the `...` arguments
- Use a single IPC lock when writing `coef` and `se.coef` to RealizationSink. Previously, process A could write to `coef` and process B could write to `se.coef` simultaneously, but this can create a race condition if, for example, both `coef` and `se.coef` are in the same HDF5 file.
This change means that, in this example, process 'A' must wait for process 'B' to finish before being able to begin writing `coef` to the RealizationSink.
- Update `BSmooth()` documentation 
Package: bsseq
Commit: 0adebae6b1ae7ff6e051a309b0d065a4856c3ab3
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-11 09:08:45 -0400
Commit message:

 Tidy

 
Package: bsseq
Commit: b2034fcb6155d1f77b02d5efd8c603e896b81b6d
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-10 10:37:16 -0400
Commit message:

 Update 'Collate' in DESCRIPTION

 
Package: bsseq
Commit: 0c45dd4ec9ad4ee2576f3b1da72918f187a89992
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-10 10:31:38 -0400
Commit message:

 Initial implementation of findCytosines()

 
Package: bsseq
Commit: 6339d1112cc47b90811b1a17c53fdb947fab9560
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-10 10:31:16 -0400
Commit message:

 Use a single IPC lock when writing M and Cov to RealizationSink

Previously, process A could write to 'M' and process B could write to 'Cov' simultaneously, but this can create a race condition if, for example, both 'M' and 'Cov' are in the same HDF5 file.
This change means that, in this example, process 'A' must wait for process 'B' to finish before being able to begin writing 'M' to the RealizationSink. 
Package: bsseq
Commit: 441a63d86d023277e4482e2b8f72d4cf20a2da6b
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-10 10:29:08 -0400
Commit message:

 Improve progress bar in .contructFWGRangesFromBismarkFiles()

 
Package: bsseq
Commit: f086668f2aceef80e76b5b9c5c9392e0a81cfc76
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-06 09:45:11 -0400
Commit message:

 Add TODOs

 
Package: bsseq
Commit: f4c5710c7a5648e8850155c755c9a16dcaa6ed0a
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-05 19:31:37 -0400
Commit message:

 More tweaks to read.bismark() and co

 
Package: bsseq
Commit: 81bbcb4b9ea980b2e3f0621e1f73a496d03902b9
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-05 16:30:04 -0400
Commit message:

 Rename 'gr' argument in read.bismark() as 'loci'

 
Package: bsseq
Commit: 65f8a16f7c1c39e5f9960e656aa3632874cd6ed6
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-05 16:28:32 -0400
Commit message:

 Remove loci_dt and bsseq_dt

These are superseded by FWGRanges, which implement the correct strand-matching behaviour that is surprisingly difficult to achieve otherwise. 
Long term, I'd like to support FWGRanges as the rowRanges in a BSseq object. 
Package: bsseq
Commit: 1aef3bd98096cb7c64f4f304fbe522c6a5399a00
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-06-05 14:36:20 -0400
Commit message:

 Add FWIRanges and FWGRanges, use in read.bismark()

 
Package: bsseq
Commit: 9725691b1e7e345ac5739e639db541bdfd9229ac
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-05-31 15:23:36 -0400
Commit message:

 Add TODO 
Package: bsseq
Commit: 3c2dce42f654f8b5f01f679a21097cd2b7b57f3d
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-05-31 15:23:24 -0400
Commit message:

 Split out R/read.bismark.R

Slightly formalise intermediate objects lociDT and BSseqDT.
Split these out into their own files.
Refine construction of 'gr' from Bismark files. 
Package: bsseq
Commit: 04be7a8c47fd8524b6dd95655e3a231d5e92328b
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-05-29 15:26:41 -0400
Commit message:

 Continue refactoring read.bismark() 
Package: bsseq
Commit: 588e496cae0d6fa1642ab58eb11160327ed30c73
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-05-29 15:26:19 -0400
Commit message:

 Add TODOs 
Package: bsseq
Commit: 31f7d3b8ac14440596d922e544c8a4595ff3a5a4
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-05-29 08:56:37 -0400
Commit message:

 Merge branch 'refactor-read.bismark' into refactor 
Package: bsseq
Commit: 866ab76fd69f9f0edd3872c217033b585d052c80
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-05-28 19:42:18 -0400
Commit message:

 Work in progress: refactoring bsseq

- BSseq objects can once again use ordinary matrix objects as assays.
- Reimplement `BSmooth()` more-or-less from scratch:
  - Switch from 'parallel' to 'BiocParallel' for parallelization. This brings some notable improvements:
    - Smoothed results can now be written directly to an on-disk realization backend by the worker. This dramatically reduces memory usage compared to previous versions of 'bsseq' that required all results be retained in-memory.
    - Parallelization is now supported on Windows through the use of a 'SnowParam' object as the value of `BPPARAM`.
    - Improved error handling makes it possible to gracefully resume `BSmooth()` jobs that encountered errors by re-doing only the necessary tasks.
    - Detailed and extensive job logging facilities.
  - Fix bug in `BSmooth()` with the `maxGap` parameter.
- Re-factor BSseq() constructor and add fast, internal .BSseq() constructor.
- Re-factor collapseBSseq() and combine(). Should be much more performant.
- Use beachmat to implement fast validity checking of 'M' and 'Cov' matrices.
- Resave BS.chr22 (supplied data) using integer for storage mode of assays to reduce size.
- Switch from RUnit to testthat. testthat has better integration with code coverage tools that help when refactoring. 
Package: bsseq
Commit: 3b038a97bfd43d57ca77e815e1bc0b8eb9eb4cf1
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-05-04 14:31:03 -0400
Commit message:

 Initial re-write of read.bismark()
 
Package: bsseq
Commit: cc2028663443c2ae3f135bf1c1ed27e27f5c92ab
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-17 21:13:04 +1000
Commit message:

 Merge

 
Package: bsseq
Commit: b841efcb5a26cea1eacf2ef6f979580550b4301f
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-07-18 10:35:25 +1000
Commit message:

 Update installation instructions in README 
Package: SEPIRA
Commit: 3600c7e3e89c74c8f1b3417e109fb4814b6a2cb8
Author: YC3 <35122685+YC3@users.noreply.github.com>
Date: 2018-09-17 16:47:42 +0900
Commit message:

 s
 
Package: SEPIRA
Commit: 53bc07dd392bfaca8951a04896090044a84932e3
Author: YC3 <35122685+YC3@users.noreply.github.com>
Date: 2018-09-17 16:44:44 +0900
Commit message:

 s
 
Package: SEPIRA
Commit: 22e67587bc7ce3f5ad5830a571f0059918224557
Author: YC3 <35122685+YC3@users.noreply.github.com>
Date: 2018-09-17 16:38:05 +0900
Commit message:

 d
 
Package: SEPIRA
Commit: ff560b8f4d018705c34d92fe5d0539cfb1f3b6f5
Author: YC3 <yuting@dev-genet.novalocal>
Date: 2018-09-17 16:34:41 +0900
Commit message:

 des
 
Package: SEPIRA
Commit: d2efe55ce573d54b865d1edcbfe94bf708cece16
Author: YC3 <yuting@dev-genet.novalocal>
Date: 2018-09-17 15:39:29 +0900
Commit message:

 sepira
 
Package: SEPIRA
Commit: 34220afcae7a3d3805fec122c6f1b3252970efff
Author: YC3 <yuting@dev-genet.novalocal>
Date: 2018-09-17 14:07:07 +0900
Commit message:

 citation added
 
Package: SEPIRA
Commit: e4875be60dc866da38f7c2213cd3cacb31f2c71f
Author: YC3 <35122685+YC3@users.noreply.github.com>
Date: 2018-09-02 20:06:12 +0900
Commit message:

 Merge pull request #10 from YC3/18sept

18sept 
Package: SEPIRA
Commit: f2cb923b20a7bbb28e57b3a3de126aba36919d3c
Author: YC3 <35122685+YC3@users.noreply.github.com>
Date: 2018-09-02 19:56:59 +0900
Commit message:

 Add files via upload 
Package: SEPIRA
Commit: 73447c1cc80dc13db5a29e44e7289a01c19a7a70
Author: YC3 <35122685+YC3@users.noreply.github.com>
Date: 2018-09-02 19:54:26 +0900
Commit message:

 Add files via upload 
Package: DMRcate
Commit: 0f4142ab2439b0d5900f1ec2970823dc81d17c94
Author: Tim Peters <t.peters@garvan.org.au>
Date: 2018-09-17 14:14:52 +1000
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: DMRcate
Commit: d96d1d59172e70235331a698844045a6eb5da7ed
Author: Timothy John Peters <t.peters@garvan.org.au>
Date: 2018-09-11 18:49:32 +1000
Commit message:

 LICENSE bump 
Package: DMRcate
Commit: c05b98183a7f705a9a008778f21c36e47ed73864
Author: Timothy John Peters <t.peters@garvan.org.au>
Date: 2018-09-11 18:48:59 +1000
Commit message:

 1.16.2 bump 
Package: DMRcate
Commit: ce0fd3da0ffb2b38ff0aca3b802b90e0d6bd73f9
Author: Timothy John Peters <t.peters@garvan.org.au>
Date: 2018-09-11 18:44:31 +1000
Commit message:

 Update DMR.plot.R

genome Ideogram change 
Package: DMRcate
Commit: 9602cf226ea080f8c7b03b0ca0650c9d94529477
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-06-01 13:06:44 +1000
Commit message:

 Shorten WGBS input for vignette
 
Package: DMRcate
Commit: 83b917c5ab7e3eb49259a89ac0a4205bc811c42a
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-05-30 14:32:17 +1000
Commit message:

 DMRcate_1.12.1_vignettefix
 
Package: DMRcate
Commit: a9b5a6c2ab5d1bb2d83f74da05eb5e3c8be54cee
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-05-30 11:16:55 +1000
Commit message:

 DMRcate_1.12.1
 
Package: DMRcate
Commit: 9dab34aa0fedbe9b55daa22701bab8490eb2b113
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-03-31 15:48:21 +1100
Commit message:

 Update DMRcate-internal.Rd 
Package: DMRcate
Commit: 070436ee2c93d154600f9fb1cfbc64b9129c5b14
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-03-31 15:40:29 +1100
Commit message:

 DMRcate_1.10.10
 
Package: DMRcate
Commit: 83d868e51dcc990c03c3d11178b609c7f13e139b
Author: Michael Buckley <michaelmikebuckley@gmail.com>
Date: 2017-03-28 17:07:28 +1100
Commit message:

 Main function, dmrcate(), re-organised and sped up.
 
Package: DMRcate
Commit: a5aedc50a4f26c1995c896e7896dd804d9d0da90
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-03-28 15:17:34 +1100
Commit message:

 Update cpg.annotate.R 
Package: DMRcate
Commit: a1233a7c955f733519836f4998d3dd03c7524c2c
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-03-28 15:07:40 +1100
Commit message:

 DMRcate_1.10.9, ty to Jenny Drnevich for bugspot
 
Package: DMRcate
Commit: 844615c312adbccc8659cfbeb11244943c8018bc
Author: Michael Buckley <michaelmikebuckley@gmail.com>
Date: 2017-03-17 07:57:26 +1100
Commit message:

 Unloop promoters part of extractRanges.
 
Package: DMRcate
Commit: 640ef3876e59e335702d0732ef84ac5554da7f8a
Author: Michael Buckley <michaelmikebuckley@gmail.com>
Date: 2017-03-15 15:17:54 +1100
Commit message:

 Faster version with no 'apply' calls.
 
Package: DMRcate
Commit: a27acf0ca498d0b2086e1847fbfcfd1558e19f47
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-03-13 11:40:21 +1100
Commit message:

 DMRcate_1.10.8
 
Package: DMRcate
Commit: 052c73ec7d9f4f3265351525b4a370697da9a3bc
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-03-03 14:02:53 +1100
Commit message:

 DMRcate_1.10.7
 
Package: DMRcate
Commit: 8c5a1be81c33d884a57438596165d67088c36786
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-02-07 14:19:37 +1100
Commit message:

 DMRcate_1.10.6, ty to Michael Prummer for bugspot
 
Package: DMRcate
Commit: f1d877fd179ebabec955463b33e0ad1dbaa18bd4
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-01-23 09:47:45 +1100
Commit message:

 DMRcate_1.10.5
 
Package: DMRcate
Commit: 19a032fe2429f7a576249170f9f10293d0967348
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-01-22 18:15:56 +1100
Commit message:

 bracketfix
 
Package: DMRcate
Commit: 6fd3b72d8acfac16b918e101e953d82962e9b3cf
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-01-18 17:34:40 +1100
Commit message:

 DMRcate_1.10.4, ty to Xavier Pastor for patch
 
Package: DMRcate
Commit: a8f2b03eb17119f0776b7ea9ca227acfa9e9320c
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-01-11 15:03:08 +1100
Commit message:

 DMRcate_1.10.3
 
Package: DMRcate
Commit: e6ca4d7a87c58119a576e5353f3506daa1be19a0
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-01-03 12:57:54 +1100
Commit message:

 Messages in cpg.annotate()
 
Package: DMRcate
Commit: 2f0008bc9f81c1187348295c70bf221578b84793
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-01-03 12:27:05 +1100
Commit message:

 DMRcate_1.10.2
 
Package: DMRcate
Commit: 5bbf220e9922efa2ed66ce47b84d45a946b3e9ae
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2017-01-03 12:19:02 +1100
Commit message:

 DMRcate_1.10.2. Thank you to Yuan Tian and Eugene Wang for bugspotting
 
Package: DMRcate
Commit: 3f63acd8dc2ea7fc7d073a8b5df919d3a36d24bd
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-10-24 13:01:54 +1100
Commit message:

 1.10.1 LICENCE 
Package: DMRcate
Commit: 64b36e0cd3f4fdacf97ed96b46b0fc8597d05f9a
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-10-24 13:01:15 +1100
Commit message:

 1.10.1 DESCRIPTION 
Package: DMRcate
Commit: 4cdca18c6dec138f6174a8dc3a9051b0811b2721
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-10-24 13:00:31 +1100
Commit message:

 1.10.1 NEWS 
Package: DMRcate
Commit: 6909bec3f1cca99ac13d8cbd1e7278057061c228
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-10-21 14:35:17 +1100
Commit message:

 DMRcate_1.8.7
 
Package: DMRcate
Commit: 6f656e6daac7a54cc718f895eae7547c6218502e
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-07-06 19:50:58 +1000
Commit message:

 DMRcate_1.8.6 (ty to Giovanni C. for the bugspot)
 
Package: DMRcate
Commit: 7e1c861fdf8bf05f4bc1eee1f9e19c915900d1da
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-05-25 14:04:20 +1000
Commit message:

 DMRcate_1.8.5
 
Package: DMRcate
Commit: c6b02e2c9b908b3e4ffc37fcb36d198abb49621e
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-05-23 14:54:46 +1000
Commit message:

 DMRcate_1.8.4
 
Package: DMRcate
Commit: 4fc76ac9e928af4b0a9842b824f945dce7bc5bd8
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-03-30 16:13:29 +1100
Commit message:

 DMRcate_1.6.53, correct environment errors
 
Package: DMRcate
Commit: 7038cbad757acf425f8ce8809a59a19acb219c43
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-03-10 17:14:55 +1100
Commit message:

 Merge branch 'master' of https://github.com/timpeters82/DMRcate-devel
 
Package: DMRcate
Commit: 0bedac4cfd4d7e5f184dff6ea604ff06e4532160
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-03-10 17:11:32 +1100
Commit message:

 DMRcate_1.6.52, ty to Jesper Maag for finding a bug in DMR.plot()
 
Package: DMRcate
Commit: 6b2ec9dc7d4a32b388a6c2ab9a536b6858e36dd8
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-03-10 17:11:32 +1100
Commit message:

 DMRcate_1.6.52
 
Package: DMRcate
Commit: 9541af9ae426368d886f27e53eb553459e0bb86e
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-02-01 16:16:32 +1100
Commit message:

 DMRcate_1.6.5, ty to Eric Smith for bug report
 
Package: DMRcate
Commit: b0a6928febec6bc216fb037f0fa94d5f47b57621
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-01-18 16:26:40 +1100
Commit message:

 DMRcate_1.6.4
 
Package: DMRcate
Commit: c2684e04c22baa031a758a980b21d25c077de37a
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-01-11 11:36:09 +1100
Commit message:

 namespace update
 
Package: DMRcate
Commit: ca4dc4d35d0e4fa4a17e5c4435a7a73a26033037
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-01-08 11:54:01 +1100
Commit message:

 DMRcate_1.6.3
 
Package: DMRcate
Commit: a40485d7af20eb1be051488863a51295cdf2e8ea
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-01-04 12:58:14 +1100
Commit message:

 DMRcate_1.6.2
 
Package: DMRcate
Commit: e8c952aea3d0333349ca494bb5e0cc722f62b7cb
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2016-01-04 12:52:16 +1100
Commit message:

 Bugfix for when gaps=0
 
Package: DMRcate
Commit: 364a0a840468a8f8b2f71180defd763ba3349959
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-12-14 12:48:50 +1100
Commit message:

 dummy removal
 
Package: DMRcate
Commit: f521930f699701b9b0f4e04cdb1a03fb780a529a
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-12-10 11:23:58 +1100
Commit message:

 Dummy push
 
Package: DMRcate
Commit: 69b24bb14b81a040d881b944939d21263603ed9a
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-11-26 17:09:40 +1100
Commit message:

 DMRcate_1.6.1 (release)
 
Package: DMRcate
Commit: 017720b71cde1a3b3c14c82bedf3a6e06b7d65a2
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-11-23 15:46:16 +1100
Commit message:

 DMRcate_1.7.3
 
Package: DMRcate
Commit: 0bd4b4f4de8312b082330dd8bd8e7f3e13638221
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-11-09 09:47:02 +1100
Commit message:

 Delete extraneous files
 
Package: DMRcate
Commit: 9ed137da253d74d9c47dbc0542760780a9343fea
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-11-06 12:06:22 +1100
Commit message:

 DMRcate_1.7.2
 
Package: DMRcate
Commit: 3298a9bd9f261b886952a6d7817aa4c51a2f8ad3
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-11-05 22:54:45 +1100
Commit message:

 DMRcate_1.7.1 again
 
Package: DMRcate
Commit: d9773cdb3b07c0a00979ad16e2fe701bec3a6a70
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-11-05 22:50:25 +1100
Commit message:

 DMRcate_1.7.1
 
Package: DMRcate
Commit: 8241440afe0a1a7581f29c85afe0b648de1250b6
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-07-13 09:54:40 +1000
Commit message:

 DMRcate_1.5.61
 
Package: DMRcate
Commit: ebfead988c0e9cb0a4be71cd37ce273fc311fabf
Author: timpeters82 <t.peters@garvan.org.au>
Date: 2015-07-06 11:46:06 +1000
Commit message:

 Merge pull request #1 from ttriche/master

A few patches  
Package: DMRcate
Commit: c6e51f2ba5db44a0f28e455f1dc671cc190a0ee5
Author: Tim Triche, Jr. <tim.triche@gmail.com>
Date: 2015-06-26 15:01:55 -0700
Commit message:

 add devtools, git2r to install directions 
Package: DMRcate
Commit: ba9e160fdc392c38151d892276d6ff9c74d39783
Author: Tim Triche, Jr. <tim.triche@gmail.com>
Date: 2015-06-26 15:01:08 -0700
Commit message:

 add devtools 
Package: DMRcate
Commit: 65da44588db6674a8508ea2322f0319c3ad04101
Author: Tim Triche, Jr. <tim.triche@gmail.com>
Date: 2015-06-26 14:59:00 -0700
Commit message:

 Add explicit installation directions 
Package: DMRcate
Commit: 4d4013ef941e2ec796836ef4b437c41c04a7004a
Author: Tim Triche, Jr. <tim.triche@gmail.com>
Date: 2015-06-26 11:59:51 -0700
Commit message:

 Create README.md 
Package: DMRcate
Commit: 984ea2072c68f3726491052d1bc4af128fb1063f
Author: ttriche <tim.triche@gmail.com>
Date: 2015-06-26 11:57:09 -0700
Commit message:

 initial checkin of patches to mainstream DMRcate
 
Package: DMRcate
Commit: 9e294a204c982a507d0e05fbd306c1fb82a8fdc5
Author: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>
Date: 2015-04-16 21:33:55 -0700
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.

Consists of 0 commit.

Commit information:
 
Package: DMRcate
Commit: dec284c17caa2fdc399200e52851a8b3f4c2fa2b
Author: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>
Date: 2015-04-16 12:51:13 -0700
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.

Consists of 1 commit.

Commit information:

SVN Revision number: 102591
Commit message:
Bump versions prior to creating 3.1 branch.

Committed by d.tenenbaum
Committed at: 2015-04-16T19:42:01.524374Z
 
Package: DMRcate
Commit: cfcec38d9475134547736bcc045663a2ae11eab2
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2015-04-13 18:29:17 +1000
Commit message:

 DMRcate_1.3.1 bump again with licence
 
Package: DMRcate
Commit: c70212386b67e83aba9838baaf0e30011d36ca65
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2015-04-13 18:20:50 +1000
Commit message:

 DMRcate_1.3.1 bump again
 
Package: DMRcate
Commit: 6eee3eddf700d2cec325997ff78b9e53aeee42ed
Author: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>
Date: 2015-03-27 04:28:11 -0700
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.

Consists of 0 commit.

Commit information:
 
Package: DMRcate
Commit: 75e8eb52cfead2a1203f561bd2e2e65ad5f39298
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2015-03-27 19:10:18 +1100
Commit message:

 DMRcate_1.3.1 again
 
Package: DMRcate
Commit: 0763a155246250d0ddeb29e9cf65a24540776513
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2015-03-27 19:08:01 +1100
Commit message:

 Merge remote-tracking branch 'origin/master'

Conflicts:
	DESCRIPTION
 
Package: DMRcate
Commit: 3369af65bc3ad7a2498650992c0ec211c535813e
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2015-03-27 19:06:05 +1100
Commit message:

 DMRcate_1.3.1
 
Package: DMRcate
Commit: d187734333c38bebdc89e6388861a281a6ddcfd1
Author: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>
Date: 2014-10-13 14:57:36 -0700
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.

Consists of 1 commit.

Commit information:

SVN Revision number: 95443
Commit message:
Bumping versions after creating 3.0 release branch.

Committed by d.tenenbaum
Committed at: 2014-10-13T21:47:41.382147Z
 
Package: DMRcate
Commit: 1dc041dcee84b2a921cf1daf1c017310a5e42ab8
Author: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>
Date: 2014-10-13 14:48:25 -0700
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.

Consists of 1 commit.

Commit information:

SVN Revision number: 95439
Commit message:
Bump package versions prior to creating the 3.0 branch.

Committed by d.tenenbaum
Committed at: 2014-10-13T21:38:33.867451Z
 
Package: DMRcate
Commit: b123c8097e5e05dadad01ada32de6da61bdbd4a2
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-08-29 13:33:38 +1000
Commit message:

 DMRcate_1.1.6
 
Package: DMRcate
Commit: 3cafb3ff7729a026e1980aa344578ce89d2aa3e0
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-08-14 15:01:08 +1000
Commit message:

 DMRcate_1.1.5
 
Package: DMRcate
Commit: ba33983cf6c7204e9ca33b17c7570fd80c2fd43b
Author: t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-04-24 06:23:37 +0000
Commit message:

 conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@89436 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: DMRcate
Commit: c433a2180933cb2fe54491e01416bfbeb1c148fb
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-04-24 11:33:35 +1000
Commit message:

 DMRcate_1.1.3

<- becomes = in data.frame creation
 
Package: DMRcate
Commit: 05544e263ec36ada876235b87aaecd7776908ba6
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-04-24 11:19:26 +1000
Commit message:

 DMRcate_1.1.2

Bugfix in variability and hypermethylation
 
Package: DMRcate
Commit: 4c617418d76c5dffa6b8111bc97d4196a4017b8d
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-04-22 15:12:19 +1000
Commit message:

 DMRcate version 1.1.1

Removed sentence in vignette relating to development version
 
Package: DMRcate
Commit: 541499c76be6dc3c4a86a5df806fdf0f95038010
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-04-11 21:21:21 +0000
Commit message:

 Second version bump after creating 2.14 release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@88840 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: DMRcate
Commit: 2d2652262740e67f6ecac1e3050c1f4091486c0a
Author: t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-26 07:33:39 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: 61e6a247ce01002959a3a373b10ea07c59254547
    Commit message:
    DMRcate_0.99.11

    - Beta fold-change incorporated into annotate()
    - maxbetafc added to returned results
    - grey lines added to DMR.plot at beta = {0, 0.5, 1}
    - Formula slightly changed in vignette
    Committed by timpeters82 
    Commit date: 2014-03-26T18:33:22+11:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87929 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    
Package: DMRcate
Commit: 61e6a247ce01002959a3a373b10ea07c59254547
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-03-26 18:33:15 +1100
Commit message:

 DMRcate_0.99.11

- Beta fold-change incorporated into annotate()
- maxbetafc added to returned results
- grey lines added to DMR.plot at beta = {0, 0.5, 1}
- Formula slightly changed in vignette
 
Package: DMRcate
Commit: a6194e68fdeff98a8202a1610a644b958de4a30a
Author: t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-24 23:38:03 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: f3f03c12bde0606c57d304f566486d3c9b67c1b6
    Commit message:
    DMRcate_0.99.10

    Updated vignette to reflect DMRcate still being in R-devel
    Committed by timpeters82 
    Commit date: 2014-03-25T10:37:46+11:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87821 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    
Package: DMRcate
Commit: f3f03c12bde0606c57d304f566486d3c9b67c1b6
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-03-25 10:37:39 +1100
Commit message:

 DMRcate_0.99.10

Updated vignette to reflect DMRcate still being in R-devel
 
Package: DMRcate
Commit: 86f7b928b94521c45dcde855078f3c5f641bdafe
Author: t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-21 06:26:40 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commit(s).

Commit information:

    Commit id: 532bded6d65aac5f3cc0f58895582c5fba70ed6c
    Commit message:
    DMRcate_0.99.9

    Clarification over preference of M-values in vignette, plus one instance
    of formatting in man page
    Committed by timpeters82 
    Commit date: 2014-03-21T17:26:26+11:00

    Commit id: e2d6b32524217e1b7d53775d74d74e2569b1a981
    Commit message:
    Bumping DESCRIPTION

    bump to 0.99.9 in DESCRIPTION
    Committed by timpeters82 
    Commit date: 2014-03-21T17:26:26+11:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87687 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    
Package: DMRcate
Commit: e2d6b32524217e1b7d53775d74d74e2569b1a981
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-03-21 17:26:17 +1100
Commit message:

 Bumping DESCRIPTION

bump to 0.99.9 in DESCRIPTION
 
Package: DMRcate
Commit: 532bded6d65aac5f3cc0f58895582c5fba70ed6c
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-03-21 17:24:34 +1100
Commit message:

 DMRcate_0.99.9

Clarification over preference of M-values in vignette, plus one instance
of formatting in man page
 
Package: DMRcate
Commit: dd0281cebcaf2938430838e936182274d777184e
Author: t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-19 00:26:43 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: 5f8f365fba5c85d38d27e2fd63aa373da6c8f789
    Commit message:
    DMRcate_0.99.8

    Minor changes in formatting surrounding \textit{p}-value
    Committed by timpeters82 
    Commit date: 2014-03-19T11:26:22+11:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87590 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    
Package: DMRcate
Commit: 5f8f365fba5c85d38d27e2fd63aa373da6c8f789
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-03-19 11:26:14 +1100
Commit message:

 DMRcate_0.99.8

Minor changes in formatting surrounding \textit{p}-value
 
Package: DMRcate
Commit: aa78d72febd1be650d301741f28935c37806f28f
Author: t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-17 06:23:43 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: 3437a6f80a2c0db27b9ebdbb6590f12aac339987
    Commit message:
    DMRcate_0.99.7

    Changed bad formatting and obsolete object names in the man pages.
    Committed by timpeters82 
    Commit date: 2014-03-17T17:23:22+11:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87496 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    
Package: DMRcate
Commit: 3437a6f80a2c0db27b9ebdbb6590f12aac339987
Author: timpeters82 <Tim.Peters@csiro.au>
Date: 2014-03-17 17:23:22 +1100
Commit message:

 DMRcate_0.99.7

Changed bad formatting and obsolete object names in the man pages.
 
Package: DMRcate
Commit: 59bc62ef514f1b5de78dd2cf03cc664b86b2e21a
Author: mtmorgan@fhcrc.org <mtmorgan@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-08 06:50:46 +0000
Commit message:

 add DMRcate to repository and manifest


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87230 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: powerTCR
Commit: 7067a0a109cfec09974975275bc4e1d917662bf8
Author: Hillary Koch <hillary.koch01@gmail.com>
Date: 2018-09-17 00:12:47 -0400
Commit message:

 removed excess in vignettes
 
Package: FGNet
Commit: 511e6e7065f9f427d2637050864b563c7dbef04b
Author: Sara Aibar <sara.aibar@kuleuven.vib.be>
Date: 2018-09-16 23:15:06 +0200
Commit message:

 v 3.15: Deprecate plotKegg()
 
Package: QuaternaryProd
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Author: kolonel <carlfakhry@gmail.com>
Date: 2018-09-16 12:11:40 -0500
Commit message:

 added a check for progressBar
 
Package: scran
Commit: 8ad777bd151bc12baf8d4c9f8c9926bd7e166839
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 16:12:11 +0100
Commit message:

 Moved combining method details from ?combineVar to ?combinePValues.
 
Package: scran
Commit: 87dfd62d22c480b36593d570924a073d16949e8d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:55:02 +0100
Commit message:

 Rebuilt NAMESPACE, bumped version number and date, updated NEWS.
 
Package: scran
Commit: 29845ef2cdcdad276ca011a09f3dab64b3fe1d6b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:51:40 +0100
Commit message:

 Removed obsolete .combine_pvalues utility.
 
Package: scran
Commit: 02febaa91e45b66480d49e027d73855348ddf332
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:50:59 +0100
Commit message:

 Switched pairwiseTTests to use combinePValues for Stouffer's.
 
Package: scran
Commit: 136214c6ed41b3b32e07565de5d5449a2cb56aa7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:48:40 +0100
Commit message:

 Shortcut for only one vector in combinePValues.
 
Package: scran
Commit: 5bee1049f6c50232878fabdafefe1684c4a65d14
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:36:08 +0100
Commit message:

 Split testVar and combineVar tests to separate files.
 
Package: scran
Commit: 53ce38474b923936db1571109f99ba09d78e306d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:35:06 +0100
Commit message:

 Switched combineVar to use combinePValues internally.
 
Package: scran
Commit: d93d1902cb0bb1deb9b90dc506fe29680d4179ba
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:34:24 +0100
Commit message:

 Protect against p=0 and 1 in Z method for combinePValues.
 
Package: scran
Commit: 8a6552ce8aa9c11da1937ea68f63170f980221b1
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:29:27 +0100
Commit message:

 Support weights as a list in combinePValues.
 
Package: scran
Commit: 5d0e3ec3602beb23abdf1d15c704e4ea81de80bd
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:16:18 +0100
Commit message:

 Switched combineMarkers to use combinePValues.
 
Package: scran
Commit: 45ab45b00180f4d803443425c6521d9932d650f8
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:02:29 +0100
Commit message:

 Fixed a log bug in combinePValues.
 
Package: scran
Commit: f87bbfccb09e5f524aa8e84af6f9221aa71f7879
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 15:01:08 +0100
Commit message:

 Added explicit tests for combinePValues.
 
Package: scran
Commit: d107154ef21b87a6f697138bf9b4cc82dad8b3fa
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 13:07:51 +0100
Commit message:

 Documented combinePValues.
 
Package: scran
Commit: 05c97fc28dd3e40648d1fea1495cf5a097917fff
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 13:06:53 +0100
Commit message:

 Updated Simes C++ code to accept a list.
 
Package: scran
Commit: 535cbd0792381db3f2baa3f76058ee2970fc3650
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-16 12:56:13 +0100
Commit message:

 Rolled out specific function for p-value combining.
 
Package: chimeraviz
Commit: 8948ba91129ec08a65472a7563740b089639377b
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-09-16 16:53:01 +0200
Commit message:

 Fix small stuff
 
Package: chimeraviz
Commit: 05c968870a62fb79a3a754e7012ca62932ab43b8
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-09-16 15:53:08 +0200
Commit message:

 Fix typo
 
Package: chimeraviz
Commit: e4f8ae759eaf25d102ba4cf7f59f04cf560798fd
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-09-16 15:32:06 +0200
Commit message:

 Link to citations
 
Package: chimeraviz
Commit: 039349785903e8e1d9b81f78f411c16537b6d39d
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-09-16 15:31:59 +0200
Commit message:

 Bump version
 
Package: chimeraviz
Commit: bd3f6fd2f7bf40e9fddbfa25fc25bb9384136095
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-09-16 15:25:10 +0200
Commit message:

 Avoid readr because of https://github.com/tidyverse/readr/issues/750
 
Package: plotGrouper
Commit: aec3c83f20914954df3c9749af125d1edd58093e
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-15 21:51:59 -0700
Commit message:

 Fix placement of comparison segments
 
Package: plotGrouper
Commit: ff7e3fbe14c99556ec7c95016d39047df4dcfa8c
Author: jdgagnon <jgagnon@vpn-10-48-4-203.ucsf.edu>
Date: 2018-09-15 09:47:16 -0700
Commit message:

 udpate README
 
Package: mzR
Commit: 59a4c51a7a90c712c7adf7e83055510e1d2b547a
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-15 23:11:27 +0200
Commit message:

 reference correct issue number
 
Package: mzR
Commit: f77fa9ea0d9bec67003fa37d00768e8258642eaf
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2018-09-15 22:48:48 +0200
Commit message:

 Merge pull request #182 from sneumann/fix181

Closing #181 
Package: mzR
Commit: 6e6b87d510d366f18b9ba24669bb13a0adddd7c6
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2018-09-15 22:34:04 +0200
Commit message:

 More elegant fix for #181
 
Package: mzR
Commit: 00f65ff95c67a28cac504c827ac4ba2227b8291f
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2018-09-15 22:11:56 +0200
Commit message:

 Closing #181
 
Package: mzR
Commit: e7ed4bd57e8087a7333d08a6521ed463ee1cddf8
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 23:15:13 +0200
Commit message:

 bump gh devel version
 
Package: amplican
Commit: 64c05b4dab96f4cfed5c1f129b8e78d95bb58a22
Author: JokingHero <kornellabun@gmail.com>
Date: 2018-09-15 21:48:21 +0200
Commit message:

 bump version
 
Package: amplican
Commit: 349e91a28d7dae930c7e62f290d9bdd6f66c5c4f
Author: JokingHero <kornellabun@gmail.com>
Date: 2018-09-15 21:47:26 +0200
Commit message:

 hopefully will fix inconsistent behaviour of knitr when plotting grid objects from child
 
Package: amplican
Commit: 31b17fd6f27d942a9a2ce7e84342f8ead68fb129
Author: JokingHero <kornellabun@gmail.com>
Date: 2018-09-15 21:10:43 +0200
Commit message:

 fixed naming of the vignette FAQ
 
Package: scran
Commit: 8e3daadb1a60d653291286258182e20ecbb89d1d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 18:14:39 +0100
Commit message:

 Merge branch 'master' of https://github.com/MarioniLab/scran
 
Package: scran
Commit: f11e2ec67da8038315d62aa0f9f7fcc80e8e7d6f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 18:05:12 +0100
Commit message:

 Documented log-behaviour of findMarkers.
 
Package: scran
Commit: b1c9ca4493cd754984c6567ec48d2bf48dc69cba
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 18:04:57 +0100
Commit message:

 Updated doubletCluster tests for new log behaviour of findMarkers.
 
Package: scran
Commit: dcf6c9248b0052d78e917a98e3973de07528cc94
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 18:02:15 +0100
Commit message:

 Updated doubletCluster for log-p-values from findMarkers.
 
Package: scran
Commit: ee16c29085572383a61f747e91153dad66c273d9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 17:49:19 +0100
Commit message:

 Added Details and Examples for combineMarkers documentation.
 
Package: scran
Commit: 31902fd5b97e8b667097734edcd5321558764042
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 17:43:04 +0100
Commit message:

 Discarded redundant findMarkers tests, small updates.
 
Package: scran
Commit: f61cfe56d65aeb2f3d86cb7f1e0f85342caa403c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 17:42:22 +0100
Commit message:

 Bugfix to findMarkers for passing log-p values.
 
Package: scran
Commit: 4dc81afb145aff7e3fe8c58e91b2a0efd7bb3700
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 17:39:13 +0100
Commit message:

 Protect linear model t-test from discreteness.
 
Package: scran
Commit: bf1cccfbca9019b937fe3cd4ea2b6d8d84c723b5
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 17:30:20 +0100
Commit message:

 Added tests for all modes of pairwiseTTests.
 
Package: scran
Commit: 7a25226c47e344019809fdf349f41a74a1accb52
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 17:06:01 +0100
Commit message:

 Bugfix for linear model t-test standard error.
Remove intercept check, require intercept-free design as input.
 
Package: scran
Commit: 70f97531e17a16fb748b129d5dbc1118c09895bf
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 15:40:02 +0100
Commit message:

 Bugfix for Stouffer's method in pairwiseTTests.
 
Package: scran
Commit: 125e9ab185b80aeccba730d3ab6d87802c8bbd58
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 14:51:44 +0100
Commit message:

 Bugfix when lfc!=0 for pairwiseTTests.
 
Package: scran
Commit: ecee82097fe98f41094d11651c1cf61208e2a7cc
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 13:47:44 +0100
Commit message:

 Migrated docs from findMarkers to pairwiseTTests.
 
Package: scran
Commit: 1327f9e64e8b6755664b7cb0e7efd6d3e7e8abd7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 12:17:01 +0100
Commit message:

 Migrated testing code from findMarkers to pairwiseTTests.
 
Package: scran
Commit: 4184722d05bce9c4c3ce2191482a60978cb6bc8f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 19:25:15 +0100
Commit message:

 Rebuilt NAMESPACE.
 
Package: scran
Commit: d7a875b7e726dd351c358f5cd71dd2b4c9a83bda
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 19:24:54 +0100
Commit message:

 Bugfix for returning full stats, added tests for full.stats=TRUE.
 
Package: scran
Commit: 1a1b546e14ce1f9048109285a0d9dd200c5f6c9a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 19:15:26 +0100
Commit message:

 Documented combineMarkers (except for example).
 
Package: scran
Commit: aa7b599ffab51271b76a51b0b63cdbc6024954fe
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 18:58:26 +0100
Commit message:

 Added tests for combineMarkers.
 
Package: scran
Commit: df56fd2ce34c6cead8102f1af4f07fe0cb1909d0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 18:58:17 +0100
Commit message:

 Protect against silly inputs, streamling multiple testing correction.
 
Package: scran
Commit: 28f9b5c600a7744082113ae3af0f863c10a11ec7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 16:01:02 +0100
Commit message:

 Added separate source file for marker-related utilities.
 
Package: scran
Commit: 4313ca91a05ca18326be5634933c7a151ada4807
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 15:59:00 +0100
Commit message:

 Split off marker list combining code into a separate function.
 
Package: scran
Commit: c119c7d2fdf3a423031c01a278f81b043825afed
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-09-13 09:13:31 +0100
Commit message:

 Merge pull request #19 from PeteHaitch/patch-1

Typo 
Package: scran
Commit: 3c1e7cde96b047e48f4e50d74a586f8b1fb80e9d
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-09-13 09:59:19 +1000
Commit message:

 Typo 
Package: scran
Commit: 1722bef6f00771deb9b55ea32e13c57dc0924a74
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-12 16:35:16 +0100
Commit message:

 Bumped version number, date.
 
Package: scran
Commit: 676c496fd4ded1c90128622be661537f53c62a19
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-12 16:34:28 +0100
Commit message:

 Protect against numerical imprecision in score comparisons.
 
Package: simpleSingleCell
Commit: 0a60fed6edf17d863da77d2f0ac7d74c16487706
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-15 18:13:42 +0100
Commit message:

 Fixed vignette order on the landing page... again.
 
Package: plotGrouper
Commit: ca153db2d277aef9cfa1c16caec36d2ed191e33e
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-15 09:27:21 -0700
Commit message:

 Version bump
 
Package: scruff
Commit: 859a3ccb941d3ce9b5daf4f81ac97955afef4b28
Author: zhewa <314100793@qq.com>
Date: 2018-09-15 11:23:07 -0400
Commit message:

 version bump
 
Package: scruff
Commit: 7107eba2122a22faa3bf693ada6c81902d7cc2a6
Author: zhewa <314100793@qq.com>
Date: 2018-09-15 11:16:02 -0400
Commit message:

 include = c("filtered", all) in tenxBamqcplot
 
Package: IsoformSwitchAnalyzeR
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Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2018-09-15 08:45:34 +0100
Commit message:

 Minor update to isoformSwitchTestDEXSeq
 
Package: plotGrouper
Commit: b4af0a581b4c9e5d1f1b9210399247568848dc28
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-14 16:39:43 -0700
Commit message:

 update README & vignette
 
Package: flowWorkspace
Commit: 84b753b68fc15dd89362d91fe45be7ec454443b2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-14 15:15:57 -0700
Commit message:

 Merge branch 'trunk' into devel
 
Package: flowWorkspace
Commit: ebb13af5f4e6b992704b3ff25906da1fd29f4126
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-14 15:15:15 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: 8d90c229049cf91596f76a1560916f32a1bd8254
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-14 15:14:26 -0700
Commit message:

 add plot_diff_tree
 
Package: amplican
Commit: 47f1ed16efd193df85b539c2ae766cea1686845a
Author: JokingHero <kornellabun@gmail.com>
Date: 2018-09-14 21:48:38 +0200
Commit message:

 fix for description merge confict
 
Package: amplican
Commit: 1d300cc8356fb4aeb59efc1cf69b838aca576fe9
Author: JokingHero <kornellabun@gmail.com>
Date: 2018-09-14 21:37:24 +0200
Commit message:

 some bug fixes, improvemnets to HDR, example of base editor
 
Package: amplican
Commit: f1d302d3bd1b0159438e0aa86dc73d511bd72988
Author: JokingHero <kornellabun@gmail.com>
Date: 2018-08-15 15:28:17 +0200
Commit message:

 export min_freq to the amplicanPipeline for easier manipulation
 
Package: sesame
Commit: fdea046245eda3438391f7d3bced190e1e5f40a2
Author: Wanding Zhou - Bioinformatics <zhouwanding@gmail.com>
Date: 2018-09-14 13:48:30 -0400
Commit message:

 Merge pull request #5 from ttriche/master

fix build issue (cheezy kludge: use \dontrun) and add CITATION (S00PER IMPORTANT!!1) 
Package: sesame
Commit: ace8f9e337c93a877e8619d1a63a92d07087825c
Author: ttriche <tim.triche@gmail.com>
Date: 2018-09-14 13:05:18 -0400
Commit message:

 typo in CITATION format, fixed
 
Package: sesame
Commit: 8649febbde921ba963487294056bc0daafddd4dd
Author: ttriche <tim.triche@gmail.com>
Date: 2018-09-14 13:03:33 -0400
Commit message:

 quote year in citation
 
Package: sesame
Commit: f87a94b79a7e6360b9e98fb084def07d307cf96f
Author: ttriche <tim.triche@gmail.com>
Date: 2018-09-14 13:02:26 -0400
Commit message:

 added CITATION for citation("sesame")
 
Package: sesame
Commit: 218a8f0f850f61e5c837f8872026b45b898e1984
Author: ttriche <tim.triche@gmail.com>
Date: 2018-09-14 12:55:53 -0400
Commit message:

 add citation
 
Package: sesame
Commit: 0448c8f7c9a1a1de8d1911cac17bbfded256ea07
Author: ttriche <tim.triche@gmail.com>
Date: 2018-09-14 12:52:25 -0400
Commit message:

 fix build issue
 
Package: HDF5Array
Commit: a124ba38844c2911dd5bc388ea4acf190ea24048
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-14 10:24:46 -0700
Commit message:

 write_array_to_sink() was renamed BLOCK_write_to_sink() in DelayedArray
 
Package: DelayedArray
Commit: 998fa6af9f1f9ff78691ce00ae8cab0a3542f32a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-14 10:21:20 -0700
Commit message:

 Rename (and improve) write_array_to_sink() -> BLOCK_write_to_sink()

Also add "type" method for RleRealizationSink objects.
 
Package: QuaternaryProd
Commit: ba370fb48763a385e8b9173b4a877c0ce1082ea4
Author: kolonel <carlfakhry@gmail.com>
Date: 2018-09-14 12:00:29 -0500
Commit message:

 update version number
 
Package: QuaternaryProd
Commit: 08cd88baa9a807d317a97323780d45098e93782b
Author: kolonel <carlfakhry@gmail.com>
Date: 2018-09-13 23:15:22 -0500
Commit message:

 Added the option for specifying an arbitrary network and added a progress bar when computing pvalues over the causal network
 
Package: TFutils
Commit: 6da0fd696da8485b8b332cf15aa16d39bfd600b2
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-09-14 12:18:02 -0400
Commit message:

 minor changes
 
Package: seqplots
Commit: 66230d41f2bb83db21e3c524d2c65a11779fc240
Author: przemol <pstempor@gmail.com>
Date: 2018-09-14 17:17:45 +0100
Commit message:

 version bump to 1.19.3
 
Package: TabulaMurisData
Commit: 6bc3af4418d9351d1732ef0741927d5ce2a7be53
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-09-14 18:01:27 +0200
Commit message:

 Add iSEE to Suggests
 
Package: seqplots
Commit: bef58872272f297b1dd6222237b7de066e876e02
Author: przemol <pstempor@gmail.com>
Date: 2018-09-14 16:58:20 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/seqplots
 
Package: seqplots
Commit: cf9e0c3de82678847a3ad61429f449850dc9e5d8
Author: przemol <pstempor@gmail.com>
Date: 2018-09-14 10:45:30 +0100
Commit message:

 clusters are properly assigned in single thread mode, fixes #38
 
Package: seqplots
Commit: 08cd0dd6bd568b6627fbde536eb9d01eab65c1d4
Author: przemol <pstempor@gmail.com>
Date: 2018-09-13 19:02:12 +0100
Commit message:

 use single core calculations by default, fixes #43
 
Package: seqplots
Commit: 750edb43525370c33d00fb5ed260df06810570f9
Author: przemol <pstempor@gmail.com>
Date: 2018-05-02 11:11:07 +0100
Commit message:

 remove test for unused features
 
Package: seqplots
Commit: b50e5ff3f16fa2f410f5de64938add4b744fa3c5
Author: przemol <pstempor@gmail.com>
Date: 2018-05-02 11:07:42 +0100
Commit message:

 add parameter to determine sorting distance
 
Package: seqplots
Commit: 43546b89e597d0fb0b68cd7569f8545826d87f68
Author: przemol <pstempor@gmail.com>
Date: 2018-05-01 19:17:03 +0100
Commit message:

 heatmap plotting function takes options to sort by specific tracks, sort by anchored distance and cluster based on anchored distance, and annotate clusters using external vector
 
Package: seqplots
Commit: d7863b832833d754e0391491d5a745b6c3bacd2c
Author: przemol <pstempor@gmail.com>
Date: 2018-03-01 12:24:52 +0000
Commit message:

 removed "library' or 'require' calls for: ‘BSgenome’ ‘RSQLite’ ‘rtracklayer’
 
Package: seqplots
Commit: 99e521ba38cec7b4b45532a2fc9bfe8321436722
Author: przemol <pstempor@gmail.com>
Date: 2018-02-28 20:18:18 +0000
Commit message:

 export for getREF function
 
Package: seqplots
Commit: 0e5aeb2225bd7bef2a2b605e31f3f134d779f157
Author: przemol <pstempor@gmail.com>
Date: 2018-01-27 17:04:16 +0000
Commit message:

 getPlotSetArray: if track list is named, use the names instead of paths to annotate the output
 
Package: seqplots
Commit: 893d5432eac27b46e45c6971891d8cd64ae3c900
Author: przemol <pstempor@gmail.com>
Date: 2018-01-09 20:03:47 +0000
Commit message:

 add_local_file - function to add files to local SeqPlots installation
 
Package: seqplots
Commit: c8f1f33e42d1762141e769449dd157d2f2f44896
Author: przemol <pstempor@gmail.com>
Date: 2017-11-02 16:47:54 +0000
Commit message:

 docs update
 
Package: seqplots
Commit: 40789caf89521a561588fa6c2893aaf71fb5177a
Author: przemol <pstempor@gmail.com>
Date: 2017-09-27 17:28:57 +0100
Commit message:

 further support for chromosome check for genomes in FASTA files - TODO: add support for motif plots
 
Package: seqplots
Commit: d494a83decdf8e629df2d465910df7f1f1aa4688
Author: przemol <pstempor@gmail.com>
Date: 2017-09-27 15:30:34 +0100
Commit message:

 support for uploading narrowPeak files
 
Package: seqplots
Commit: e06362e752ccfba80861db21a7f334106c70f47b
Author: przemol <pstempor@gmail.com>
Date: 2017-09-27 15:26:50 +0100
Commit message:

 docs update
 
Package: seqplots
Commit: 2dc11b4ba81a66655cc6527320a18cf0af10208c
Author: przemol <pstempor@gmail.com>
Date: 2017-09-27 15:26:31 +0100
Commit message:

 Import function for narrowPeak format
 
Package: seqplots
Commit: f40a0cfd7acd3cc2cfeca343085581555e23c019
Author: przemol <pstempor@gmail.com>
Date: 2017-09-27 15:21:14 +0100
Commit message:

 use FASTA genomes for uploaded files
 
Package: seqplots
Commit: d297808bbfa0dc1e1aee5cf75d1a234c56f099dc
Author: przemol <pstempor@gmail.com>
Date: 2017-09-27 15:01:18 +0100
Commit message:

 Logic for adding FASTA files in GUI
 
Package: seqplots
Commit: cdeef028fdd7c1cfbfd8b2061759221e6ff7845a
Author: przemol <pstempor@gmail.com>
Date: 2017-09-20 14:52:54 +0100
Commit message:

 Merge branch 'master' of github.com:Przemol/seqplots

# Conflicts:
#	inst/seqplots/server.R
 
Package: seqplots
Commit: a70d2e15c1ee9d8d8470344ffa0c1110aee0c830
Author: przemol <pstempor@gmail.com>
Date: 2017-09-20 14:49:44 +0100
Commit message:

 adding BW files from Query String - bugfix
 
Package: seqplots
Commit: a8f355e174bb314d22d2a09bef55e3b254c98bbb
Author: przemol <pstempor@gmail.com>
Date: 2017-09-20 14:49:44 +0100
Commit message:

 adding BW files from Query String - get metadata info from query string
 
Package: seqplots
Commit: 9a160b2b680269444121123bebd0981871489cd0
Author: przemol <pstempor@gmail.com>
Date: 2017-09-20 14:18:04 +0100
Commit message:

 adding BW files from Query String - error handling
 
Package: seqplots
Commit: faa74fa3b630d3c978e0ea2b55d95dd31f5a641b
Author: przemol <pstempor@gmail.com>
Date: 2017-09-20 13:49:27 +0100
Commit message:

 adding BW files from Query String - modal dialog and session self closing
 
Package: seqplots
Commit: ad7fb036eada0094738be3dd8cd417dddb3e1e7f
Author: przemol <pstempor@gmail.com>
Date: 2017-09-19 17:11:50 +0100
Commit message:

 adding BW files from Query String
 
Package: seqplots
Commit: 5ee60e81ddefbe46dc1507ee4582dc9229c61c26
Author: przemol <pstempor@gmail.com>
Date: 2017-09-19 16:41:51 +0100
Commit message:

 fix for converting custom genomes files from wig to bigwig files - seqinfo object is created based on data in wig file
 
Package: seqplots
Commit: 0231349947378b0480ec323a1c95c7a9abdfb40b
Author: przemol <pstempor@gmail.com>
Date: 2017-09-19 13:28:29 +0100
Commit message:

 further reduction in warnings while testing
 
Package: seqplots
Commit: 86b0d8ef4c3c612a9963c3f550cc39aa67b5af3b
Author: przemol <pstempor@gmail.com>
Date: 2017-09-18 17:57:24 +0100
Commit message:

 initial support for genome in FASTA format plus various warnings suppressed
 
Package: seqplots
Commit: 61cff9733c503bf1af30e093c3eab5cfe054792b
Author: przemol <pstempor@gmail.com>
Date: 2017-09-18 16:08:41 +0100
Commit message:

 fixed url filed in CITATION
 
Package: plotGrouper
Commit: 33393b35902497ce34990ebda5c6b3d136c2bd45
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-14 08:13:17 -0700
Commit message:

 Update DESCRIPTION
 
Package: plotGrouper
Commit: 6603cc8a35a6e79f3061b7a5a338fb63daaa0eee
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-14 08:03:03 -0700
Commit message:

 update README
 
Package: Onassis
Commit: 5d738704823330833555c046c91504ff16a75d44
Author: egaleota <eugenia.galeota@ieo.eu>
Date: 2018-09-14 16:06:24 +0200
Commit message:

 Bug fix: removed some rmarkdown not showing correctly the vignette text
 
Package: maEndToEnd
Commit: 2e5cae5f8221ce0cd75cdf8237b7dfce57a847d3
Author: klaus <bernd.klaus@embl.de>
Date: 2018-09-14 11:50:32 +0200
Commit message:

 small change to reactome output
 
Package: maEndToEnd
Commit: 0bf62d07b1821f48296bfaa51f5a0cf0f357ce35
Author: klaus <bernd.klaus@embl.de>
Date: 2018-09-14 11:14:06 +0200
Commit message:

 minor firxes to the RLE section
 
Package: maEndToEnd
Commit: ab2f87f9ef667dab25ea3bc0fb21a24bf1c36beb
Author: klaus <bernd.klaus@embl.de>
Date: 2018-09-14 09:58:22 +0200
Commit message:

 modified the latex conversion check so that it does not throw an error when working interactively
 
Package: maEndToEnd
Commit: 589fdd67b9ec66967cff0b74577cff8b0ee6f99b
Author: Steffireise <steffi[at]reisenauer-online.de>
Date: 2018-09-03 13:10:26 +0200
Commit message:

 changed book name "genomics class" to "Biomedical Data Science" and "Michael Irizarry" to "Rafael Irizarry"
 
Package: maEndToEnd
Commit: 321faefd8137514b84c89ef907e48333b3f86f5b
Author: Steffireise <steffi[at]reisenauer-online.de>
Date: 2018-09-03 12:44:02 +0200
Commit message:

 remove section on target options "full" and "extended"
 
Package: tRNAscanImport
Commit: bc7dc2592832b05da243a1bf574b6c1b50f61ac9
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2018-09-14 09:52:20 +0200
Commit message:

 vignette update
 
Package: tRNAscanImport
Commit: 4902d7b9e52e1bcbebd717357dcb9ec529d73bc2
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2018-09-14 08:44:17 +0200
Commit message:

 README.md update
 
Package: IsoformSwitchAnalyzeR
Commit: 1e2bbac107d91821a772d85579cd8b6390a790b0
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2018-09-14 08:51:34 +0200
Commit message:

 Version bump for Bioconductor
 
Package: PREDA
Commit: 4b14ed727389d171fc2b423b3eafe3c17b3411d9
Author: itagliaf <itagliaf@node1.cluster.ifom.eu>
Date: 2018-09-14 08:30:18 +0200
Commit message:

 bug fix: removing samr dependency as no more available
 
Package: M3C
Commit: 329b333fe8901dce807183e5d4e7abb4069c24fa
Author: crj32 <chris.r.john86@gmail.com>
Date: 2018-09-14 07:17:05 +0100
Commit message:

 removed html file
 
Package: M3C
Commit: 47e0919a6ee80d34e16089a3bd8e2e545812db2c
Author: crj32 <chris.r.john86@gmail.com>
Date: 2018-09-14 07:15:26 +0100
Commit message:

 vignette edits
 
Package: M3C
Commit: 76bdec6551cf646a3ad31c8e526261732ce987f2
Author: crj32 <chris.r.john86@gmail.com>
Date: 2018-09-14 07:06:09 +0100
Commit message:

 fixed vignette error
 
Package: RCy3
Commit: e477941a0edc27200d8fb29856bbb15561b02d17
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-09-13 22:57:50 -0700
Commit message:

 version bump
 
Package: RCy3
Commit: 4c68141c77eeeda3d7032799e866146d61a07dfe
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-09-13 22:57:30 -0700
Commit message:

 replaced sapply with vapply; replace factors in dfs
 
Package: RCy3
Commit: cdbd07c0520d6d1ee37fc4f285b73c6891cb88fc
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-09-13 20:43:56 -0700
Commit message:

 rotate deprecated and updated news; version bump
 
Package: MSnbase
Commit: bd951d064df0cb8eab004a9a83fdff361d708348
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 23:52:24 +0200
Commit message:

 no docs on Bioc
 
Package: MSnbase
Commit: 01e6144523387f225444225fb2ed97ca5653cd81
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 23:51:19 +0200
Commit message:

 merge master and update pkgdown
 
Package: MSnbase
Commit: 7a0b1804465a8b82cf303582fc0f0a2746564b8a
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 23:27:10 +0200
Commit message:

 add scan.number.s. numeric test
 
Package: MSnbase
Commit: 56635ba78ae3064799d9912ff71a7cbed6303c59
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 16:21:58 +0200
Commit message:

 don't assume charge in plotDensity (issue #359)
 
Package: MSnbase
Commit: de90cc36be6c5545f0f8d3bb2e1c163f56ddaf2e
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-04 07:25:47 +0200
Commit message:

 add note about parallel processing
 
Package: MSnbase
Commit: 448d33fc052893050678540a8401c5e966560993
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-08-21 12:40:17 +0200
Commit message:

 bump version for gh devel
 
Package: mzR
Commit: ac3bc6fffe30151733e3b116a515677ac7cf88ac
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 23:14:04 +0200
Commit message:

 update news
 
Package: mzR
Commit: 55057452e20b0c253041231d988166c3b485744d
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 23:12:02 +0200
Commit message:

 Merge branch 'master' of github.com:sneumann/mzR
 
Package: mzR
Commit: 38c8544318263a84b9876c2ec4af1bd712ead50c
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-09-13 23:11:52 +0200
Commit message:

 specParams returns numeric scan.number.s.
 
Package: mzR
Commit: d00e3cace0e4dd1721f6dc515e9f213c966f7789
Author: sneumann <sneumann@ipb-halle.de>
Date: 2018-09-13 14:02:39 +0200
Commit message:

 Merge pull request #179 from sneumann/featureRemovelibnetCDF

Feature removelibnet cdf 
Package: mzR
Commit: 523282dbcc0fb617522b445df14a9d912340b942
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2018-09-12 08:47:30 +0200
Commit message:

 Bump version. Merged changes close #178
 
Package: mzR
Commit: 87f92cbc09c1d6730a6c880ca139f67339df0506
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2018-09-11 17:54:45 +0200
Commit message:

 Remove leftover static netCDF for windows
 
Package: mzR
Commit: 187568290d8671cc181666858adf7a418ba5316d
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2018-09-11 17:27:38 +0200
Commit message:

 Add runinfo and instrumentinfo to test_cdf
 
Package: mzR
Commit: dfbd825f35f1c66cf69c980662a6bc3b02413f4b
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2018-09-10 10:41:50 +0200
Commit message:

 Removed netCDF.h, can already be used by xcmsRaw
 
Package: HiCcompare
Commit: abe677b6bd4b2aae559487190439d60f338935c9
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2018-09-13 16:43:36 -0400
Commit message:

 add warning for inter-chr interactions
 
Package: HiCcompare
Commit: cc2181e57af12795059bf89fb570d1ce0614a68f
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2018-09-13 16:19:19 -0400
Commit message:

 add cluster example to vignette
 
Package: BiocOncoTK
Commit: 84c7716d48ba9cf48dbd44d2198ef09684cd8812
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-09-13 16:33:39 -0400
Commit message:

 add option to exclude mss from bindMSI
 
Package: sesame
Commit: e9d5fb3d1f2c00629def03398b012381021eae15
Author: zwdzwd <zhouwanding@gmail.com>
Date: 2018-09-13 16:22:06 -0400
Commit message:

 version bump 0.99.5
 
Package: sesame
Commit: f1e2cde9af43033b6b194ffd8775a5ea359f8815
Author: zwdzwd <zhouwanding@gmail.com>
Date: 2018-09-13 13:08:41 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: sesame
Commit: 2a23fdc6ec3dcd0783ea92adb30967695af73cc6
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-09-10 18:30:03 -0400
Commit message:

 minor, message omitted
 
Package: sesame
Commit: 2d26aad382b95cf04c2d9ef19bb1b51f22292412
Author: Wanding Zhou - Bioinformatics <zhouwanding@gmail.com>
Date: 2018-08-30 17:18:15 -0400
Commit message:

 Merge pull request #4 from ttriche/patch-1

fix sesamize 
Package: sesame
Commit: 321e9e77f4e2c445bf81bcae361db96d4ba31d7b
Author: Tim Triche, Jr <tim.triche@gmail.com>
Date: 2018-08-30 17:16:08 -0400
Commit message:

 fix sesamize 

this was driving me insane 
Package: sesame
Commit: bc6b3eea7690f33d120ffd76cf13f18aa65b264e
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-08-06 14:52:38 -0400
Commit message:

 minor, message omitted
 
Package: sesame
Commit: 07f2cb30b4ba6980652be7e9534fafb2e2ebfd58
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-08-04 09:59:41 -0400
Commit message:

 added parameters to opensesame
 
Package: sesame
Commit: c8d664ad6da378cc6c0fc51f17899cf8a433f0a8
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-08-02 16:53:16 -0400
Commit message:

 document regeneration
 
Package: sesame
Commit: 577023386ac83de61f27442ca573f45720106aa5
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-08-01 23:29:47 -0400
Commit message:

 update to openSesame and sesamize, incorporate Tim's code
 
Package: sesame
Commit: 4ca1319dd1d7656d786645e4664445d8b6b6bfe2
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-07-17 21:30:17 -0400
Commit message:

 minor, message omitted
 
Package: sesame
Commit: 9cd2a699e3264d6b8fc61707074d1bd382d2edaa
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-07-17 21:30:04 -0400
Commit message:

 openSeSAMe pipeline
 
Package: sesame
Commit: 35e094fa6e5ba5d2999a0393243e9058b40d6eef
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-06-12 14:56:55 -0400
Commit message:

 exported getNormCtls
 
Package: sesame
Commit: 84eeb09c05a7aeb6e70bcebcff52759cffe399f5
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-06-11 22:01:10 -0400
Commit message:

 Merge branch 'ttriche-master'
 
Package: sesame
Commit: 67fef74187d0d0f0d73b8631f054bcc249f290ed
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-06-11 22:00:52 -0400
Commit message:

 minor fix to stop message
 
Package: sesame
Commit: 3f6f9c24917be61d26118dcf995dd21df2c0f0a4
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-06-11 22:00:00 -0400
Commit message:

 fix to sapply usage, plugged in searchIDATprefixes to SigSetListFromIDATs, added \value etc.
 
Package: sesame
Commit: ed926929fc9d961d4b6a50d9041de3592d4e4e64
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-10 14:50:36 -0400
Commit message:

 fix formatting in `show` method for SigSetList
 
Package: sesame
Commit: 6c3e14220197dd4d22684926d55a9fa6923734dc
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-10 14:46:33 -0400
Commit message:

 refactor SigSetListFrom* to take a list of IDAT stubs
 
Package: sesame
Commit: 63d730088af94fe67c19937fc0f0023bd330fa49
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-09 19:12:05 -0400
Commit message:

 be more selective about importing methods from S4Vectors
 
Package: sesame
Commit: 30ff1bf653e508d546670ac2626a4a0b1946707b
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-09 19:08:47 -0400
Commit message:

 let the user know how long a load is likely to take
 
Package: sesame
Commit: 649fb476e4ceb7dc0f90dc2265f5dc960d37b54f
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-09 19:05:33 -0400
Commit message:

 cleanup SigSetListFromPath
 
Package: sesame
Commit: 8428dedc4bae52148c7876039998c5234b4d140f
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-09 18:32:51 -0400
Commit message:

 more SigSetList cleanup, and some progress messages
 
Package: sesame
Commit: 52fb020689e881e75a458584eb8949cbdac62b3e
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-09 18:28:25 -0400
Commit message:

 more SigSetList cleanup
 
Package: sesame
Commit: d83f7bbdad5f02455a87c3efb28d1391e87da564
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-09 18:14:01 -0400
Commit message:

 derrrrrrp... left some old cruft in SigSetList `show` method
 
Package: sesame
Commit: ef391c3a6e6ab7d642ca049bd1f18d6c4b23ec94
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-09 18:11:35 -0400
Commit message:

 debuggina and slimming down SigSetList
 
Package: sesame
Commit: ffa90cd3e1e3a7baf2efaad42369f991822c36d9
Author: ttriche <tim.triche@gmail.com>
Date: 2018-06-09 18:03:58 -0400
Commit message:

 add SigSetList class
 
Package: sesame
Commit: 9f66eaf79a4600baff3b21058147c2961efa1910
Author: Tim Triche, Jr <tim.triche@gmail.com>
Date: 2018-06-09 17:14:12 -0400
Commit message:

 Merge pull request #1 from zwdzwd/master

load gzipped IDAT 
Package: sesame
Commit: e77935e175c36cee4f9c87daa58ac12f6a4780d6
Author: Wanding Zhou <wanding.zhou@vai.org>
Date: 2018-06-09 17:08:36 -0400
Commit message:

 load gzipped IDAT
 
Package: sesame
Commit: 41ace372ce8fcf1fc4b326d17c1aad6831b92302
Author: Wanding Zhou - Bioinformatics <zhouwanding@gmail.com>
Date: 2018-06-09 13:27:40 -0400
Commit message:

 Merge pull request #2 from ttriche/patch-2

Begin cleanup of vignette 
Package: sesame
Commit: ab310bfdf7cc664f932f09c41cee2bf11cba3ca7
Author: Tim Triche, Jr <tim.triche@gmail.com>
Date: 2018-06-08 15:14:14 -0400
Commit message:

 Begin cleanup of vignette

Great vignette -- almost too complete!  Just some minor copy editing 
Package: BiocParallel
Commit: 13c2187c2569ebbbe8a3853cd8bc8853c18923f9
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-09-13 16:07:07 -0400
Commit message:

 implement bpexportglobals()

- export options() to workers
- default TRUE
 
Package: DelayedArray
Commit: 643acc55cae3ab9d04b66c80b8e86b5d34f1ce8c
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-13 10:22:55 -0700
Commit message:

 Add bplapply2()

bplapply2() is a simple wrapper to BiocParallel::bplapply() that
propagates base::.Options to the workers. Not exported because
DelayedArray is obviously the wrong place for this (a better place
would be in BiocParallel).
 
Package: DelayedArray
Commit: c1d49e7247ea7ea2be12d541cd33bd5533d2bedb
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-13 09:46:49 -0700
Commit message:

 Disable feature implemented in last 2 commits

No more in-house mechanism for automatic propagation of DelayedArray
user-controlled global options to workers (fails on some clusters).
DelayedArray options are stored again in base::.Options.
 
Package: logicFS
Commit: a98a2c782b2e08b7b06eb1dfbf71584c188923d3
Author: holgerschw <holger.schw@gmx.de>
Date: 2018-09-13 17:32:09 +0200
Commit message:

 Just testing
 
Package: DESeq2
Commit: 600c6c20fca6c2d54148bea17ac31c424ac69336
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-09-13 10:56:36 -0400
Commit message:

 add Wolfgangs linear model mu
 
Package: methylKit
Commit: e379aaa79779752fbdf66765f584dec563d32df4
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-09-13 15:46:47 +0200
Commit message:

 update NEWS and version bump to 1.7.8
 
Package: methylKit
Commit: aea7cc7069ccceadd179f92f4362123eaedaf803
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-09-13 15:43:34 +0200
Commit message:

 add tests for applyTbxByOverlap
 
Package: methylKit
Commit: d057cadac6a27438043d7e2c6b853e7bfeae432a
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-09-13 15:42:54 +0200
Commit message:

 fix for applyTbxByOverlap

Fixes https://github.com/al2na/methylKit/issues/131
 
Package: Pi
Commit: 2424b7236b9117c0e2b964e83f6c698135b3af47
Author: Hai Fang <hfang.shanghai@gmail.com>
Date: 2018-09-13 10:35:20 +0100
Commit message:

 Update to the version 1.9.3
 
Package: simpleSingleCell
Commit: a75668988ff7b4c03e90fa9adfc6ba9daa1565a7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 09:30:58 +0100
Commit message:

 Bumped version number, date.
 
Package: simpleSingleCell
Commit: dcf31ab53a0b9be6baf2abc3f75c1d68fe51f15e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 09:30:42 +0100
Commit message:

 Fixes to doublet workflow, added standard ending text.
 
Package: simpleSingleCell
Commit: e1ade84db7280d98c917d169561cde10a4f498fe
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-13 09:24:37 +0100
Commit message:

 Fixed ordering of index entries.
 
Package: ChAMP
Commit: a1e6cdc421cf74c6072dddf79d609617ecf3e422
Author: JoshuaTian <tianyuan1991hit@gmail.com>
Date: 2018-09-13 14:54:00 +0800
Commit message:

 Fixed bug in champ.CNA()
 
Package: ChAMP
Commit: be71ab8e85176526af2678ebb27bacda3ba4a179
Author: JoshuaTian <tianyuan1991hit@gmail.com>
Date: 2018-09-13 14:45:43 +0800
Commit message:

 Fixed bug in champ.CNA()
 
Package: DelayedArray
Commit: 625a795c6258c2ea91bccd38d4b2fedce12e3069
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-12 22:31:48 -0700
Commit message:

 Tweak to propagation of user-controlled global options to workers

Fail early and graciously if a worker fails to inherit DelayedArray
user-controlled global options (which will happen on a cluster where
the nodes don't have access to the tempdir() of the head).
 
Package: plotGrouper
Commit: 4eae95c5b7de8ef609f12a6a0fb247fc28d24735
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-12 19:49:45 -0700
Commit message:

 Merge pull request #69 from jdgagnon/develop

fix typo in DESCRIPTION 
Package: plotGrouper
Commit: a3ea9117f5ff934ed712ccf4cb7f1a469a56cf32
Author: jdgagnon <jgagnon@vpn-10-48-1-102.ucsf.edu>
Date: 2018-09-12 19:49:11 -0700
Commit message:

 fix typo in DESCRIPTION
 
Package: plotGrouper
Commit: 147ee1709c254d2a6774db1c234d0f5d243c216f
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-11 13:18:20 -0700
Commit message:

 Merge pull request #68 from jdgagnon/develop

Fix README 
Package: plotGrouper
Commit: 32b16fd13919232663d6e20fe71f10f21ee880ed
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-11 13:17:53 -0700
Commit message:

 Fix README
 
Package: plotGrouper
Commit: c03d8ca84a5bdb4509cce8539184f02238bebebb
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-11 12:46:20 -0700
Commit message:

 Merge pull request #67 from jdgagnon/develop

Update vignette/README & version bump 
Package: plotGrouper
Commit: cb4d0ee221d9186f69b1adb14fc0347eca480ea5
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-11 12:45:13 -0700
Commit message:

 Update vignette/README & version bump
 
Package: plotGrouper
Commit: f4cf5f3965ecc54b9557e7581429a97108a4da66
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-11 12:05:22 -0700
Commit message:

 Merge pull request #66 from jdgagnon/develop

Merge pull request #65 from jdgagnon/master 
Package: plotGrouper
Commit: 45ab87fa3d87664c67fc9d43613a1b1df17651f2
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-11 12:05:04 -0700
Commit message:

 Merge pull request #65 from jdgagnon/master

pull from master 
Package: plotGrouper
Commit: dd88ac87d833a29619bcfbfdfcc670af6361092c
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-11 12:03:48 -0700
Commit message:

 Update README
 
Package: plotGrouper
Commit: de6edf1f0c60d07a9fba29cf8a52ba0e65385d33
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-11 09:06:07 -0700
Commit message:

 Merge pull request #63 from jdgagnon/develop

Add build info from Bioconductor to README 
Package: plotGrouper
Commit: c9ced34d2eaf5351999cab4d409322759ddb5631
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-11 08:59:56 -0700
Commit message:

 Add build info from Bioconductor to README
 
Package: plotGrouper
Commit: 4e45a9c45b4965ebe8e2e7b5cbb7ff2e203e9374
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-10 21:01:28 -0700
Commit message:

 Merge pull request #62 from jdgagnon/develop

Develop 
Package: plotGrouper
Commit: 6d71b57099e7dba002a9289dd38a1af54e1e2771
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-10 21:00:55 -0700
Commit message:

 version bump
 
Package: plotGrouper
Commit: 427bad547bb19f7e96278ce3cae2d38d5b7238be
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-10 20:59:26 -0700
Commit message:

 improve look of log transformations
 
Package: plotGrouper
Commit: e7b9eb30e670b0212723094370332ec2b5d7f49d
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-10 20:59:05 -0700
Commit message:

 Add bioconductor build info to README
 
Package: plotGrouper
Commit: d7cf2f0fe7e6e707ce019d3b15b3b231bd442895
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-10 10:40:34 -0700
Commit message:

 Merge pull request #61 from jdgagnon/develop

fix non-ascii quotes in readme file 
Package: plotGrouper
Commit: 55e16d536efe782ab9f63e0f78bad194c90aecf2
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-10 10:40:07 -0700
Commit message:

 fix non-ascii quotes in readme file
 
Package: plotGrouper
Commit: e16a7120dcf9057b7e926f038a1fd050843eedd1
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-09 21:53:04 -0700
Commit message:

 Merge pull request #60 from jdgagnon/develop

updated sessionInfo() 
Package: plotGrouper
Commit: b2dcb15414d230d135f6d03b0d55713840c7c244
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-09 21:48:10 -0700
Commit message:

 updated sessionInfo()
 
Package: plotGrouper
Commit: d7d7ad1df92951f286e5ea0a60e57f8ffe9907d4
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-09 12:55:55 -0700
Commit message:

 Merge pull request #59 from jdgagnon/develop

Version bump 
Package: plotGrouper
Commit: 118ca7fae2498edd5dd52fca84307da975e85a7a
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-09 12:55:24 -0700
Commit message:

 Version bump
 
Package: plotGrouper
Commit: 43ef35b55dc24ede9e78eed678fca7de00cec463
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-09 11:06:19 -0700
Commit message:

 Merge pull request #58 from jdgagnon/develop

Use png with transparency for GitHub page. 
Package: plotGrouper
Commit: 8c5cb47c414721b57c330133707b644e0e5877e2
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-09 11:04:53 -0700
Commit message:

 Use png with transparency for GitHub page.
 
Package: plotGrouper
Commit: 18a5c4ac5ea3fb5469bfff31fccf76c269c66e75
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-07 12:30:13 -0700
Commit message:

 Merge branch 'master' of https://github.com/jdgagnon/plotGrouper
 
Package: plotGrouper
Commit: 419fa7aee55943d6a65d9c4c306ed9803e49a188
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-07 12:29:54 -0700
Commit message:

 Cleanup master
 
Package: plotGrouper
Commit: acb7a3130c2b89e3e1b75fe0638b41ac3221cb4e
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-07 12:25:51 -0700
Commit message:

 Merge pull request #57 from jdgagnon/develop

allow Rproj on github 
Package: plotGrouper
Commit: 7185636f9d99ecb5cc7777b5ec86a9fb045d868b
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-07 12:24:01 -0700
Commit message:

 allow Rproj on github
 
Package: plotGrouper
Commit: d69bb2a75184372f31cf15184cdc4f9f534f87a0
Author: John Gagnon <john.gagnon.42@gmail.com>
Date: 2018-09-07 12:18:16 -0700
Commit message:

 Merge pull request #56 from jdgagnon/develop

Develop 
Package: plotGrouper
Commit: 2b9cff991ce0e070d6406d4cf08e00b825ab4dc1
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-07 12:17:50 -0700
Commit message:

 Fix README logo
 
Package: plotGrouper
Commit: 3dc28c091fbe85dc9fb14f4f6985266dea07fc95
Author: jdgagnon <jgagnon@Johns-MacBook-Pro-3.local>
Date: 2018-09-07 12:16:43 -0700
Commit message:

 Fix logo in readme
 
Package: DelayedArray
Commit: 31cc4290fdd72acd1d9de796cbda4df16b43211e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-12 16:18:18 -0700
Commit message:

 Workers now inherit DelayedArray user-controlled global options

In the context of BiocParallel::bplapply() and family, workers now inherit
the user-controlled options defined on the master. Workers can also modify
the inherited options or define new user-controlled options but this does
not affect the options defined on the master (one-way communication).
This mechanism works with nested levels of parallelization i.e. if workers
start subworkers and so on.
 
Package: flowWorkspace
Commit: b5745306a5113db947071bc0afca9bab5d5e6dfe
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-12 15:31:15 -0700
Commit message:

 Merge branch 'trunk' into devel
 
Package: flowWorkspace
Commit: ae7097d307dea6480182dbf3b5d1c372c87eb46f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-12 15:30:47 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: 7a8527e8c34e601b5b5983df883ce5d781f15156
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-12 15:10:50 -0700
Commit message:

 fix typo. #242
 
Package: debrowser
Commit: f5aa3b5442b360a6c3ce02c16e4fff4840a2931c
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2018-09-12 18:14:57 -0400
Commit message:

 Merge branch 'RELEASE_3_7'
 
Package: debrowser
Commit: b8da70c0a78104e950ff29e7914f25ac3ae81479
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2018-09-12 18:13:08 -0400
Commit message:

 Bug fixes
 
Package: methylKit
Commit: 77aa6c7acf9845c869fa60ce7b34b7252dd50113
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-09-12 23:14:36 +0200
Commit message:

 update NEWS and version bump to 1.7.7
 
Package: methylKit
Commit: dcac7ee0d34a95bb0809b68cb3fdbb7f32770560
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-07-17 17:53:41 +0200
Commit message:

 omit .checkTabixFileExists for destranding
 
Package: methylKit
Commit: aee5da5712746ccd88b914d042ded29c38276683
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-06-18 10:54:16 +0200
Commit message:

 update NEWS and version bump
 
Package: methylKit
Commit: 46833e3e8abc352106c6841a21cab6cbff5e16ee
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-06-18 10:35:15 +0200
Commit message:

 update documentation
 
Package: methylKit
Commit: 14fc0281054613abeee91258c958c926a49f6692
Author: Alexander Gosdschan <alexg9010@users.noreply.github.com>
Date: 2018-06-16 11:29:16 +0200
Commit message:

 Update methSeg.R

Remove duplicate check for sample size. 
Package: methylKit
Commit: 6a4dc7d3f336967d2f0ed5964a7efe94a09e1a25
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-06-14 18:06:17 +0200
Commit message:

 Updates to @katwre pull request:
- changed parameter name from `estimate.params.density` to `initialize.on.subset`
- allow for values higher than 1, which directly yields number of samples
- priorize Mclust argument `initialization`
- check for to few samples, 9 seems to be the magic number
- add tests
 
Package: methylKit
Commit: d84a677f2e120e699affb5b38b4eb27d66544561
Author: Kasia Wreczycka <katarzyna.wreczycka@mdc-berlin.de>
Date: 2018-06-14 13:17:50 +0200
Commit message:

 fix previous commit
 
Package: methylKit
Commit: 17bfae99df33b9e9156c628b787bd96949dd4add
Author: Kasia Wreczycka <katarzyna.wreczycka@mdc-berlin.de>
Date: 2018-06-14 12:48:21 +0200
Commit message:

 remove if clause
 
Package: methylKit
Commit: d87f446e47c22800c7267d748312040b2ab9ef79
Author: Katarzyna Wreczycka <katwre@gmail.com>
Date: 2018-06-13 16:51:58 +0200
Commit message:

 added estimate.params.density param to methSeg
 
Package: MultiAssayExperiment
Commit: 1556af77e4c06abae42c8f8673be2b267c277e46
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-12 17:35:32 -0400
Commit message:

 update c method to allow MultiAssayExperiment concat, add tests
 
Package: MultiAssayExperiment
Commit: c9bbe7272ec1e51797752a887a513cc0210dc415
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-12 17:34:35 -0400
Commit message:

 bug fix: use a named vector when merging replicates
 
Package: MultiAssayExperiment
Commit: 536db3c7c2ea89f7a3e85f1352e623546f2081b3
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-12 17:33:19 -0400
Commit message:

 update format, remove unchanged metadata from replaceSlots
 
Package: MultiAssayExperiment
Commit: 7f32e967bf7a293ebbdeb931daba59b5207a968a
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-10 20:51:36 -0400
Commit message:

 update wercker.yml file again
 
Package: MultiAssayExperiment
Commit: f2c7aa86413d5a84919eb2c5eb5c46b44505c7e6
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-10 20:46:04 -0400
Commit message:

 update wercker.yml file
 
Package: MultiAssayExperiment
Commit: 94eee7859da597ddb7cb6faf5aac0c4ad61591a1
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-10 18:06:35 -0400
Commit message:

 Merge branch 'master' of github.com:waldronlab/MultiAssayExperiment
 
Package: MultiAssayExperiment
Commit: cdd69545bab74c36dd2488089af9d6f57cc570f0
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-09-10 18:05:52 -0400
Commit message:

 bug fix: avoid Inf by using min on TRUEs, closes #249
 
Package: ORFik
Commit: e762b10e58746f210d9bb10340c068646c1a0e89
Author: Kornel Labun <kornellabun@gmail.com>
Date: 2018-09-12 18:50:29 +0200
Commit message:

 Merge pull request #55 from JokingHero/orfScannerUpdate2

Orf scanner update2 
Package: ORFik
Commit: 45f1f13e9f334887eef3c1bc4ca1d56bdd540034
Author: Kornel Labun <kornellabun@gmail.com>
Date: 2018-09-12 18:50:11 +0200
Commit message:

 Fix description 
Package: ORFik
Commit: 05d68446822b350d98d8c773501a2f276b6a36a9
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2018-09-12 18:30:17 +0200
Commit message:

 version bump
 
Package: ORFik
Commit: 9b7468152f699c24d61bb3f23a806c034bfe1385
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2018-09-12 18:26:10 +0200
Commit message:

 added more docs, some logic fixup on orfScanner
 
Package: DelayedArray
Commit: e4534a7c0ffdc5d738958b706b6617d0f7859c6a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-09-12 08:39:19 -0700
Commit message:

 Add TODO for "is_sparse" method for DelayedUnaryIsoOpWithArgs objects
 
Package: DMRcaller
Commit: 0744d4ec2d136df04a873b0fcbf07f9282c8946c
Author: nrzabet <n.r.zabet@gen.cam.ac.uk>
Date: 2018-09-12 15:39:05 +0100
Commit message:

 bug fix
 
Package: DMRcaller
Commit: e6585817fc7493fc7c95c0a99a6ee2593dcc843c
Author: nrzabet <n.r.zabet@gen.cam.ac.uk>
Date: 2018-09-12 15:36:17 +0100
Commit message:

 bug fix
 

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