Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

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

This list is also available as an RSS feed (master branch), and RSS feed (release branch)

Package: biobroom
Commit: 8981fd5d7c3a337080e3a144d734cf347522cba2
Author: Andrew Bass <ajbass@princeton.edu>
Date: 2018-01-22 22:29:23
Commit message:

 updated testthat
 
Package: flowWorkspace
Commit: a39046cd80d1708bf2082d2f484b70bd517e592d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-01-22 21:16:37
Commit message:

 Merge branch 'trunk' into devel
 
Package: flowWorkspace
Commit: 7143b34990bbc2e4e8c5b1eb7360ea0aba45d7d0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-01-22 21:16:14
Commit message:

 bump
 
Package: flowWorkspace
Commit: c41a38065dc7b8641222cb1fd11f829a6baac741
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-01-22 21:05:18
Commit message:

 throw error when character expression passed to booleanFilter constructor to avoid confusion
 
Package: ATACseqQC
Commit: 9a69bb60b75e7574374de3c6824175cd0e0d8560
Author: Jianhong Ou <jianhongou@dhcp-152-16-223-142.research.duhs.duke.edu>
Date: 2018-01-22 21:01:13
Commit message:

 fix the conflict part in help document.
 
Package: ATACseqQC
Commit: 512158e75a85f84a2a04d38ec4c4e6d178ff1e87
Author: Jianhong Ou <jianhongou@dhcp-152-16-223-142.research.duhs.duke.edu>
Date: 2018-01-22 20:59:56
Commit message:

 remove the conflict parts.
 
Package: ATACseqQC
Commit: 174f05747394f9b1dcc16d2a1dd126b4946e98a9
Author: Jianhong Ou <jianhongou@dhcp-152-16-223-142.research.duhs.duke.edu>
Date: 2018-01-22 20:57:44
Commit message:

 merge the change from upstream

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

# Conflicts:
#	R/readBamFile.R
#	man/readBamFile.Rd
 
Package: ATACseqQC
Commit: 3508a6ad6c456c7bf5ca2b1c38e2ab40ac22cd96
Author: Jianhong Ou <jianhongou@dhcp-152-16-223-142.research.duhs.duke.edu>
Date: 2018-01-22 20:54:15
Commit message:

 fix the missing links in documentation.
 
Package: GenomicTuples
Commit: 8eee9fb33922e72fcaae4f7a8ac2bbdcfd20c44d
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-01-22 20:42:26
Commit message:

 Merge upstream

Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
#	man/GTuples-class.Rd
#	man/GTuples-comparison.Rd
#	man/findOverlaps-methods.Rd
 
Package: GenomicTuples
Commit: 96de4cc3d156fa8bdb85cef97b303c0d008af7a7
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-01-22 20:18:49
Commit message:

 Minor edit to trigger Travis
 
Package: GenomicTuples
Commit: 31b4001e3f335a3f11709e8f25cf98c74f04c6bb
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-01-22 20:02:51
Commit message:

 - Follow recent changes in IRanges
- Tidy up man pages
- Update min. version of dependencies
- Import all of 'methods' to simplify NAMESPACE
 
Package: apeglm
Commit: 7453afccac06742f5ddf3a20c0275a2d5e1b9df9
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-22 20:16:49
Commit message:

 use log1p
 
Package: apeglm
Commit: 1dd5505573d1250369a8dab6045b98da4f38ccda
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-22 20:13:06
Commit message:

 update docs
 
Package: BASiCS
Commit: ae2330446d9e277e97f8ab86c159dc3dd0544af7
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2018-01-22 19:24:22
Commit message:

 version 1.1.31: (2018-01-22)
- Updated documentation for `BASiCS_showFit` method
 
Package: BASiCS
Commit: 03466de66aa059cb1e8b8820e3e69a4c8c718197
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2018-01-22 18:46:38
Commit message:

 version 1.1.30: (2018-01-22)
- Commit to triger a new built
 
Package: BASiCS
Commit: 5d25c6882bae53411abc4a7417c312a68fb37391
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-21 16:41:44
Commit message:

 Merge branch 'Devel'
 
Package: BASiCS
Commit: e4e3750b6beffbc9ef09f3cf5514ddf4e2548329
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-21 16:40:37
Commit message:

 version 1.1.29: (2017-12-21)
- `showFit` generic renamed as `BASiCS_showFit` (to avoids potential conflicts)
 
Package: BASiCS
Commit: e214f19525bf67f940db95413c2f04eac61d1b84
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-20 15:40:16
Commit message:

 version 1.1.28: (2017-12-20)
- Vignette header as in BiocStyle
- In `BASiCS_TestDE` function: `ProbThresholdE` argument renamed as `ProbThresholdR`
- In `BASiCS_TestDE` function: `ProbThresholdE` argument renamed as `ProbThresholdR`
- Updated documentation for example `BASiCS_Chain` objects
- Minor additional changes to the documentation
 
Package: BASiCS
Commit: ec8f1187ee7ccdf3aa4a87d0f07b635f63e1fb3c
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-20 14:11:52
Commit message:

 version 1.1.27: (2017-12-20)
- Minor typo resolved in `displayChainBASiCS` method
- Reduced size of example objects
- Unit tests updated accordingly
- In `BASiCS_TestDE` function: `PsiE` argument renamed as `EpsilonR`
 
Package: BASiCS
Commit: 29233a3ac7d17431157747bdb01ede6daf6bcb5d
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-20 01:39:46
Commit message:

 version 1.1.26: (2017-12-20)
- Vignette bibliography moved to .bib file
- Added diagram to summarise different implementations
- Reduced size of example objects
- Unit tests updated accordingly
- `subset` method created for `BASiCS_Chain` objects
- Removal of parameter `lambda` from `BASiCS_Chain` objects (for storage)
- R/Methods.R + R/Classes.R updated accordingly
- `newBASiCS_Chain` updated accordingly.
- Code format for `showFit`
 
Package: BASiCS
Commit: 04c279f5d7216ef213788baa2b5cb58402772dfd
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-19 18:59:45
Commit message:

 version 1.1.25: (2017-12-19)
- Vignette bibliography moved to .bib file
- Added diagram to summarise different implementations
- Reduced size of example objects
- `subset` method created for `BASiCS_Chain` objects
 
Package: BASiCS
Commit: f19aadb8a20e03d24d800502da00c5f730fc6980
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-19 00:21:50
Commit message:

 version 1.1.24: (2017-12-18) - WIP
- Reduced no of iterations in unit test for quicker testing
- library `hexbin` added to imports (required for `showFit`)
- Vignette edits (simplification of Quick Start)
 
Package: BASiCS
Commit: 653b8589cea1f9efdf1b2b219d6352995bdf75b4
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-19 00:20:34
Commit message:

 version 1.1.24: (2017-12-18) - WIP
- Reduced no of iterations in unit test for quicker testing
- library `hexbin` added to imports (required for `showFit`)
- Default value set for `Tech` in `newBASiCS_Data` function
- Vignette edits (simplification of Quick Start)
 
Package: BASiCS
Commit: 1674021d3540d37ec81a21ff20cdd52e03f73aab
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-18 19:26:55
Commit message:

 version 1.1.24: (2017-12-18) - WIP
- Reduced no of iterations in unit test for quicker testing
- library `hexbin` added to imports (required for `showFit`)
- Vignette edits
 
Package: BASiCS
Commit: c9bb2f655a97c1aac0f76d328fa54ea6c876d964
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-18 18:27:31
Commit message:

 version 1.1.24: (2017-12-18)
- Reduced no of iterations in unit test for quicker testing
- library `hexbin` added to imports (required for `showFit`)
 
Package: BASiCS
Commit: b187040aa05cad4241f04985255abd891973bd45
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-18 15:14:45
Commit message:

 version 1.1.23: (2017-12-18)
- Minor improvements to documentation
 
Package: BASiCS
Commit: 77b26e793cee11b5f4ed7d58f38c5695bcec64d1
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-16 15:05:13
Commit message:

 Conflicts resolved
 
Package: BASiCS
Commit: 56dfde91d0aafbf797247f0f8694c5cf41098771
Author: nilseling <nils.eling@gmx.de>
Date: 2017-12-15 19:01:55
Commit message:

 Fixed annotation problems to pass R CMD check
 
Package: BASiCS
Commit: e594481adfd1d1340a0c3266c62d7da3be49b4d5
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-13 16:58:20
Commit message:

 version 1.1.21: (2017-12-13)
- `ConstrainProp` added as an optional argument for `BASiCS_MCMC` (no-spikes)
 
Package: BASiCS
Commit: 5e8ba8ba1c1fe9015c3919682d45fce0d8575aee
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-11 14:02:27
Commit message:

 version 1.1.20: (2017-12-11)
- Updated dpi option in vignette to reduce .html size
 
Package: BASiCS
Commit: dd996590c0989eec50d076e9486ddec9f84f7e6c
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-12-09 13:39:42
Commit message:

 Fixed typo in roxygen header
 
Package: BASiCS
Commit: d6e9a5a4565e7fe3bd75ab5e8a1804063dc7a554
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-12-09 13:31:23
Commit message:

 Deleted preliminary no-spike vignette
 
Package: BASiCS
Commit: 83a1c7d6ddcf60a6dc71fc1a852ce015ae5891aa
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-12-09 13:30:25
Commit message:

 Added new man pages for regression case and additional functions to plot Summary parameters
 
Package: BASiCS
Commit: 8c6b23d6ff2a84e1ae23311c6496ea219933a294
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-12-09 01:07:35
Commit message:

 Added extra files for regression part of vignette
 
Package: BASiCS
Commit: f520130659e92bcc23b696de62236dc572b7c830
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-08 10:06:32
Commit message:

 version 1.1.18: (2017-12-08)
- Minor typo in `HiddenBASiCS_MCMC_NoSpikesParam` resolved
 
Package: BASiCS
Commit: 29752f214ebc759da19728b021dc51d8af778322
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-12-07 23:37:32
Commit message:

 version 1.1.17: (2017-12-07)
- Stop scaling of size factors for no-spikes case (`HiddenBASiCS_MCMC_Start`)
- Unit testing updated accordingly
- Extra unit test to ensure that no-spikes results match for objects
with/without spikes when setting `WithSpikes = FALSE`
- Modified constrain for no-spikes cases (to deal with non-zero genes)
- Default value of `ConstrainType` set to 1 in `BASiCS_MCMC` (no-spikes only)
 
Package: BASiCS
Commit: 056ffb3c60998be9eb0eb628c21976e4b7ea3ba6
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-29 23:09:28
Commit message:

 version 1.1.16: (2017-11-29)
- Change in `BASiCS_MCMC` no-spikes so that only genes with zero total
counts are excluded from the identifiability constrain
 
Package: BASiCS
Commit: 3a212e395c39b2e8c41da18fce437cee0c35270d
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-29 09:14:58
Commit message:

 version 1.1.15: (2017-11-29)
- Typo fixed in `AtLeast2Cells` (`BASiCS_MCMC` function)ndefinition for
no-spikes + regression case when original data has spikes
 
Package: BASiCS
Commit: 761c52da63f6871c5272dfb815753ba755f1f89d
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-29 00:06:30
Commit message:

 version 1.1.14: (2017-11-29)
- Minor bug resolved for no-spikes case when original data has spikes
- New unit test to assess that case
 
Package: BASiCS
Commit: c6cd81b9634510a8110a5a1355e96cbab15d149b
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-28 12:06:57
Commit message:

 version 1.1.13: (2017-11-28)
- Fixed storage of `RefGene` in no-spikes when `StochasticRef = FALSE`
 
Package: BASiCS
Commit: 4aff17afab37a15764aa193d4bea393cfe4bd11f
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-28 10:47:03
Commit message:

 version 1.1.12: (2017-11-28)
- Additional changes to improve usage of no-spikes case
 
Package: BASiCS
Commit: 1a697c7c8955575ef66405baf4c40c4d988f04a0
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-27 15:02:10
Commit message:

 version 1.1.11: (2017-11-24)
- Minor typo in the call to `HiddenBASiCS_MCMCcppNoSpikes` has been resolved
 
Package: BASiCS
Commit: 8f8b4efb11cf6584f2c5e8c5244e98ad24bce8b7
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-27 14:47:09
Commit message:

 version 1.1.11: (2017-11-24)
- Minor typo in the call to `HiddenBASiCS_MCMCcppNoSpikes` has been resolved
 
Package: BASiCS
Commit: 6661a9ebfedd13a40f55d513af485e4301e9efdf
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-27 13:56:22
Commit message:

 version 1.1.10: (2017-11-27)
- `HiddenBASiCS_MCMC_Start` updated to remove regression-related hyper-params
- `HiddenBASiCS_MCMC_ExtraArgs` updated to include regression-related hyper-par
- `BASiCS_MCMC` modified accordingly
- Storage of adaptive variances fixed for the no-spike case
- Minor typo in the call to `HiddenBASiCS_MCMCcppNoSpikes` has been resolved
 
Package: BASiCS
Commit: 983edd1edbe192a06195ed20f9ed193a07402cbc
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-27 11:49:14
Commit message:

 Unused file removed
 
Package: BASiCS
Commit: d7c48edb5f1e74c664f4c9f391b460d3c18e0262
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-27 11:48:45
Commit message:

 version 1.1.10: (2017-11-27)
- `HiddenBASiCS_MCMC_Start` updated to remove regression-related hyper-params
- `HiddenBASiCS_MCMC_ExtraArgs` updated to include regression-related hyper-par
- `BASiCS_MCMC` modified accordingly
- Storage of adaptive variances fixed for the no-spike case
 
Package: BASiCS
Commit: 98a3af5086f4f5b2f39238b5d250b2a2719238c6
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-24 01:07:06
Commit message:

 version 1.1.9: (2017-11-24)
- `means` only updated when needed (regression case); unit test updated accordingly
- `deltaUpdateNoSpikes` + `deltaUpdateRegNoSpikes` removed as no longer required
- Simplification of terms in `deltaUpdateReg`
- Small changes to unify code format in C++ file
- Notation change: `phi` replaced by `s` in no-spikes implementation
- Unit test changed accordingly (no-spike)
- Minor style changes in `BASiCS_MCMC`
- `BASiCS_MCMC` function broken into smaller functions (easier to read). This
creates the following hidden functions: `HiddenBASiCS_MCMC_InputCheck`,
`HiddenBASiCS_MCMC_ExtraArgs`, `HiddenBASiCS_MCMC_NoSpikesParams`,
`HiddenBASiCS_MCMC_OutputStore` and `HiddenBASiCS_MCMC_RefFreqStore`
- Merge between no-spikes and regression case completed (code to be tested)
- Minor change in storage of reference frequency (no spikes only)
 
Package: BASiCS
Commit: 3c81280336fb64b14035ef14602f131835ccdd94
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-24 01:03:30
Commit message:

 version 1.1.9: (2017-11-24)
- `means` only updated when needed (regression case); unit test updated accordingly
- `deltaUpdateNoSpikes` + `deltaUpdateRegNoSpikes` removed as no longer required
- Simplification of terms in `deltaUpdateReg`
- Small changes to unify code format in C++ file
- Notation change: `phi` replaced by `s` in no-spikes implementation
- Unit test changed accordingly (no-spike)
- Minor style changes in `BASiCS_MCMC`
- `BASiCS_MCMC` function broken into smaller functions (easier to read). This
creates the following hidden functions: `HiddenBASiCS_MCMC_InputCheck`,
`HiddenBASiCS_MCMC_ExtraArgs`, `HiddenBASiCS_MCMC_NoSpikesParams`,
`HiddenBASiCS_MCMC_OutputStore` and `HiddenBASiCS_MCMC_RefFreqStore`
- Merge between no-spikes and regression case completed (code to be tested)
 
Package: BASiCS
Commit: bf3f572e079973d5254a1fffb17342f60c6323c3
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-23 19:01:15
Commit message:

 version 1.1.9: (2017-11-23) - WIP
- `means` only updated when needed (regression case); unit test updated accordingly
- `deltaUpdateNoSpikes` + `deltaUpdateRegNoSpikes` removed as no longer required
- Simplification of terms in `deltaUpdateReg`
- Small changes to unify code format in C++ file
- Notation change: `phi` replaced by `s` in no-spikes implementation
- Unit test changed accordingly (no-spike)
- Minor style changes in `BASiCS_MCMC`
- `BASiCS_MCMC` function broken into smaller functions (easier to read). This
creates the following hidden functions: `HiddenBASiCS_MCMC_InputCheck`,
`HiddenBASiCS_MCMC_ExtraArgs`
 
Package: BASiCS
Commit: af0d1a965f292f36d33478cdd1b84a24c8c3f27a
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-23 16:52:36
Commit message:

 version 1.1.9: (2017-11-23) - WIP
- `means` only updated when needed (regression case); unit test updated accordingly
- `deltaUpdateNoSpikes` + `deltaUpdateRegNoSpikes` removed as no longer required
- Simplification of terms in `deltaUpdateReg`
- Small changes to unify code format in C++ file
- Notation change: `phi` replaced by `s` in no-spikes implementation
- Unit test changed accordingly (no-spike)
- Minor style changes in `BASiCS_MCMC`
- `BASiCS_MCMC` function broken into smaller functions (easier to read). This
creates the following hidden functions: `HiddenBASiCS_MCMC_InputCheck`,
`HiddenBASiCS_MCMC_ExtraArgs`
 
Package: BASiCS
Commit: 0c5d50dbe9348bb151d9af2e2bd8c7ef14b14822
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-23 16:00:13
Commit message:

 version 1.1.9: (2017-11-23) - WIP
- `means` only updated when needed (regression case); unit test updated accordingly
- `deltaUpdateNoSpikes` + `deltaUpdateRegNoSpikes` removed as no longer required
- Simplification of terms in `deltaUpdateReg`
- Small changes to unify code format in C++ file
- Notation change: `phi` replaced by `s` in no-spikes implementation
- Unit test changed accordingly (no-spike)
- Minor style changes in `BASiCS_MCMC`
- `BASiCS_MCMC` function broken into smaller functions (easier to read). This
creates the following hidden functions: `HiddenBASiCS_MCMC_InputCheck`
 
Package: BASiCS
Commit: b6924cbc3af0db92ad7a9ccbbce6759b1bb4cc85
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-23 15:28:58
Commit message:

 version 1.1.9: (2017-11-23) - WIP
- `means` only updated when needed (regression case); unit test updated accordingly
- `deltaUpdateNoSpikes` + `deltaUpdateRegNoSpikes` removed as no longer required
- Simplification of terms in `deltaUpdateReg`
- Small changes to unify code format in C++ file
- Notation change: `phi` replaced by `s` in no-spikes implementation
- Unit test changed accordingly (no-spike)
 
Package: BASiCS
Commit: c8f0979227208a765614d27620a25df472c518d3
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-23 15:17:15
Commit message:

 version 1.1.9: (2017-11-23) - WIP
- `means` only updated when needed (regression case); unit test updated accordingly
- `deltaUpdateNoSpikes` + `deltaUpdateRegNoSpikes` removed as no longer required
- Simplification of terms in `deltaUpdateReg`
- Small changes to unify code format in C++ file
 
Package: BASiCS
Commit: cbb315a24696f2d5c58240c41fc9564a6fe76a96
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-22 18:09:19
Commit message:

 version 1.1.9: (2017-11-22) - WIP
- `means` only updated when needed (regression case); unit test updated accordingly
- `deltaUpdateNoSpikes` + `deltaUpdateRegNoSpikes` removed as no longer required
- Simplification of terms in `deltaUpdateReg`
 
Package: BASiCS
Commit: bc39b5672ec49249d0fbb937092beb2b5e785e3d
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-22 13:18:29
Commit message:

 version 1.1.9: (2017-11-22) - WIP
- `means` only updated when needed (regression case); unit test updated accordingly
 
Package: BASiCS
Commit: dfd99c156ffd12b67eb8892e6fca3138a0c780ec
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-21 23:48:20
Commit message:

 version 1.1.8: (2017-11-21)
- `muUpdateRegNoSpikes` and `deltaUpdateRegNoSpikes` added to C++ code
- Clean-up of C++ code (repeated debug checks made into function)
- `lambdaUpdateReg` created as a separate function
- Vectorization of calculations related to regression implementation
- Global quantities (e.g. inv(V0)) taken outside the look (regression case)
- `sigma2UpdateReg` created as a separate function
- `betaUpdateReg` created as a separate function
- Fixed typo in sigma2 updates (regression case); unit test updated accordingly
 
Package: BASiCS
Commit: cb5b432b564d737c71dca97112cb8c6893b22fb6
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-21 18:55:23
Commit message:

 version 1.1.8: (2017-11-20) WIP
- `muUpdateRegNoSpikes` and `deltaUpdateRegNoSpikes` added to C++ code
- Clean-up of C++ code (repeated debug checks made into function)
- `lambdaUpdateReg` created as a separate function
- Vectorization of calculations related to regression implementation
- Global quantities (e.g. inv(V0)) taken outside the look (regression case)
 
Package: BASiCS
Commit: ec8b070f3935a6e712f67744d182c0e0da1df967
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-21 00:59:59
Commit message:

 version 1.1.8: (2017-11-20)
- `muUpdateRegNoSpikes` and `deltaUpdateRegNoSpikes` added to C++ code
- Clean-up of C++ code (repeated debug checks made into function)
 
Package: BASiCS
Commit: cc83d62169761a1b922cb4baf02bf71310686b5d
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-20 23:03:39
Commit message:

 version 1.1.7: (2017-11-20)
- Nils added as author in cpp file
- Updated unit test for no-spikes case (changes due to change in stoch ref)
- Change in `BASiCS_MCMC` so that only biological counts go to C++
- Added factorizations in `muUpdateReg` and `deltaUpdateReg` (C++ code)
 
Package: BASiCS
Commit: 951e76ad8e2779efb658b9ccaf3a8a76e99a62f6
Author: nilseling <nils.eling@gmx.de>
Date: 2017-11-15 18:00:46
Commit message:

 Merge branch 'Devel' of https://github.com/catavallejos/BASiCS into Devel
 
Package: BASiCS
Commit: 68c764ed2322e8104e7b604b5ac11b2f096ce88d
Author: nilseling <nils.eling@gmx.de>
Date: 2017-11-15 18:00:20
Commit message:

 Added unit test for regression case
 
Package: BASiCS
Commit: 974b40dfdd952ce548d53bc6f87a3c9b21cde4f4
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-15 17:23:51
Commit message:

 version 1.1.6: (2017-11-15)
- Added prototype for regression + no-spikes sampler
 
Package: BASiCS
Commit: 710e4dc9b58c5e57aa9d47167df099b8e0cf9404
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-15 15:00:58
Commit message:

 version 1.1.5: (2017-11-15)
- Removal of collapsed sampler prototype (from C++ and R) - moved to
`CollapsedSampler` branch
- Number of genes used for stochastic reference increased to 10% of genes (no spikes only)
 
Package: BASiCS
Commit: 9ec944ffa6fc95eab8477f4fd99d19c131d9be19
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-15 14:57:00
Commit message:

 version 1.1.5: (2017-11-15)
- Removal of collapsed sampler prototype (from C++ and R) - moved to
`CollapsedSampler` branch
- Number of genes used for stochastic reference increased to 1000 (no spikes only)
 
Package: BASiCS
Commit: 4d104ece7c598bae2db65fd2fa65bd00234f754d
Author: nilseling <nils.eling@gmx.de>
Date: 2017-11-13 11:40:23
Commit message:

 Updated NEWS file
 
Package: BASiCS
Commit: c65125a0d34db9941863eaad8daa284e96bff9ba
Author: nilseling <nils.eling@gmx.de>
Date: 2017-11-13 11:38:29
Commit message:

 Corrected ordering of TableResDisp
 
Package: BASiCS
Commit: 32be77fbc4bb1fa1cef53000d9303dc963610976
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-11-13 00:24:03
Commit message:

 Reduced the epsilon test to genes that are expressed in 2 cells
 
Package: BASiCS
Commit: 7ce31267a82bf4b24a93a32292049fe64eea34fe
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-11-12 01:27:20
Commit message:

 Changed NA values in epsilon chain to 0 to allow EFDR and EFNR gridsearch
 
Package: BASiCS
Commit: f19dd8c2d8bfc9c75623f5b7c55ce96422a20ec3
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-10 08:15:32
Commit message:

 Debugging collapsed sampler
 
Package: BASiCS
Commit: 17f48da3a2f51ee211ba6661d2ec494e4d9a49a9
Author: nilseling <nils.eling@gmx.de>
Date: 2017-11-09 11:58:39
Commit message:

 Changed directionality of epsilon testing and fixed output
 
Package: BASiCS
Commit: b6c728896dc606dba9290573db4a123ea54c807f
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-08 18:47:36
Commit message:

 version 1.1.3: (2017-11-08)
- Collapsed sampler implemented (to be tested)
- Unit tests reverted to original case
- Version number bump
 
Package: BASiCS
Commit: d4caf45a47a741293be77c456f9d31dfddce8935
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-08 15:49:16
Commit message:

 Debug messages added
 
Package: BASiCS
Commit: 1983211046b200bebdfacdacb923174da23c48c8
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-08 15:31:21
Commit message:

 version 1.1.3: (2017-11-08)
- Collapsed sampler implemented (to be tested)
 
Package: BASiCS
Commit: 4e744b9140f94baf28196c496e9509f9dda33ef4
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-08 15:31:11
Commit message:

 version 1.1.3: (2017-11-08)
- Collapsed sampler implemented (to be tested)
 
Package: BASiCS
Commit: e1ed95cb534c9b6f3bf53dabb1107695c489ee3d
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-08 12:09:10
Commit message:

 version 1.1.2: (2017-11-08)
- Skeleton for sampler with integrated out s
 
Package: BASiCS
Commit: b91c55fd9fd7681422ba064a53bcb1c1b009c44d
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-08 11:03:05
Commit message:

 version 1.1.1: (2017-11-08)
- 'ggplot2' added to imports
- Default value for SpikeInfo changed to NULL in `newBASiCS_Data` function
- Cleaning of `HiddenBASiCS_MCMCcppNoSpikes`
- Cleaning of full conditionals for no-spikes implementation
- Fixed bug in stochastic reference implementation
- Added unit test for no-spikes case (estimation)
- Minor tyle changes to merge regression case
- 'Eta' parameter removed from `Summary` method (regression case only)
- Corrected HPD interval calculation for epsilon and sigma2 (regression case)
- Added mark for 'ExcludedFromRegression' genes in `BASiCS_TestDE`
 
Package: BASiCS
Commit: 1dea6914398608d4dcdbc39bbdebe3b891a8144f
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-08 11:00:01
Commit message:

 version 1.0.0: (2017-10-30)
- Bioconductor 3.6 release

version 1.1.0: (2017-10-30)
- Version number bump after bioconductor 3.6 release
 
Package: BASiCS
Commit: 74e24d1208f8b0232fee3968737526eb9a52013a
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2017-11-08 10:51:07
Commit message:

 Merge branch 'master' into Devel
 
Package: BASiCS
Commit: d1b16cdead0b68581014296d5ebb2eb4d565c2e8
Author: nilseling <nils.eling@gmx.de>
Date: 2017-11-07 17:04:10
Commit message:

 Added GeneSelect option to residual over-disp testing
 
Package: BASiCS
Commit: a97e813eae6e13fc280145dcfb15d1b61678a5b7
Author: nilseling <nils.eling@gmx.de>
Date: 2017-11-07 15:42:58
Commit message:

 Corrected HPD calculation for epsilon and sigma2
 
Package: BASiCS
Commit: 102a74c9a28a6472ff3723326c32f9397d6565f6
Author: nilseling <nils.eling@gmx.de>
Date: 2017-11-06 13:42:54
Commit message:

 Removed eta from Summary function
 
Package: BASiCS
Commit: f2bd72bdd5330d0f85d781529e6d335716ddbad3
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-27 19:10:55
Commit message:

 Devel changes (version number once merged with master)
- 'ggplot2' added to imports
- Default value for SpikeInfo changed to NULL in `newBASiCS_Data` function
- Cleaning of `HiddenBASiCS_MCMCcppNoSpikes`
- Cleaning of full conditionals for no-spikes implementation
- Fixed bug in stochastic reference implementation
- Added unit test for no-spikes case (estimation)
- Minor tyle changes to merge regression case
 
Package: BASiCS
Commit: d855c1750e17b7ec699a5b435d7ef682bbb677b7
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-27 09:00:23
Commit message:

 Devel changes (version number once merged with master)
- 'ggplot2' added to imports
- Default value for SpikeInfo changed to NULL in `newBASiCS_Data` function
- Cleaning of `HiddenBASiCS_MCMCcppNoSpikes`
- Cleaning of full conditionals for no-spikes implementation

To-do
- Add unit test for no-spikes case
- Check issue with stochastic ref
 
Package: BASiCS
Commit: 0f8c06cad997ab9a63ff0a20d0140377f4ea0484
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-26 21:53:18
Commit message:

 Devel changes (version number once merged with master)
- 'ggplot2' added to imports
- Default value for SpikeInfo changed to NULL in `newBASiCS_Data` function
- Cleaning of `HiddenBASiCS_MCMCcppNoSpikes`

To-do
- Add unit test for no-spikes case
- Check full conditionals for no-spikes case (replace the one for nu
by spikes case)
 
Package: BASiCS
Commit: 15a915142a25b848f69f45b6f4e82118b1c1895d
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-26 20:17:01
Commit message:

 Devel changes (version number once merged with master)
- 'ggplot2' added to imports
- Default value for SpikeInfo changed to NULL in `newBASiCS_Data` function
- Partial cleaning of no-spikes case (removed unused args)
 
Package: BASiCS
Commit: 3ccae6be6e5e932e285baebe9f6b1a9ad9aaf989
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-26 17:00:07
Commit message:

 Merge branch 'Devel' of https://github.com/catavallejos/BASiCS into Devel
 
Package: BASiCS
Commit: d1f184da1f47a9577118956d748155c6739293c0
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-26 16:59:41
Commit message:

 Changed SpikeInfo default to NULL
 
Package: BASiCS
Commit: 35aa6c43b25ffdba13f6ad1acfc016de4740fd88
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-26 16:51:41
Commit message:

 Merge branch 'master' into Devel
 
Package: BASiCS
Commit: 87736f247b97235cbde7a68c7914cdfe88a11250
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-23 13:09:35
Commit message:

 Added ggplot2
 
Package: BASiCS
Commit: 4a3c0d8b8d6555f102877b1f9797f010faca196f
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-17 10:14:10
Commit message:

 All conflics resolved after merge
 
Package: BASiCS
Commit: 5742e36d19dae244c5a9758eba228b69154f6ac9
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-17 10:11:47
Commit message:

 More conflicts resolved

Pending files:
#	R/HiddenBASiCS_MCMC_Start.R
 
Package: BASiCS
Commit: e41a88a60e7760eab60e4600b72c80889ed2d4e8
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-17 10:05:25
Commit message:

 More conflict resolving

Pending files:
#	R/HiddenBASiCS_MCMC_Start.R
#	R/Methods.R
 
Package: BASiCS
Commit: ca1fddbdc3a13699914e973de4b86af842d03a08
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-17 09:59:45
Commit message:

 conflicts partially resolved after merge

Pending files:

#	R/HiddenBASiCS_MCMC_Start.R
#	R/Methods.R
#	R/newBASiCS_Chain.R
#	man/BASiCS_Chain-methods.Rd
#	man/BASiCS_Chain.Rd
#	man/BASiCS_Summary.Rd
#	man/BASiCS_TestDE.Rd
#	man/newBASiCS_Chain.Rd
#	tests/testthat/test_parameter_estimation.R
#	tests/testthat/test_parameter_estimation_batch.R
#	vignettes/BASiCS_nospikes.Rmd
 
Package: BASiCS
Commit: c2383275e980196d33dff8b04381bae3dea7a7e3
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2017-10-17 09:39:56
Commit message:

 Merge branch 'master' into Devel

# Conflicts:
#	NAMESPACE
#	R/BASiCS_MCMC.R
#	R/BASiCS_TestDE.R
#	R/Classes.R
#	R/HiddenBASiCS_MCMC_Start.R
#	R/Methods.R
#	R/newBASiCS_Chain.R
#	man/BASiCS_Chain-methods.Rd
#	man/BASiCS_Chain.Rd
#	man/BASiCS_Summary.Rd
#	man/BASiCS_TestDE.Rd
#	man/newBASiCS_Chain.Rd
#	tests/testthat/test_parameter_estimation.R
#	tests/testthat/test_parameter_estimation_batch.R
#	vignettes/BASiCS_nospikes.Rmd
 
Package: BASiCS
Commit: 14dc11bb6758a00912f1812a0ca268805bc920d9
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-10-17 08:44:29
Commit message:

 Adjusted test reference values and debug
 
Package: BASiCS
Commit: b9520c817536ded33a325daf2256bddb59efa30f
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-10-16 15:01:35
Commit message:

 Bug fixes for checks
 
Package: BASiCS
Commit: a4d42a3e518c822a28afa02ee964883c3f246c3a
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-10-16 09:10:28
Commit message:

 New man files
 
Package: BASiCS
Commit: 7b53e56917f33a5ad2175c91371e369b42cdb0ca
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-10-16 09:08:37
Commit message:

 Updated annotation
 
Package: BASiCS
Commit: 4019b3f334a9af020f7702168b835de7f28ef494
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-10-16 08:55:16
Commit message:

 Added updateObject function
 
Package: BASiCS
Commit: 6c5afe401f1ea440771722fbaf4bd661866dea1c
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-10-16 08:26:16
Commit message:

 Added versioning
 
Package: BASiCS
Commit: 3007d734ff176c67c42fffc471ed32fd99ae71a1
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-10-12 22:13:01
Commit message:

 Commented out the code from vignette
 
Package: BASiCS
Commit: d582c0c3b2963861bdb0cbd972962d26e85eab6a
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 15:44:37
Commit message:

 Added new MCMC sampler for regression case
 
Package: BASiCS
Commit: 1ab866e76ac88b5188c9fb2d37b46b6a3fcb448c
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 15:40:33
Commit message:

 Added showFit function to exports
 
Package: BASiCS
Commit: 07921d1dc5a110c0584df0110bdb712fdcc613c6
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 15:34:28
Commit message:

 Added parameter attribute
 
Package: BASiCS
Commit: 6c262fb128e42187d4b169b447f4afaa6c45dcd7
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 15:28:37
Commit message:

 Added showFit function to visualize the regression trend
 
Package: BASiCS
Commit: b6a5ea2584c25651175aa2754945583a359c3ecb
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 15:24:30
Commit message:

 Added the parameters call due to changed chain class
 
Package: BASiCS
Commit: 27098aae29c82baab245fc43a9d38b020f24eff1
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 15:11:32
Commit message:

 Added parameters call due to changed Chain class
 
Package: BASiCS
Commit: 8fb369bd14aa6dff271ecb3cd45b10ed41db4117
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 15:04:18
Commit message:

 Added the parameters call due to changed Chain class
 
Package: BASiCS
Commit: e13852eba55bb7505802aac4c51373271fdde4f0
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 14:54:40
Commit message:

 Added differential residual dispersion testing
 
Package: BASiCS
Commit: 7ba1802aa15e1f85463286524493267bffc02e91
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 11:44:10
Commit message:

 Adjusted to new version of chain class
 
Package: BASiCS
Commit: 89b705e524c21f827ccde183603dadd6e725f55c
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 11:03:04
Commit message:

 Changed slot call due to changed Class structure
 
Package: BASiCS
Commit: f0e0475ec79a0c7039b9e2072147803e9ef5642f
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 10:51:11
Commit message:

 Changed the Chain call due to updated class structure
 
Package: BASiCS
Commit: 6cf246b3d86785afc35f323bbcff83a1995435f9
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 10:48:10
Commit message:

 Changed from single slots to parameters slot (list)
 
Package: BASiCS
Commit: 8abfb5f9065fc4e7cce84a6713ee9ca4017cb7bb
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-11 10:32:17
Commit message:

 Added starting value initialization
 
Package: BASiCS
Commit: d2d3058e1f30d5320b2d126e24ea5dbca8e89ff2
Author: Nils Eling <nils.eling@gmx.de>
Date: 2017-10-10 18:18:46
Commit message:

 Added regression case for MCMC sampler
 
Package: BASiCS
Commit: 28c7fedac6eafc4f2258d9697b3088bea6f058f3
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 16:16:31
Commit message:

 Started merging the new and old version
 
Package: BASiCS
Commit: 72252c78a89883386c1d105b03236928916485b8
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 16:00:20
Commit message:

 Removed priordelta from attributes
 
Package: BASiCS
Commit: 4c94f2436768ff052fec096eed5c4ba540489a0d
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 15:18:12
Commit message:

 Bug fixes
 
Package: BASiCS
Commit: ffbe3c885038afa6a9119a15f90f595ac6b5b019
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 15:02:30
Commit message:

 Added the output for regression parameters
 
Package: BASiCS
Commit: f4504095003dd70745393d8d86d93670a60b057f
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 14:54:34
Commit message:

 Added the updates of regression parameters
 
Package: BASiCS
Commit: 1bd845bce4546d91e9757387e0c229282d1dac2d
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 14:27:15
Commit message:

 Changed delta and mu update functions to new version
 
Package: BASiCS
Commit: c0fdecb51d90734536c786f3022d8a879aba7304
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 13:43:54
Commit message:

 Added initialization section for regression approach
 
Package: BASiCS
Commit: 202c7d42ca366cdf3d02f87f686eeafc94ea64b1
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 13:22:03
Commit message:

 Fixed MCMC sampler attributes
 
Package: BASiCS
Commit: 95b86ce7f8903865db4891398b4d2235af0724ff
Author: nilseling <nils.eling@gmx.de>
Date: 2017-10-10 11:52:37
Commit message:

 Added functions for regression approach
 
Package: HDF5Array
Commit: ad3e48caac5a233af2ace69a49a3ebc0c3946862
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 18:14:55
Commit message:

 add 'check' argument (TRUE by default) to internal utility h5dim()
 
Package: nucleR
Commit: 044ae2c3ab93c83c3b31e1943a10bac0d4215b56
Author: gthar <r.illa.pujagut@gmail.com>
Date: 2018-01-22 17:13:31
Commit message:

 fixed version number
 
Package: EBImage
Commit: 12c7d7cdcfcec5b0c4edeb9e4c22cb21a1a916e9
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-22 16:41:23
Commit message:

 version 4.21.2
- silence "Undefined global functions or variables" NOTE during R CMD check
 
Package: trackViewer
Commit: 059a2f3bc86b6902f25513a0ed7d3048aea4b53c
Author: Jianhong Ou <jianhongou@riboimager.research.duhs.duke.edu>
Date: 2018-01-22 16:25:32
Commit message:

 fix the warning in windows documentation.
 
Package: Uniquorn
Commit: 1a4938d976ee65e7c3b21e0de12721d6ea7b0453
Author: RaikOtto <fubioinf@gmail.com>
Date: 2018-01-22 16:00:28
Commit message:

 update
 
Package: EBImage
Commit: f0808e7e92b9116fdcecd645c3982daae77fdc21
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-22 15:57:09
Commit message:

 version 4.21.1
- update call to BiocStyle format function
 
Package: annotatr
Commit: eb608bb78e58d1e1b2b6ac3e13ea6740c854e34b
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2018-01-22 15:44:55
Commit message:

 Add gene / CpG support for galGal5 (chicken)

* Correspondingly, because GenomeInfoDb::Seqinfo() fails for galGal5 because it's not a valid genome yet, I added tryCatch statements to parts that used it so that the seqinfo slot is left blank.
* You need to reevaluate the way this works and make it more general so it's not so difficult to add new organisms. 
Package: netReg
Commit: 4651fc3fda76f3e910d9430a006a277c13b8687d
Author: dirmeier <simon.dirmeier@bsse.ethz.ch>
Date: 2018-01-22 15:36:43
Commit message:

 Added BSL to DESCRIPTION and updated LICENSE file
 
Package: netbenchmark
Commit: 2e5e840c0afc9d0a6bb2ea702fba29017773d97d
Author: Pau Bellot <pau.bellot@upc.edu>
Date: 2018-01-22 10:56:56
Commit message:

 Bump version

- Bumping development version
- Fixing C3net wrapper (Thanks to Gokmen Altay)
- Adding  package namespaces 
Package: netbenchmark
Commit: 55085511707432f46a32859d8ffb3e57ba81534d
Author: Pau Bellot <pau.bellot@gmail.com>
Date: 2018-01-20 19:41:54
Commit message:

 Merge pull request #1 from sysbio-vo/genenet-fix

GeneNet ggm.estimate.pcor function wrong argument 
Package: netbenchmark
Commit: d2ba54d5b68ef1fb2ad7bf990b6a3311bbaf8b59
Author: Pau Bellot <pau.bellot@upc.edu>
Date: 2018-01-20 19:38:08
Commit message:

 Replacing Genie3 code by the package

- Now, it's aviable a bioconductor package that implements Genie3 method. 
- Replace the old R code by the call to the package in the wrapper. 
Package: netbenchmark
Commit: e07b557e6baaf064e5b8b057e987e28f5cd938eb
Author: Pau Bellot <pau.bellot@upc.edu>
Date: 2018-01-19 16:44:57
Commit message:

 Bug fixes in network evaluation

Bugs in network evaluation were discovered by https://github.com/alnf  

* R/comp.metr.R:
-- Fix of AUROC: now it returns 1 when the inferred network is a perfect reconstruction
*R/evaluate.R:
-- extend parameter was causing some errors and unwanted behaviour 
*src/netbenchmark_init.c:
-- changes to work with Rcpp 0.12.13 http://dirk.eddelbuettel.com/code/rcpp.changelog.htm 
Package: netbenchmark
Commit: eb69c901e544f37f1adfaa2ed7c6e47e2f5be3a8
Author: aln <alnfgit@gmail.com>
Date: 2018-01-18 23:20:53
Commit message:

 ggm.estimate.pcor function from GeneNet requires observations to be in rows as all the netbenchmark in-house data, therefore transposing triggers an error, when input data matrix is not squared
 
Package: netbenchmark
Commit: 17a008351b73a2e4b966f4ac2cb2bbd2ff172b13
Author: Pau Bellot <pau.bellot@gmail.com>
Date: 2018-01-17 10:00:47
Commit message:

 Update LICENSE 
Package: netbenchmark
Commit: 6ae46a72162c28dae257cf05033e1bc6bcf9d243
Author: Pau Bellot <pau.bellot@upc.edu>
Date: 2018-01-17 09:03:28
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: netbenchmark
Commit: 0095fa0746824e22984bb34c6cf39a64924ff01c
Author: Pau Bellot <pau.bellot@gmail.com>
Date: 2018-01-16 09:19:18
Commit message:

 Update README.md 
Package: netbenchmark
Commit: c4ce6aeba9f896bea6c9f94fd2fe6b6dfc64b73c
Author: Pau Bellot <pau.bellot@gmail.com>
Date: 2018-01-16 09:17:56
Commit message:

 Initial commit 
Package: GRridge
Commit: 86178db002958b2d8ad908f116e0604695494699
Author: markvdwiel <mark.vdwiel@vumc.nl>
Date: 2018-01-22 15:07:31
Commit message:

 some changes
 
Package: methylKit
Commit: d7de840becb4eee7e5a45df7d6dfbc9a74f06ff0
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-01-22 15:03:51
Commit message:

 update NEWS and Version Bump
 
Package: methylKit
Commit: 36d54c95fd2440399a58cc9cd329393ad984f038
Author: alexg9010 <alexg9010@users.noreply.github.com>
Date: 2018-01-15 10:56:30
Commit message:

 fix #100 
Package: methylKit
Commit: 0f4baf86d9a612775729db2bb6c9070f4d86a5dd
Author: alexg9010 <alexg9010@users.noreply.github.com>
Date: 2018-01-15 10:55:31
Commit message:

 fix #99 
Package: methylKit
Commit: 32f8e053d832a1f7ff1d06b3280da70114ea00f8
Author: alexg9010 <alexg9010@users.noreply.github.com>
Date: 2018-01-15 10:54:21
Commit message:

 fix #97 
Package: methylKit
Commit: 82b1972a4c4c94773cf5610c7aec3e1d44dd5a87
Author: Altuna Akalin <aakalin@gmail.com>
Date: 2017-11-08 15:45:54
Commit message:

 updated readme links 
Package: methylKit
Commit: 2ce4ddbe767a611e5a155989e5b71f1d1fdf39e2
Author: Altuna Akalin <aakalin@gmail.com>
Date: 2017-11-08 15:42:58
Commit message:

 Update README.md 
Package: MAGeCKFlute
Commit: 9e3e68e057243dc6450febd659b88414b6ee8bba
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-01-22 13:44:42
Commit message:

 capitalize the first letter
 
Package: vsn
Commit: a69451a994386bf5edf71aff9517a9a32d292ca4
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-22 11:59:50
Commit message:

 Update calls to BiocStyle format functions
 
Package: IRanges
Commit: 0c4a7f12cc0ffdefcf83c8779ddb0e926a8f2eba
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 10:33:34
Commit message:

 make the SimpleIntegerRangesList class VIRTUAL
 
Package: IRanges
Commit: d1a748ba4145feb50f4f52ce87dc8372ad0bb6a5
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 10:23:19
Commit message:

 deprecate the RangesList() constructor
 
Package: MCbiclust
Commit: 9214142e23aaeb940843bd67432d021a041b643d
Author: rbentham <robert.bentham89@gmail.com>
Date: 2018-01-22 10:13:42
Commit message:

 Changed to Vignette style to html_documentS
 
Package: brgedata
Commit: 415089a199f46fd6bf1d363d3843cc517bc2a504
Author: Carlos Ruiz <yocra3@gmail.com>
Date: 2018-01-22 10:11:02
Commit message:

 Add LICENSE file, bump version
 
Package: rtracklayer
Commit: 3a6864529207144c2ed90bc7efcbd7360f92a6d1
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 10:00:37
Commit message:

 better to use the most specific class name when instanciating
 
Package: Repitools
Commit: ec5a04ee9e6be4c7775dc2ac1bc2990fc1dc195c
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 09:48:39
Commit message:

 The 'regions' slot of a ChromaResults object now is an IRangesList
instead of an IntegerRangesList.
 
Package: microbiome
Commit: 22eb7a7789f2ccc41c5fe490cbdc8ce984372223
Author: lei <lei@savu>
Date: 2018-01-22 09:35:09
Commit message:

 ok
 
Package: microbiome
Commit: 59250f553f14ad375fd481d7d376abab2bed107a
Author: lei <lei@savu>
Date: 2018-01-19 12:31:01
Commit message:

 Fixed the version number
 
Package: rtracklayer
Commit: 3efa8ef104ef8b508f8c7f35f952f37e225a5c58
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 09:21:53
Commit message:

 Follow renaming of SimpleRangesList class -> SimpleIntegerRangesList in
IRanges 2.13.13
 
Package: IRanges
Commit: cf38237f44d313a96957512e87a2007c5c7aefa9
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 09:17:53
Commit message:

 rename SimpleRangesList class -> SimpleIntegerRangesList
 
Package: Repitools
Commit: b5d340454b479284c27ccff1f7f88d7fc684da4d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 09:06:28
Commit message:

 use coercion to IRangesList rather than calling RangesList()
 
Package: CNVrd2
Commit: 9da358d04a92ad34694cd7d5f96e420464d1951e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 09:01:55
Commit message:

 use IRangesList() rather than RangesList()
 
Package: CODEX
Commit: ebbbc43cb3986cfaf2c96637323fc9f146f65c40
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 09:00:24
Commit message:

 use IRangesList() rather than RangesList()
 
Package: rtracklayer
Commit: a15d7beba796095e9fef4b7acad2cf92f641814e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 08:58:59
Commit message:

 use IRangesList() rather than RangesList()
 
Package: htSeqTools
Commit: 2e63bb10a6fa24bd1e8f5d18d581fe0bf5313554
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 08:56:50
Commit message:

 use coercion to IRangesList rather than calling RangesList()
 
Package: DECIPHER
Commit: 267ed7c5430b56a8102df85fb282f33648ad6b2a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 08:54:44
Commit message:

 use coercion to IRangesList rather than calling RangesList()
 
Package: MMDiff2
Commit: 64ead779e990efa1153f2386457f0a703fc13d84
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 08:46:14
Commit message:

 use IRangesList() rather than RangesList()
 
Package: genomeIntervals
Commit: dc2ece2d0c066a724fd3ef3cc695e0491617a9e5
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 08:43:49
Commit message:

 use IRangesList() rather than RangesList()
 
Package: exomePeak
Commit: d30e00fac61e0be1b8ea1694b4ea673897d3b48b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 08:38:18
Commit message:

 use IRangesList() rather than RangesList()
 
Package: IRanges
Commit: be3b33a93af3c515e98763c82f3623fc12c92037
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 08:34:40
Commit message:

 use IRangesList() rather than RangesList()
 
Package: mCSEA
Commit: dce30227fe60c8ad84c1c951655b99123373301c
Author: Jordi Martorell Marugán <jmartorellm@gmail.com>
Date: 2018-01-22 08:03:05
Commit message:

 Update authors information
 
Package: ggtree
Commit: cf8b3bfe0a47de72924d422c0f1ca2a2c1150c10
Author: guangchuang yu <guangchuangyu@gamil.com>
Date: 2018-01-22 07:28:03
Commit message:

 fine tune y position after flip; flip compatible with collapse
 
Package: ggtree
Commit: 9b4dd3ff27be600efdeb9cb13e095d603b52b6ae
Author: guangchuang yu <guangchuangyu@gamil.com>
Date: 2018-01-22 03:49:47
Commit message:

 typo
 
Package: ggtree
Commit: 3708794e4104fe9e2509be45598d8e65d2b83fae
Author: guangchuang yu <guangchuangyu@gamil.com>
Date: 2018-01-22 03:29:54
Commit message:

 update citation
 
Package: ggtree
Commit: 3f398f6a9ec19d55170b94af5d59173a447e51df
Author: guangchuang yu <guangchuangyu@gamil.com>
Date: 2018-01-16 08:29:02
Commit message:

 new citation
 
Package: ggtree
Commit: 55824e6560d5f65b2661a2cd1ea3e2ec7f4fab77
Author: guangchuang yu <guangchuangyu@gamil.com>
Date: 2018-01-08 06:14:45
Commit message:

 update readme
 
Package: ggtree
Commit: a5086475acd984cc06afa72b63e0414cd1226d8f
Author: guangchuang yu <guangchuangyu@gamil.com>
Date: 2018-01-08 06:12:09
Commit message:

 update readme
 
Package: MAGeCKFlute
Commit: dd68d393829c1615d82653ae2989677d04a82a08
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-01-22 06:42:06
Commit message:

 add reture in man
 
Package: MAGeCKFlute
Commit: ae44cd8ade5725ab2526a1405bc483452e2c3185
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-01-22 06:09:47
Commit message:

 R 3.0 -> R 3.5
 
Package: MAGeCKFlute
Commit: 9542008c21e3a674b3b69806bfa9bd5b9c227d69
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-01-22 06:04:36
Commit message:

 0.99.18
 
Package: MAGeCKFlute
Commit: e4ab2ceb068dc97ca0856bfe4d0b6b72ef9944b7
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2017-12-13 08:30:06
Commit message:

 figure size
 
Package: MAGeCKFlute
Commit: f33f04ace7d51d9275556428c33a780965c65191
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2017-12-13 08:02:47
Commit message:

 Replace a more beautiful EnrichView
 
Package: MAGeCKFlute
Commit: 0772b7341d78152b60066dd3121f2f95189e3b71
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2017-12-12 08:41:40
Commit message:

 revision
 
Package: MAGeCKFlute
Commit: e2ec2eec51ffac2195e2d429c0aaf46c711e4f03
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2017-12-11 07:53:16
Commit message:

 Add vignettes
 
Package: MAGeCKFlute
Commit: 3d9932ca6f5966e523d65a31c93fb9d44cee5292
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2017-12-11 06:34:38
Commit message:

 Modify help document
 
Package: MAGeCKFlute
Commit: 335b0557d7d224148574b6233d2d70eb835f47e0
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2017-12-10 12:59:36
Commit message:

 0.99.18
 
Package: GenomicRanges
Commit: 910b8b16c7662b4b971f5f1c516a0b2fe3f6dc21
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 06:35:14
Commit message:

 small simplification
 
Package: groHMM
Commit: 00a8cd0752a1c92ca9b2e4d756d8a26012c73093
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 06:16:31
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: AllelicImbalance
Commit: ce286aaaf6a24469dcf8b4495493b014bde54109
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 06:11:57
Commit message:

 - Follow renaming of Ranges and RangesList classes -> IntegerRanges and
  IntegerRangesList in IRanges 2.13.12.
- Remove all references to RangedData (this class is going away soon).
 
Package: derfinder
Commit: 74689630c3f39e5d8693ba7e9d86807eeccf0757
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 06:03:34
Commit message:

 The code in derfinder does not use the RangesList() constructor so no
need to import it.
 
Package: wavClusteR
Commit: 7aa37e41e8f7313fadbb26f43849da2a65755cf0
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 05:59:59
Commit message:

 - Follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12.
- Remove all references to RangedData (this class is going away soon).
 
Package: ATACseqQC
Commit: 4c5acadf07cdb6384a6057e1a2253a247c8c41f2
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 05:45:34
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: methylKit
Commit: 3d9b86d41098145a620476619373982f40179bd8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 05:38:30
Commit message:

 The code in methylKit does no use the RangesList() and RangedData()
constructors so no need to import them.
 
Package: easyRNASeq
Commit: 336bced0f15c1a47a2dc6b184647790d8d767518
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 05:22:36
Commit message:

 The code in easyRNASeq does not use the RangesList() constructor so no
need to import it.
 
Package: R3CPET
Commit: 9861ef6d72c9dab5538f21ed3bc81c08cc2dee01
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 05:16:27
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: chipseq
Commit: c866ab163637d92c3e681fad2168dc80aa7f8e98
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 05:10:15
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: GenomicTuples
Commit: 85a460665622505473e8669954e93f0afb053b41
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 05:04:32
Commit message:

 - Follow renaming of Ranges and RangesList classes -> IntegerRanges and
  IntegerRangesList in IRanges 2.13.12.
- Remove all references to RangedData (this class is going away soon).
 
Package: RaggedExperiment
Commit: 8e8b14b5085d06969b9a08e968873ea1ed5507a7
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 04:45:33
Commit message:

 Follow renaming of Ranges and RangesList classes -> IntegerRanges and
IntegerRangesList in IRanges 2.13.12
 
Package: OrganismDbi
Commit: 3a314d5440342935f0797573ec9061af0d3111a4
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 04:38:55
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: loci2path
Commit: c295e3ab671f19c5a1535b2a9b61ff73c5639e4d
Author: StanleyXu <xutianlei@outlook.com>
Date: 2018-01-22 03:23:54
Commit message:

 update biocStyle; old defunct.
 
Package: R453Plus1Toolbox
Commit: bf258168ec2acd2f8ec2d3977042ce7933be1499
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:44:41
Commit message:

 no more "append" method to import from the Biostrings package
 
Package: SGSeq
Commit: 32ffd97feb12fd83cbd2353770a7fc4a713cd168
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:33:19
Commit message:

 oops, needs to be (>= x.y.z), not (x.y.z)
 
Package: ChIPseeker
Commit: b62d7922fb61e58620bbb685e4def4fb863c8e81
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:28:57
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: systemPipeR
Commit: 0332bdc5284fdb2e8b06b5cede9e0426f33a32d9
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:25:34
Commit message:

 oops, needs to be (>= x.y.z), not (x.y.z)
 
Package: systemPipeR
Commit: 36d01352f35a570b2c4fc887e001f1d33ed502c5
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:23:14
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: R453Plus1Toolbox
Commit: 56beb47661abc38926b851a2a61581ef02c5821d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:18:23
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: Repitools
Commit: 58b4f5f8c25d092c2357d8164a498d4ab30340ea
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:11:41
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: genomation
Commit: 3c41561a57c411d0423ab1c5b90a22e78f768ed8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:06:44
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: SGSeq
Commit: 1486b825da516438a50d6cefa72a8acb95a9dae1
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 01:01:00
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: girafe
Commit: 9a3264572fe10926c4cb5aa885ad3cca7572e5b3
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:57:52
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: VariantTools
Commit: 94cdcbb702b8e9026b20d9590bf27ffe26df079a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:50:28
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: ChIPpeakAnno
Commit: b3a40f320d869cce534ac4cbdd097b5dfd56dcfb
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:41:49
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: ShortRead
Commit: 3ea9ecb43ff27c8c5e30722e4aea93cdcefe21d7
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:31:32
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: gmapR
Commit: c08711413e1b500c2a54e8d8cec564206a4da6a6
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:24:43
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: VariantAnnotation
Commit: db9cb3b7212ebd9c5f6f3e1082274cadfde003ec
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:05:30
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: GenomicFeatures
Commit: 194806b42fcba78e3ccaea51bfd82bc00b66ad0a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:05:02
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: BSgenome
Commit: d2a0a158b8de84b947d1759b65006385731cc18a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:04:49
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: rtracklayer
Commit: 52e04e9e2260070ccd6c07c2c827cc28366c804e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:04:33
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: GenomicAlignments
Commit: 71d47f2d1d12656572ab17bf4c9da52dd21487ec
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:04:16
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: Rsamtools
Commit: dc96f913aeb5300738fb0bfb030ef40250353cea
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:03:34
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: Biostrings
Commit: 3f199204efdb686dd8ad5e1f3f829480178213da
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:03:07
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: SummarizedExperiment
Commit: b060c925edbbdeeee46ef97ca09e6e60c7abdab3
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:02:31
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: GenomicRanges
Commit: d359462fe5fac7b3225909fd12ce740e43a63085
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:02:04
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: GenomeInfoDb
Commit: 2d5bb9956087264d521109d0dd26b0f2cb1f1a33
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:01:37
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: S4Vectors
Commit: 034452c7ff4c1a92fc622733170a2e827fca405f
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-22 00:01:03
Commit message:

 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12
 
Package: IRanges
Commit: e13fadd8d5442c57e36552cc680c3c4c5e9a33b4
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-21 23:59:48
Commit message:

 rename RangesList class -> IntegerRangesList
 
Package: GreyListChIP
Commit: 5a776dc07e0242c725eae2ff6b3d6e798b6e1690
Author: Gord Brown <gdbzork@gmail.com>
Date: 2018-01-21 19:03:58
Commit message:

 fixing documentation bugs, testing bugs
 
Package: apeglm
Commit: bffab98f1aac8ee4917da64e200265348d1e7efc
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-21 16:06:55
Commit message:

 run the new code
 
Package: diffuStats
Commit: e1329c93bcbb96ee13e98643f9893146ae4c885c
Author: Sergi Picart <elpicart@gmail.com>
Date: 2018-01-21 12:42:16
Commit message:

 Bug fixes again
 
Package: diffuStats
Commit: 096e454aff0ca858c3478d06843746e42ad6d2fc
Author: Sergi Picart <elpicart@gmail.com>
Date: 2018-01-21 11:30:20
Commit message:

 Bug fixes
 
Package: IdeoViz
Commit: 24136654015bd9132511a64e9d39a735ad76970a
Author: Shraddha Pai <shraddha.pai@utoronto.ca>
Date: 2018-01-20 16:04:51
Commit message:

 Merge remote-tracking branch 'upstream/master'

Conflicts:
	DESCRIPTION
	R/plotChromValuePair.R
	R/plotOnIdeo.R
	man/avgByBin.Rd
	man/getBins.Rd
	man/getIdeo.Rd
	man/plotChromValuePair.Rd
	man/plotOnIdeo.Rd
	vignettes/Vignette.Rnw
 
Package: IdeoViz
Commit: ae2e7bb9d7dcd9792a7c42e2486fef0c4859f85a
Author: Shraddha Pai <shraddha.pai@utoronto.ca>
Date: 2017-12-08 16:53:25
Commit message:

 moving BioC repo to github
 
Package: IdeoViz
Commit: cd168c87a483624af930f8dc1185c6cc02affab1
Author: Shraddha Pai <shraddha.pai@utoronto.ca>
Date: 2017-12-08 16:51:34
Commit message:

 Initial commit 
Package: netReg
Commit: 6b33746c6308116e067c3324b9747fe55ebdb595
Author: dirmeier <simon.dirmeier@bsse.ethz.ch>
Date: 2018-01-20 14:04:28
Commit message:

 Added new version of dlib, replaced deprecated html_document with new version, updated to 1.3.1
 
Package: MLInterfaces
Commit: 208b5827414ad21e08bf1fe2d7e683b4cf1171e9
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-01-20 14:05:50
Commit message:

 removing rgl import and answering BiocCheck; rgl will not load for me, stymieing development
threejs may substitute fully but that has not been done with projectLearner...
 
Package: GenomicFeatures
Commit: 9de41080c9bc2b3d57bcb229a9fc60eeb19c32c2
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 13:12:09
Commit message:

 minor edit
 
Package: GenomicRanges
Commit: 4147f6192940f5d8697f601cf5e4fdb794911067
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 13:07:52
Commit message:

 some leftovers after renaming of Ranges class -> IntegerRanges
 
Package: IRanges
Commit: bcd57928e27fb6332659461a8b55b458c286c037
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 13:01:04
Commit message:

 one more leftover after renaming of Ranges class -> IntegerRanges
 
Package: IRanges
Commit: b83b32d37a643a119d4c0abd4a72ea36d9c4fce0
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:54:12
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/IRanges
 
Package: IRanges
Commit: 00e6b732e98479960e25798d0ba031d677ea1008
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:54:00
Commit message:

 some leftovers after renaming of Ranges class -> IntegerRanges
 
Package: ArrayExpressHTS
Commit: b87eea7435c6bbbad5eada9d50bdd588384b69a7
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:46:22
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: Pbase
Commit: 86817ba4581afab4a26ed0fa31a623311596bcbf
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:41:59
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: rtracklayer
Commit: e6b2880df962fcd73b648d4fc72e7ca962634973
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:37:25
Commit message:

 requires GenomicRanges >= 1.31.7
 
Package: girafe
Commit: e5c5c2bbb535ca365caaeafc2c0b57829a360af0
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:31:36
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: IRanges
Commit: cfb2e963b7938424cac52fea4852941fc12dc462
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:25:02
Commit message:

 requires S4Vectors >= 0.17.24
 
Package: VariantAnnotation
Commit: eaaa54e76d9a3b1ded5abfb6e31b86c6483bee58
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:08:42
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: SummarizedExperiment
Commit: 3e35d74fe91e6162341f23cf5d42b897261cb222
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 11:50:44
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: SpidermiR
Commit: ce3274fdc98f6c745bfcf8f7d2a7c81b9230f27e
Author: claudiacava <claud.cava@gmail.com>
Date: 2018-01-20 11:47:11
Commit message:

 update
 
Package: GenomicFeatures
Commit: 45f2da5416f871b883032d9e22e999c96e7560fa
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 11:38:08
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: GenomicAlignments
Commit: acb5da89130f4e1d1873c865132613df95d69e28
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 11:07:19
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: BSgenome
Commit: 59c467e3fe88e1420b063b64d85c3b6771964ae6
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:35:31
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: rtracklayer
Commit: ab349d990247d6878155f7c953e8ed5187f74556
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:35:14
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: Biostrings
Commit: 88954cbfa7c4eaede805ca44e70928543ec27b50
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:34:36
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: XVector
Commit: 897120c1c07c97fbd09631b0b762d7932f81a542
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:33:31
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: GenomicRanges
Commit: 1c8943016498691b7da775530a108321bf16fe65
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:32:24
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: S4Vectors
Commit: 1b6d23da1dda0a101a62d796bf199f78ce04d815
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:31:21
Commit message:

 follow renaming of Ranges class -> IntegerRanges in S4Vectors 2.13.11
 
Package: IRanges
Commit: 6f87c2f362b37466ad18b1dccf861317562e43fb
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:27:43
Commit message:

 Rename Ranges and RangesORmissing classes -> IntegerRanges and
IntegerRanges_OR_missing classes, respectively.
 
Package: bacon
Commit: 117818895c2bfb5d550801979db3c78b52fc3cf7
Author: mviterson <mviterson@gmail.com>
Date: 2018-01-20 07:19:44
Commit message:

 bug fix: changed html_document2 -> html_document
 
Package: derfinder
Commit: 256d7a772207706faff4ca74e9e061706ce336d3
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-20 00:50:27
Commit message:

 v1.13.5 -- fix more links
 
Package: derfinderPlot
Commit: 760e162a53dfac1a11363531d50a8abd3b0b8cd5
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-20 00:39:17
Commit message:

 v1.13.2 -- fix more links
 
Package: regionReport
Commit: 311def55c4dbbe1f0f5898ff795e8a001c990056
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-20 00:32:50
Commit message:

 v1.13.2 -- fix a link to Ideogram (has a weird name)
 
Package: apeglm
Commit: 5b9b77499ff85cbfdf6e94ad82a5f10d90a1d7d4
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-19 23:48:49
Commit message:

 small cleaning up
 
Package: apeglm
Commit: a93197656b04e6bc2e4107ad8ba9edea6b8dee1c
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-19 23:48:24
Commit message:

 small cleaning up
 
Package: Pigengene
Commit: 61f99eb72224006f548792f3a92022df2e87a65e
Author: Habil Zare <habil_zare@yahoo.com>
Date: 2018-01-19 23:04:53
Commit message:

 C50:::as.party.C5.0 to comply with version 0.1.1
 
Package: hpar
Commit: 7553ac54645e4fe6fa670dbaa08e1c5a61a89e0a
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-19 22:02:49
Commit message:

 use BiocStyle::html_document (Bioc commit)
 
Package: cosmiq
Commit: 027805244c3ad44c5ad8da861b8934a10674d137
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:13:22
Commit message:

 version inc
 
Package: cosmiq
Commit: 19982a267139a726a97705c64c1279f6dd1d11a3
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:13:00
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/cosmiq
 
Package: cosmiq
Commit: 382a128608ed183920673380e3505d096ec89c02
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:12:40
Commit message:

 fix
 
Package: specL
Commit: 232ef92a81e794d44e09369ef983bdc501e724c3
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:11:37
Commit message:

 version inc
 
Package: specL
Commit: cdf1da30fb36a4a8aecbcbcaa9e551781b0e72b8
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:11:00
Commit message:

 fix
 
Package: imageHTS
Commit: f5604c76e80d75b8926cca1d09a106a29002162c
Author: Joe Barry <jbarry@Joes-MacBook-Pro.local>
Date: 2018-01-19 20:04:16
Commit message:

 changed from BiocStyle latex2 to latex
 
Package: motifStack
Commit: d07623322ff125edf5cd5728d467d5b813d7c506
Author: Jianhong Ou <jianhongou@dhcp-152-16-223-142.research.duhs.duke.edu>
Date: 2018-01-19 19:57:31
Commit message:

 Fix the warning in windows.
 
Package: apeglm
Commit: 7922388817c0188381da390ca1df6e659f7c2f91
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-19 19:45:09
Commit message:

 add nbinomR support for weights
 
Package: DiffBind
Commit: 230c098844e135384fb73e233cac7b1a27d9d74c
Author: Rory Stark <rory.stark@cruk.cam.ac.uk>
Date: 2018-01-19 19:09:07
Commit message:

 bug fixes + precision and dir options -- remove setwd in vignette and man pages
 
Package: flowPloidyData
Commit: 7d598cd1dfb365ebe7e77a5d787f0c8c2b75b53c
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-19 18:51:33
Commit message:

 Version bump, added NEWS file, removed encoding from vignette

Encoding line is no longer needed in Rmd files.
 
Package: flowPloidyData
Commit: 81c19f56fda371594f2a44f8568736aca6d177f8
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-19 18:35:34
Commit message:

 Added documentation of fpBad and fpVac
 
Package: GenomicFiles
Commit: eb703f74e9c0fab087c650f5941dc35359e6aac8
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:24:43
Commit message:

 Update vignette to use latex instead of latex2
 
Package: genefilter
Commit: 8feef757de9f15435750e9691748ffe3e4696785
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:23:51
Commit message:

 Update vignette to use latex instead of latex2
 
Package: Rhtslib
Commit: d0876f8e039a43ca647be67241ffbd679644ad22
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:21:51
Commit message:

 Update vignette to use html_document instead of html_document2
 
Package: VariantAnnotation
Commit: de7f434f13d2b5a333ead0ba260b4d953102a53d
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:20:43
Commit message:

 Update vignette to use latex instead of latex2
 
Package: AnnotationFilter
Commit: bc3863a6d6b728a3ecbd9644be9e3089a655491b
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:16:16
Commit message:

 Update BiocStyle from html_document2 to html_document
 
Package: AnnotationFilter
Commit: ad642b83a5e9460425665ad38870251c3a7bdbf2
Author: Daniel Van Twisk <dvantwisk@gmail.com>
Date: 2017-11-09 20:45:29
Commit message:

 Merge pull request #23 from Bioconductor/DoubleFilter

Add virtual DoubleFilter class 
Package: AnnotationFilter
Commit: 543cb176fd73457048b2c18596a3f6ae6de25aab
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-11-07 12:09:56
Commit message:

 Add virtual DoubleFilter class

- Add the virtuel DoubleFilter class.
- Add related documentation.
 
Package: annotatr
Commit: 80083985848f29e355785af6d5c84bd62b2d5c11
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2018-01-18 21:32:08
Commit message:

 Add the ability to facet over two variables in plot_numerical

 
Package: HelloRanges
Commit: 4d88c6f8f236970fa4081cb1febec5c9011a8fa0
Author: Michael Lawrence <michafla@gene.com>
Date: 2018-01-19 18:02:20
Commit message:

 use BiocStyle::latex()
 
Package: hpar
Commit: a363d14b5482bd6feb85568817f95c2711a779fa
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-19 17:47:15
Commit message:

 test for duplicated commits
 
Package: DASC
Commit: 723ffb8e56c521c73114d1bd440cc5a30b72b3eb
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 17:47:55
Commit message:

 Deprecate package
 
Package: scater
Commit: e080bb7cd07d028e3cb1cd508dadb07bf22b9c95
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-19 13:04:00
Commit message:

 Avoid checking size factor centering when NULL.
 
Package: scater
Commit: 4e87195e051551232a2bfe49eaadbc85e47f1e5e
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-19 10:25:05
Commit message:

 Small bugfix to plotHeatmap.
 
Package: scater
Commit: d7988ac627843cc068c56cf171dd0f4f3c16aad6
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-19 10:24:25
Commit message:

 Added uniquifyFeatureNames for quick uniquification.
 
Package: scater
Commit: c510568d83907ba3de8eba2d845cb92d2f1d774a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 18:16:14
Commit message:

 Further removal of unnecessary droplet-related files.
 
Package: scater
Commit: 0d07b4c376e97b98c24d2a73add86ebd8df6863f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 18:00:53
Commit message:

 Removed old SCESet methods.
 
Package: scater
Commit: 34bebdca285019510a1ceb99b5d207c9e51f9512
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:52:15
Commit message:

 Purged all 10x functions in the test suite.
 
Package: scater
Commit: baf0e90ea5b0351d32d0d5170a93e81a8c34f3a8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:41:32
Commit message:

 Deprecated droplet functions for DropletUtils equivalents.
 
Package: scater
Commit: d005d970c8a35fe8281051f9c3c0520295692222
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:29:47
Commit message:

 Added DelayedArray to Imports list.
 
Package: scater
Commit: 30396e91a66e569083e65ad601f6f70a10f8f5d9
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:12:05
Commit message:

 Fixed bug with R^2 calculations for sparse matrix inputs.
 
Package: scater
Commit: b615be78d9052ce97e16d38995ab071baf426b24
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:07:01
Commit message:

 Switched from matrixStats to DelayedMatrixStats.
 
Package: scater
Commit: 9a64c8319082d15d1c8d71a99bab73a8a80abd83
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 13:45:56
Commit message:

 Restored legacy names for back-compatibility.
Clarified variable names for more sensible code.
Updated documentation for compact, renamed metrics.
Updated tests.
 
Package: scater
Commit: d47b43b6bd35fe6629bf90fed3f3f960515261d1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 21:54:11
Commit message:

 Renamed qc fields for better safety, sensibility.
 
Package: scater
Commit: 05de5afe63d4d8f0f4853e856b84cf88acc2812c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 21:25:56
Commit message:

 Updated NEWS.
 
Package: scater
Commit: 8c80cdf56ca7dd1196c65880ef81424b138889ad
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 21:25:22
Commit message:

 Reduced nesting of scater_qc metrics, by removing exprs_vaue layer.
 
Package: scater
Commit: 883d10e534d3282556705afac93b65241d84de9e
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 21:19:54
Commit message:

 Added tests for compactness and overwriting, minor bug fix.
 
Package: scater
Commit: 1ff520b04c86f1d9c6e70279e10c3165f3fd5c3f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 20:27:32
Commit message:

 Fixes to calculateQCMetrics with new compactness format.
 
Package: scater
Commit: 5bce2f950c46262907ae5cc9996965a7f12d8cf2
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 16:49:49
Commit message:

 Supported compact QC output with nested dataframes.
 
Package: scater
Commit: 2090154d82f5ba82c20655ba54b72abb3a68ccfc
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 11:49:57
Commit message:

 Passed total exprs in qc internal functions to avoid recalculation.
 
Package: scater
Commit: 9b3a73beb7b976193016a5ecefd70cff93a466a0
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 11:01:28
Commit message:

 Fleshed out calculateQCMetrics tests for greater rigor.
 
Package: scater
Commit: ddf25e7f3d02868b1f602c0175cbcf1988833a5a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 19:06:26
Commit message:

 Fixed updated argument naming in tests.
 
Package: scater
Commit: b43c8b9be0b903397a76d06b4a21f2380e1a370b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 19:02:02
Commit message:

 Merge branch 'master' of https://github.com/davismcc/scater

Conflicts:
	R/qc.R
 
Package: scater
Commit: 2458a217c8689a5f372babd098e09607ea56628d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:45:36
Commit message:

 Switched back to old automatic control set names for now.
 
Package: scater
Commit: abfe83558c2b22d8d28ed94d6d5f78d579b922e5
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:45:36
Commit message:

 Switched back to old automatic control set names for now.
 
Package: scater
Commit: 799d1cf142939763cffd42bb55fc15b7eec84e11
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:38:16
Commit message:

 Renamed lowerDetectionLimit to detection_limit, avoid camelcase args.
 
Package: scater
Commit: f251ee8604c982cbf8d938f575183ce67c9fa629
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:35:33
Commit message:

 Added option to specify the top percentage calculations.
 
Package: scater
Commit: 75aa477c37618fcd323217c77fd2f1deebbf801b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:00:52
Commit message:

 calculateQCMatrix rank output now goes from largest to smallest.
Renamed automatically generated control/non-control sets.
 
Package: scater
Commit: b3db62aa7b7109a9562c45a2935d9519aecfa00c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 17:58:12
Commit message:

 Removed linearity checks; all metrics are now always computed.
Added lowerDetectionLimit argument to pass to nexprs().
 
Package: scater
Commit: 06b8379bc01ed1eb16aafba0ae963acffcfbe191
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 17:42:05
Commit message:

 Updated documentation for calculateQCMetrics.
 
Package: scater
Commit: 2c567c5f8ab4de934ec41e012a9dbd9cb6349da9
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 16:36:00
Commit message:

 Bumped version number, date.
 
Package: scater
Commit: 71dcaaee0700de459c5c7eac0f373ab355e1f2f8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 16:35:12
Commit message:

 Stronger tests for normalize() (migrated from scran).
 
Package: scater
Commit: 10e77ea2a893df790dd11787a83fbecd97d23bd2
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 16:28:29
Commit message:

 Merge branch 'master' of https://github.com/davismcc/scater
 
Package: scater
Commit: b2d206552012bc5b868669e0fa827d1fc2095203
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 16:27:33
Commit message:

 Patches to nexprs() documentation, testing.
 
Package: scater
Commit: 76716a31765c64dab2001d34329b888db71cf2ae
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-01-16 14:17:59
Commit message:

 Merge pull request #44 from LTLA/master

Merging BioC history with Github history 
Package: scater
Commit: a656f397696321a01cad0b764dc6a8e333733fdc
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-02 15:11:24
Commit message:

 Added plotHeatmap wrapper around pheatmap for SCE objects.
 
Package: scater
Commit: 96de14f8c811e243f23bcc643f483430b030a5c4
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-20 11:45:51
Commit message:

 Minor fix to shut up CHECK.
 
Package: scater
Commit: 20c7cea7bb154b6929470610a950b96496eb933b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-20 11:43:54
Commit message:

 Merge remote-tracking branch 'bioc/master'

Conflicts:
	R/calculate-expression.R
	R/normalisation.R
	R/plotting.R
	R/qc.R
	tests/testthat/test-classes.R
 
Package: scater
Commit: ba91873eb480345c22db4eec760796cb1141a4a6
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-12-19 11:29:21
Commit message:

 Merge pull request #42 from LTLA/master

Further fixes to plotting 
Package: scater
Commit: 0e1dfd6792af02ac3ef078510e311445a9476223
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-14 16:34:20
Commit message:

 Fixes to C++ matrixStats-code with duplicate subsets.
Generalized subsetting tests in test-cpp.R.
 
Package: scater
Commit: 4c74fa8d88bdc7294085d54bd75c03a3190c8dfd
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-14 16:13:35
Commit message:

 Optimized matrix access by sorting subset vectors.
Modified tests to check behaviour of unsorted subset vectors.
 
Package: scater
Commit: cf2433534a5e2a8e30f510db48dc393003337a5c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-13 15:03:24
Commit message:

 Bug fix to plotScater with colours/blocks.
Bug fix to calls to nexprs().
 
Package: scater
Commit: ba91fe5f8abea1e89dc6d4dc7422168500a80c96
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-13 14:58:38
Commit message:

 Updated nexprs() docs to reflect subsetting of input.
Updated tests for C++ row/col matrix functions.
 
Package: scater
Commit: e4754697a4d27d32f8cf433dfcb60e231343043e
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-13 14:58:11
Commit message:

 Switched all .Call()s to use new matrixStats-like functions.
 
Package: scater
Commit: 5e87c527184b95cc5d0aab5e71a292e113cdc427
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-13 14:25:38
Commit message:

 Generalized C++ utility functions to their matrixStats equivalents.
 
Package: scater
Commit: 4a1c30e196df575949787c2c61c02963e7daa75d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-08 13:50:11
Commit message:

 Merge remote-tracking branch 'davis/master'
 
Package: scater
Commit: 77279f1a43433d5ffd1e2885f6906614154dd4b8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-08 13:49:38
Commit message:

 Streamlined plotScater % top calculations with existing C++ code.
 
Package: scater
Commit: d515e2f67a4d15732f8c88e9660fb60e1c401ed3
Author: davismcc <davismcc@gmail.com>
Date: 2017-12-05 18:28:20
Commit message:

 Tweaking roxygen to fix NAMESPACE
 
Package: scater
Commit: 5e5d3acf8848f0149f83f19d62a08b01a9154ff1
Author: davismcc <davismcc@gmail.com>
Date: 2017-12-03 21:09:48
Commit message:

 Merging PR from Aaron.

Merge branch 'master' of https://github.com/davismcc/scater

# Conflicts:
#	DESCRIPTION
 
Package: scater
Commit: 68d5570db5a8a15c6f00f4c3fa53e8954509cd61
Author: davismcc <davismcc@gmail.com>
Date: 2017-12-03 21:08:23
Commit message:

 Adjustments to 10x import wrapper.
 
Package: scater
Commit: a6a207c07467714716c5be1059cdfa67590af931
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-12-03 21:07:20
Commit message:

 Merge pull request #39 from LTLA/master

Modified plotHighestExprs to support alternative matrices. 
Package: scater
Commit: 597268ae37aecd70ec67be226d4693681347bb59
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:32:25
Commit message:

 Documented return value for run* functions.
 
Package: scater
Commit: 6939ca0debd52e18d075e234ef6cf466607fec3b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:27:10
Commit message:

 Minor changes to shut up CHECK.
 
Package: scater
Commit: 8346e4e885106fe54a7a1e05abde374ea2f46796
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:26:18
Commit message:

 Fixed tests for updated messages, argument names.
 
Package: scater
Commit: 5a10c1a495bc30e14c81ea03b1f0f581a40b89f0
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:05:16
Commit message:

 Renamed use.size.factors arguments in various calls.
 
Package: scater
Commit: 1a00bf58d2257936de34e5b10831a1ca8ee48538
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:03:47
Commit message:

 Fixed missing ncomponents documentation in run* functions.
 
Package: scater
Commit: 04b8f7f36e33641d01400ac4acc686910aa0f8fb
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 16:53:59
Commit message:

 Bug fixes in vignettes for new args, function calls.
 
Package: scater
Commit: 8efe366851dfd295ee382490e8f765295f101164
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 15:55:59
Commit message:

 Moved details from plot* to run* documentation.
Mentioned metrics used in PCA for QC.
Mentioned deprecation of arguments in plot* functions.
 
Package: scater
Commit: 9677f60628f814523b13b6600773f97eea001185
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 15:40:52
Commit message:

 Cleaned up warning messages in plotPCA for QC.
 
Package: scater
Commit: 113155e426af2dea0f5fdbf436ba5dccd3e2bfa1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 15:33:49
Commit message:

 Softened transition to new '...' behaviour in plot*.
Minor bug fixes to plot/run calls in MDS, DiffusionMap.
 
Package: scater
Commit: ffed3e9d55275cbdf721e0c922ddc1c54da91c65
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 17:07:26
Commit message:

 Added documentation for read10xResults.
 
Package: scater
Commit: aa01f9d215eaede0708b96698acacc432a39f6ef
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 17:05:30
Commit message:

 Separated documentation for run* functions for dim. red.
Minor rewording of dim. red. plot* documentation.
Required specification of run_args when re-running dim.red.
Automatic passing of plotting arguments via ... in plot*.
Exported plotMDS, added documentation.
Deprecated return_SCE in favour of explicit run*.
 
Package: scater
Commit: 1aa7a3e110d4602b41b6cc9ef9e2a1b19eeac45a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 16:33:45
Commit message:

 Made axis ticks optional.
 
Package: scater
Commit: 9cee24fc288f862e6617ac78ddd65bda7a9d3536
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 14:52:54
Commit message:

 Fixed centering bug in normalizeSCE.
 
Package: scater
Commit: 3a85b7274868078d1bdc86bd7e2d31d435917c8e
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 14:41:58
Commit message:

 Fixed bug of not checking centering of default size factors.
 
Package: scater
Commit: 88384feb7f012e984c21ae283ec317109ecbb4b5
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 14:19:38
Commit message:

 Updated various documentation on size factor treatment.
 
Package: scater
Commit: 80f984830f450c862c3d506e63449a6d1d5929ef
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 14:07:40
Commit message:

 Streamlined handling of control-specific size factors, centering.
 
Package: scater
Commit: 9f48e2dadcf7ad59e10e94b447b8ad002b54e079
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-30 17:54:55
Commit message:

 Fixed missing comma.
 
Package: scater
Commit: d68f3a8b1bc3bb40658be01afe87197ab607b015
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-30 17:44:48
Commit message:

 Minor streamlining of code.
 
Package: scater
Commit: cf8a2136b462d7efc24e7bd1e92bfd3e1aaf3d8f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-29 14:48:10
Commit message:

 Fixed inconsistency between feature_names, rownames.
 
Package: scater
Commit: df8598da8021e3e3401c00c0fb88a4416d269640
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-29 10:10:41
Commit message:

 Modified plotHighestExprs to support alternative matrices.
Streamlined code to remove unnecessary errors, variables.
Added support for plotting raw values, w/o percentages.
 
Package: scater
Commit: 98cf41ea302f69abb94a0c747004531f95f2dc34
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-11-28 18:52:35
Commit message:

 Merge pull request #36 from Shians/master

Changed featureData to rowData in qc.R 
Package: scater
Commit: e963615f95afbd6a3b2ff12696c033e7fac75d5c
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-11-28 18:52:04
Commit message:

 Merge pull request #35 from LTLA/master

Force recompilation after Rcpp updates 
Package: scater
Commit: 671cd8ce6e2514d3ab0311d01331de4cac679459
Author: Shians <registertonysu@gmail.com>
Date: 2017-11-27 01:45:37
Commit message:

 Merge branch 'master' of github.com:Shians/scater
 
Package: scater
Commit: 6db2b391b284cda25b949be967e6ccb50ffed502
Author: Shians <registertonysu@gmail.com>
Date: 2017-11-27 01:45:00
Commit message:

 Recompiled documentation
 
Package: scater
Commit: eec925fd947465517b19e66d3a08d6eb4fd67f29
Author: Shians <registertonysu@gmail.com>
Date: 2017-11-27 01:44:50
Commit message:

 Changed featureData to rowData
 
Package: scater
Commit: 977beec96f1a4d2dfe76b957bae6dce46391786f
Author: Shians <registertonysu@gmail.com>
Date: 2017-11-27 01:41:42
Commit message:

 Changed featureData to rowData
 
Package: scater
Commit: 23196ba299c8694f62ee75bfc140b4e9284cf5a1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-25 16:29:21
Commit message:

 Merge remote-tracking branch 'davis/master'
 
Package: scater
Commit: 61007b0b014b90848b638f708da7aeff219f341a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-25 16:27:13
Commit message:

 Bumped version to force recompilation for Rcpp updates.
 
Package: scater
Commit: 7b9e9e63b21d338a4622b919dcb510694fa99141
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-11-21 14:49:19
Commit message:

 Merge pull request #34 from LTLA/master

Various fixes to read10xResults 
Package: scater
Commit: c47ba03731b7e87069a7d049ddc468639fec87b2
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-19 17:45:04
Commit message:

 Clarified log base during normalization.
 
Package: scater
Commit: 736d78b978c2f51efba1d159f17fe1618ade3bf1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-15 09:20:08
Commit message:

 Cleaned up calc_average C++ code slightly.
 
Package: scater
Commit: c892b9b8a3c7e8ed23f3eb6ab55589f239b00a5f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-15 09:18:42
Commit message:

 Fixed bugs with read10xResults with duplicate colnames.
Avoid dgTMatrix input prior to C++ code.
Added correct cell barcode subsetting in loop.
 
Package: scater
Commit: 93d43e92e4e8a756251456b292a026173edf7c5d
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-11-14 12:41:13
Commit message:

 Merge pull request #32 from LTLA/master

Minor fixes to calcAverage code 
Package: scater
Commit: af8630810c16ac6d9859384b82cfca224e978d3c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-04 15:13:04
Commit message:

 Merge remote-tracking branch 'davis/master'

Conflicts:
	DESCRIPTION
 
Package: scater
Commit: 85ebb2681c8b4d248e82a838ec7f08d15e34d957
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-04 15:11:35
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: scater
Commit: f444744021bb2848d2948e3522983ff7e677c784
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-04 15:10:00
Commit message:

 Minor fix to variable extraction in plotPCA for QC.
 
Package: scater
Commit: e48f7052849821e16b63efcf5c8674c76ba1c036
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-30 10:22:58
Commit message:

 Merge remote-tracking branch 'upstream/master'

Conflicts:
	DESCRIPTION
	R/normalisation.R
	man/downsampleCounts.Rd
 
Package: scater
Commit: 12fb261cb52fa15d7f38fcc5821989cfef908122
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-30 10:06:53
Commit message:

 Avoid making unnecessary matrix in calc_exprs.
 
Package: scater
Commit: be4975910403d6109618a4aab3806f43bf21ca69
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-30 09:51:54
Commit message:

 Moved margin calculations into if() block.
 
Package: scater
Commit: f2a5db934335a785b27061fce245dc00b67a15a2
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-25 17:27:02
Commit message:

 Updating docs; fixed bug in normaliseExprs
 
Package: scater
Commit: 178b3909fd18f39cd62dee546270603bc050ba2d
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-25 10:57:28
Commit message:

 Merge pull request #30 from LTLA/master

Fixes to 10X-related function documentation. 
Package: scater
Commit: 40e4286a5147de9f41af562df0870bb5363fe70a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-24 11:57:20
Commit message:

 Bug fix to ncomponents= for plotReducedDim.
 
Package: scater
Commit: 5848feb988c63ba47fc6590d1575ece2412817b1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-22 09:29:26
Commit message:

 Fixes to 10X-related function documentation.
 
Package: scater
Commit: 81ac3c85cb97a0d5de612d7a69638d355612971b
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-20 17:23:32
Commit message:

 Incorporating new downsampleCounts() function
 
Package: scater
Commit: 6bfc2326fd052bb2f3e371a90a63e41531d791c0
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-20 08:49:41
Commit message:

 Merge pull request #28 from LTLA/master

Downsampling method 
Package: scater
Commit: 0b712caa36e235bef477d9f4f74f072635c0d910
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-19 11:27:01
Commit message:

 Tested for correct statistical properties in sampler.
 
Package: scater
Commit: 18ba2ad6da5fa4f59c30e83eec52e84dd92119a0
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-19 11:14:53
Commit message:

 Added defense against very unlikely segfault.
 
Package: scater
Commit: ccde05bb64633e1354c639caf5c05984f2a5a0f6
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-19 11:09:16
Commit message:

 Implemented sampling wt. replacement, updated tests.
 
Package: scater
Commit: 251eac69bc5081c70f2b6fd67febae6cc5f537aa
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-18 13:02:30
Commit message:

 Fixed bug in downsampling, added tests.
 
Package: scater
Commit: a3418d713cff5cfb895a12fe710b8eda796b9eee
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-18 12:34:09
Commit message:

 Added function for matrix downsampling.
 
Package: scater
Commit: 968c481ec2330d8b0b2c134d3d6b9d3e5760bfc1
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-18 08:07:05
Commit message:

 Update for release
 
Package: scater
Commit: 87644c7de740c9e645750e9470d0a2c60ff47b85
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-10 14:35:04
Commit message:

 Update Appveyor badge 
Package: scater
Commit: e2b19a32072c6c462b0a0f2aff6537cbbec7f57a
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-10 14:23:11
Commit message:

 Update Appveyor badge 
Package: scater
Commit: b6af352d833034bc4ebd360471f615bcbddd3ae0
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 14:19:01
Commit message:

 Merge branch 'master' of https://github.com/davismcc/scater
 
Package: scater
Commit: a85cc4f8f88b662e2bda4d13768e2927e69672e1
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 14:18:48
Commit message:

 Updating appveyor setup
 
Package: scater
Commit: 9b88f6b1380cf27573322fccb9c8ce1b90e21e5e
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-10 14:04:52
Commit message:

 Update README with Travis CI badge 
Package: scater
Commit: 5e057e9a005fa5e7402782f6caf3841b08a9b0d9
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 13:18:42
Commit message:

 Adding codecoverage back to Travis CI settings
 
Package: scater
Commit: f605cc0f90e752943ab22ab101764d975179bc51
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 13:11:30
Commit message:

 Updating to native R support in Travis CI
 
Package: scater
Commit: feef1f010363326e6baa70836a936bbb05095df2
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 13:01:04
Commit message:

 Updating dataviz vignette
 
Package: scater
Commit: 9068effcd6052985984336e40103ad120cb0c13b
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-09 21:40:30
Commit message:

 Updating vignettes and calculateCPM code
 
Package: scater
Commit: 608bcfcc3caeb143240cd2858d3746217c457ee3
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-09 14:30:32
Commit message:

 Updating README
 
Package: scater
Commit: 643a2828553dccea517c6eacfe193c457fbec8d4
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-09 13:34:41
Commit message:

 Merge pull request #7 from LTLA/master

Compatibility fixes for sparse matrices 
Package: scater
Commit: abe3989476342055f72b7cb0f9a7fc65149cf168
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-09 13:34:00
Commit message:

 Merge pull request #4 from PeteHaitch/master

Fix potential integer overflow bug in calc_top_features_internal() 
Package: scater
Commit: ec4631587568c9280c759230bee322c5567cd6fe
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-02 17:56:00
Commit message:

 Renamed to .general_*Sums for consistency.
 
Package: scater
Commit: f321da3ff57b7c16d06b738b7818b342b63e318d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-02 17:33:35
Commit message:

 Propagated .row/colSums to remaining functions.
 
Package: scater
Commit: 9f632848b6600a152505d482ee33d2e0b28a97fd
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-02 17:30:38
Commit message:

 Merge remote-tracking branch 'upstream/master'

Conflicts:
	R/10ximport-wrapper.R
	R/qc.R
	R/utils.R
 
Package: scater
Commit: 4aa05f50511c4e9009d7d41ad05965fd5eb794cd
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 10:37:32
Commit message:

 Updated NAMESPACE.
 
Package: scater
Commit: b788e2feca6597ddba40f0e5c63ba3a7230730c8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 10:22:10
Commit message:

 Added Matrix::colSums import.
 
Package: scater
Commit: 2c4e473eb066c28e41f477c22ac90ca3e55e556d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 09:55:03
Commit message:

 Coerced read10XResults output to dgCMatrix format.
 
Package: scater
Commit: 5db1b24b0b0332ec109551b3a9ceaa5913a447c9
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 09:47:49
Commit message:

 Replaced all uses of matrixStats::*Vars with .general_*Vars.
 
Package: scater
Commit: 450be7dc276138dc7270f15745238b7abc8c6e35
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 09:42:56
Commit message:

 Added tests for correctness of some C++ code.
 
Package: scater
Commit: f44f6a1ed8e033373e3bee2619c27f8830e196fd
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 09:42:36
Commit message:

 Added C++ code to compute row/column variances.
 
Package: scater
Commit: 73e74597041361e14864309f53771ceb4077a1f9
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2017-09-15 19:31:56
Commit message:

 std::accumulate() takes its return type from init
Previously, this line would return an int that was then cast to a double. Now, the result is explicitly a double. This avoids potential integer overflow in the sum
 
Package: VariantToolsData
Commit: 5938a63d5b6a086ad55a9ca6f1badc8fc0d2d124
Author: larman <michafla@gene.com>
Date: 2018-01-19 16:54:41
Commit message:

 use BiocStyle::latex()
 
Package: ideal
Commit: 0baa438133438bda8aa89dd1ca8cf5e6cad04d39
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2018-01-19 16:55:08
Commit message:

 version bump - 1.3.1, with new vignette output format
 
Package: flowCL
Commit: 67cb8e39a7c3c019a3c1a089f207a17ac55ca91a
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-01-15 19:27:51
Commit message:

 Merge branch 'master' of https://github.com/jmeskas/flowCL
 
Package: flowCL
Commit: 0e1c99eee5310058b9354a614cd000a9fdd635af
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-01-15 19:15:46
Commit message:

 Bumped to 1.17.2 
Package: flowCL
Commit: 4b3705782a635ab1709f8d65fb8303e2a1065e14
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-01-15 19:15:06
Commit message:

 1.17.1 did not install. Conflicts in supportingFunction were not resolved. 
Package: flowCL
Commit: 217fede8f501e207f83008b22861eb3ae91021a3
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-01-15 18:52:54
Commit message:

 NEWS~ deleted 
Package: flowCL
Commit: a4fcb4e005ab295a55a07bfdc00f402d6d06a699
Author: jmeskas <jmeskas@bccrc.ca>
Date: 2018-01-15 18:34:47
Commit message:

 Delete NEWS~ 
Package: ideal
Commit: be09750504079548ae1a87b4c2ea9d158c20fe4d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2018-01-19 16:53:38
Commit message:

 correct output for the vignette, as html_document2 is now deprecated
 
Package: ideal
Commit: e393d69573521bdf7c1025c9862417bcd09c46d2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-12-18 23:04:23
Commit message:

 edited appveyor config
 
Package: ideal
Commit: f10c8e3f8369928d3c2a644c01882b370ef2d991
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-12-18 19:53:21
Commit message:

 updated travisCI config
 
Package: ideal
Commit: 3b61fd18ddf1892254d2e21b3d79b243cb1718a7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-12-18 19:51:17
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: ideal
Commit: 09f85d5358def60ed521c7935f309bb875dcb90b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 14:58:38
Commit message:

 added small note for button, which in the vignette does not trigger any tour
 
Package: ideal
Commit: 51c5ecb8defb7a583082d2c36dd63f8f52f72828
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 14:36:38
Commit message:

 listing in the vignette now corrected
 
Package: ideal
Commit: 37019fc238e9e8530b7808010c530dd9d083dc43
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 14:27:20
Commit message:

 pkgs now listed, and with links, in the vignette
 
Package: ideal
Commit: 67689f29ee351179e9f221d288c8d3942661346b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 14:19:05
Commit message:

 reduced size by removing unessential screenshots, plus removed helper func for installing orgdb and txdb packages - instead of that, there is a small section explaining the same thing in the vignette
 
Package: ideal
Commit: 865bfd7c67b5b6a8d3cbde5c38f27b0287d53a20
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 12:04:51
Commit message:

 edited vignette to explain fallback solution in case of edger/limma/simple data frames
 
Package: ideal
Commit: 791b9a24dc11ded1dfe3e570b761354205bb0960
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 08:03:02
Commit message:

 now naming man and r code consistently
 
Package: ideal
Commit: 747992798cb42c35fd9a3ea216e3dc3930731d5d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 07:59:50
Commit message:

 addressing valerie's comments
 
Package: ideal
Commit: 2ea1bd63d099cc05aa698d7f8c0c9fe251a4626b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-27 08:11:29
Commit message:

 edited some code in the vignette to avoid timeout, plus edited appveyor conf to test also on release
 
Package: ideal
Commit: 9da2fc814888e507bc55b073f2e1e0b28f7ebaed
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-27 06:53:50
Commit message:

 version bump to trigger build
 
Package: ideal
Commit: d87e52429d8c0968aee206684534363e7d98bd55
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 20:05:01
Commit message:

 version bump, 0.99.1
 
Package: ideal
Commit: bd5b7179889b97824863dde326cf16d1e4e436df
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 20:03:09
Commit message:

 edited appveyor for 64bit
 
Package: ideal
Commit: 4090e2ca0e585572e5fd98eb2f1ced2169ad0275
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 13:35:58
Commit message:

 added last edited field to vignette
 
Package: ideal
Commit: 8c907cf329ca3210ed618b10ff9b6ed8bef87a05
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 12:28:33
Commit message:

 cutting down the vignette compilation time
 
Package: ideal
Commit: 75f321909ee4b50a1e5249d15bf868622a231505
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 11:05:02
Commit message:

 Version 0.99.0 - ready for Bioc submission
 
Package: ideal
Commit: b6ebd22a9b46ebbd997bfcd33369894e135ea1fc
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 22:18:47
Commit message:

 version 0.9.1, version bump after all changes
 
Package: ideal
Commit: 2d2e60fc81fe24345d0c5b8d23db4fe32854d0bf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 21:52:20
Commit message:

 added practically  all of the downloadable objects, even more ready now :)
 
Package: ideal
Commit: 6a5c613fe4f82dfc3cf832607f0ba6822409ea40
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 17:53:00
Commit message:

 commented out unused code
 
Package: ideal
Commit: 674aa84f5632fce32b974b1babd15c886162e730
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 17:37:30
Commit message:

 added instructions as rendered from the rmd vignette, to md - keeping out the imgs and the html parts
 
Package: ideal
Commit: 3e4948b9d5d5f8772284d62cbaeb31fc596ebdb9
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 17:22:46
Commit message:

 only html vignette as output
 
Package: ideal
Commit: d222190e0965c81a9c7c53c16f8cc3495ce7db24
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 16:45:04
Commit message:

 edited section title after HB feedback
 
Package: ideal
Commit: ab695502bf242dc6a442704656efcf82edfab9ef
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 15:37:53
Commit message:

 version 0.9.0, quite close to submission. added all screenshots, vignette is now finalized. next: downloadable outputs
 
Package: ideal
Commit: e3c536a438342f6d38d4627aa4f9e39d01179776
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 13:17:41
Commit message:

 edited travis for codecov integration
 
Package: ideal
Commit: 04eefc3801b972a658c7e299cfe7993fce1745e6
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 13:14:52
Commit message:

 also added the quick viewer
 
Package: ideal
Commit: dbaf2cd3b95fae3ab09bab38b912656e31c08a36
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 10:40:31
Commit message:

 included basically all the text for the intro tours. some are not so fantastically positioned, but i cannot do that much about it..
 
Package: ideal
Commit: c64efe7208bcb7234763aba076195f722a9169d1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-20 22:28:16
Commit message:

 added all intros steps, plus some ids to the elements to make hints more readable since better connected
 
Package: ideal
Commit: 352ee34beace45b617865b0353349a198e6d2ceb
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-20 16:20:49
Commit message:

 v 0.6.2, also added func to setup all annos, plus fixed typo in readme
 
Package: ideal
Commit: aa75a9105ad256130d983b7fe0f90a60a407fc86
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-18 23:07:13
Commit message:

 working towards the tours, making them coded in dfs read from installed data. nice
 
Package: ideal
Commit: bd6651fe99083499f130b2d020ab5f585e0dbf94
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-15 15:43:01
Commit message:

 updated appveyor yaml
 
Package: ideal
Commit: e45d270ba44afbb1abe2ea8270d3b9312619567f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-15 13:28:42
Commit message:

 setting up updated version for travisCI
 
Package: ideal
Commit: 79fc91d132018b646a5fc3580e7eb53d2d95208f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-10 15:00:20
Commit message:

 v 0.6.0 - indeed using introjs. will think of how to make it effective, now not so far from very final version
 
Package: ideal
Commit: c648eb54e4b626401dc1474aed58f8e56541f48f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-06 11:00:04
Commit message:

 added textual help on data setup panel. specifies a little more in detail how the data should look like
 
Package: ideal
Commit: 781d4457557676a687745f0d5ad30419cf53b4c1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-05 23:32:25
Commit message:

 effectively transitioning to adopting rintrojs. need to decide what tours to offer, and how to code them. introbox or coded with ref to elements, need to ponder on both
 
Package: ideal
Commit: b9e2731de5bddff156fdd7cf539d3b60d8446f08
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-05 23:13:28
Commit message:

 added all help texts for bscollapse elements. better text in all other mds for the app
 
Package: ideal
Commit: 386616fcb8349db64cc965b6bc2943ea573b4a28
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-02 16:16:38
Commit message:

 finished first draft of text for vignette - only screenshots are missing. plus, edited a little the code and the docu
 
Package: ideal
Commit: 05e14b1d2ccbc58aaa6dbe2b2143df6d4227d3ed
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-01 22:51:14
Commit message:

 working on both the readme and the vignette, good point to snapshot
 
Package: ideal
Commit: 5dc6fe050796c7d3cb54e412880eda5ae7283f2c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-01 17:09:04
Commit message:

 slight edits to the report template
 
Package: ideal
Commit: 87a6122fae9e5b9b7340bf4d9c68f18d18c4a68d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-01 16:29:26
Commit message:

 edited the vignette, will use pcaExplorer as a basis
 
Package: ideal
Commit: 08090346d0eb892992111f3ee4cc207b3a19102d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-01 11:10:46
Commit message:

 added small sec for provided input in the report template
 
Package: ideal
Commit: 13b17b9b8a4aa559a44015c41e0e85341dd77468
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-02-14 11:17:02
Commit message:

 added nice backbone for template report, plus edited tab panel names
 
Package: ideal
Commit: acdf7d8076710f95c7017522ea72f3e9661c1d1b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-25 13:09:02
Commit message:

 added first implementation for heatmaps of go categories
 
Package: ideal
Commit: de9baab1f7ee6dd14baddfd95b17931bfaa68753
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 15:37:45
Commit message:

 restore first tests, will build upon this later
 
Package: ideal
Commit: fc15d6e6a05a95e95b33c64830f9690c948a90b2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:45:39
Commit message:

 added documentation in roxygen comments for all funcs
 
Package: ideal
Commit: 6609c3233fb27c063f61e324762c3cee3d31f919
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:45:11
Commit message:

 one only maplot function with support for providing vector of genes to be plotted
 
Package: ideal
Commit: 9781fa460a1333d0b020761791cc39cc7f77549c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:44:23
Commit message:

 added maplot with custom list, plus commented PoP for bsplus with carousel - for images displaying features
 
Package: ideal
Commit: 7b01eb68b8f502bebd8147a3552cb00cafc5261f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:43:40
Commit message:

 exports correctly in the namespace
 
Package: ideal
Commit: a1a5df400a816f7cc0fcc3fefe538d1a772ccef8
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:43:14
Commit message:

 added documentation for exported functions
 
Package: ideal
Commit: d37e73ad2cc3ea2f4b4412f92674d6adbe334d29
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:41:52
Commit message:

 added example text files for sepguesser examples
 
Package: ideal
Commit: d0f89a73f58d2b0be023b12d89ea51dc628997a4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-16 12:46:44
Commit message:

 added rug option for the ma plot
 
Package: ideal
Commit: ef9f125cfb6bf5c2a2c70522db610edcfcd2ed0f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 16:03:44
Commit message:

 removed footer where not necessary, there is already one at the very bottom
 
Package: ideal
Commit: 4b9054d73619488b378cfbfcdf376f10dd927792
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 15:40:46
Commit message:

 removed ideal_ ui and server, not using that structure anymore - for now :)
 
Package: ideal
Commit: a0b226b0eccb74c111905c1dd91f96cd01bede69
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 15:38:11
Commit message:

 moved the aux ideal files to the dedicated AUX_ideal folder, also in the devel folder
 
Package: ideal
Commit: 485f737db178b1339b21d883c8e2661c7d8a989e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 15:37:39
Commit message:

 topgo now in the depends. it looks kind of ugly but it seems to work just so afaik
 
Package: ideal
Commit: 3d9a7d83ec4f1266b957270c7bde0f012c5f758c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 14:55:11
Commit message:

 fixed heatmap brushing, fixed and made robust the goana with functions from AnnotationDbi. also putting now topGO explicitly called, maybe move to depends?
 
Package: ideal
Commit: 402e245e0b98a87ee9e31f7ed23735f3d63f15ec
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 13:50:51
Commit message:

 version 0.4.0 - massive moving of code to the one file, to avoid sourceing. coord cartesian instead of limits, gene box info now works correctly and with extra link. also correct display of exp design if dds provided
 
Package: ideal
Commit: 36b71e01c4ec8d9d49c94bed481b09cac4b7680e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 13:17:48
Commit message:

 added explicitly helpers.R file, plus using aes_string to avoide NSE notes
 
Package: ideal
Commit: 6f9df90f3e57483886b6044fbfdd25d8a48781b4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:47:16
Commit message:

 gene symbols now taken correctly by unnaming the vector, plus on the way to replace ylim with coord_cartesian limits - this will only zoom in
 
Package: ideal
Commit: c7e06d29287c251eaf3925446223019f0c436388
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:46:11
Commit message:

 volcano plot edited as for plot ma
 
Package: ideal
Commit: 7f95e46d3f8f96d87fbbaf0aec95881c46c88d58
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:45:44
Commit message:

 backbone for entrez based retrieval of info
 
Package: ideal
Commit: 2da6ab4e0557cbedf6689779c62b1cd5e32303bb
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:45:00
Commit message:

 using base funcs where possible
 
Package: ideal
Commit: 3d4fd5888fb288cc323c3dc702203b2633311a1f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:44:32
Commit message:

 ma plots now more robust
 
Package: ideal
Commit: 194e08af11d54b2f14b79e20378f61f2fc6eb50c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:43:59
Commit message:

 reworked ggplotcounts
 
Package: ideal
Commit: 84bdf81185cb4c7fc8e589a32d259bc7080f2c1e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 14:33:03
Commit message:

 added biocparallel in the imports, and better code indenting
 
Package: ideal
Commit: 8aeb7b68608e4e93503557150f1636646769ab67
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 14:13:19
Commit message:

 edited NEWS
 
Package: ideal
Commit: 9ab1b95ce2439a0200649aefbe7781dc33ad2be1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 14:03:41
Commit message:

 renamed main func to ideal.R
 
Package: ideal
Commit: beb32d59f2042c4449d1f571eaa67c0514803804
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 14:01:48
Commit message:

 cleaned up R directory
 
Package: ideal
Commit: 7de1d7131fc40aeda7427de0a4afa8b53558bc60
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 13:58:00
Commit message:

 record all .R to proceed then to cleaning
 
Package: ideal
Commit: f9e96675d093428e9edb0a0b56243c079604240e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 13:45:24
Commit message:

 version 0.3.0 - quite some massive reorganization of the files, but now way clearer
 
Package: ideal
Commit: 526a804c88d24aa9ddb0a1540391a170183612ba
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-05 17:45:45
Commit message:

 added pkg documentation file
 
Package: ideal
Commit: 45eaa3207dce65d3692c1aab2380a18c1d2a446e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-05 14:44:45
Commit message:

 restructuring, and also added backbone for heatmap by go cat plot
 
Package: ideal
Commit: 3633f50d4f7d91cee6be3d51a99c504f3a94dea7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-12-21 16:29:35
Commit message:

 added diagnostic plot of dispersion estimates with collapsible box
 
Package: ideal
Commit: fc6697c44fbc2ae3fbbb0264f19f747ed7e891cf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-28 12:30:28
Commit message:

 couple of fixes and improvements. added couple of TODOs that i will try to address, and then also things such as writing the report in temp folder
 
Package: ideal
Commit: efaca32563927b97e46a03d6ba4154624a65c080
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-24 15:50:28
Commit message:

 v 0.2.0 - made a draft that can be installed. will anyway need to extend the documentation and so on, but at least I got a source pkg archive
 
Package: ideal
Commit: 604e1fa84a4fd6bb0b2783d12e4a9a768f44fb6f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-24 09:59:27
Commit message:

 cleaning up the code for ui.R. next for server.R
 
Package: ideal
Commit: 1eb0e267e1bf6a97b501aa1875ca3d0f8cdfeb0b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-23 13:12:12
Commit message:

 css trick to have page visualized more correctly - or more nicely
 
Package: ideal
Commit: df70f9cd3d7a7861e94fecc66d2bae43bf14d43e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-21 11:13:46
Commit message:

 added topgo & goseq for GSE, respective tables, structured layout for better column usage, and also changed order of pages for having welcome screen. TODO: separate welcome and instructions to have better content thematic separation. next: work on improvements list
 
Package: ideal
Commit: 4538dc8daa2f4c9ea13e3dd66cde386b904eaaac
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-16 15:22:18
Commit message:

 use sepguesser to guess the separator, seem to be a nicely working heuristics
 
Package: ideal
Commit: 4b6273db687e0255f635669c1eb66d3dd1e4e3be
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-16 14:28:31
Commit message:

 added some formatting via fluid rows, plus change of color for valueboxes, and added some progress indicators for long running operations
 
Package: ideal
Commit: da2d57600db1e83721aaec4a18d6b61373d43b56
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-11 16:48:27
Commit message:

 boxes for main page, and corresponding restructuring to logic server. plus, progress messages now display additional detail. footer expanded for the app
 
Package: ideal
Commit: 027f03199346affd4a2b89e728c3a6669751d7b1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-10 14:41:49
Commit message:

 added progress messages here and there. also, edited layout a little with more well panels. dropdown menu now has no green badge anymore, see what happens for the header if request is accepted
 
Package: ideal
Commit: df6a9a4f66082b44ee0984f19b9d8174061d8f59
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-04 15:32:55
Commit message:

 one step less to have 3 in total, better organization of widgets in tabs. will continue on this
 

Source Code & Build Reports »

Source code is stored in Git.

Software packages are built and checked nightly. Build reports:

 

Development Version »

Bioconductor packages under development:

Developer Resources: