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GIT Logs

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

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Package: AnVIL
Commit: 5c9d8ba0fb375261e7637229dedc1e6a9b8a3c1c
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-30 13:48:34 -0400
Commit message:

 version bump
 
Package: AnVIL
Commit: bc4680ab4db86dd1bc87aba3f71e4949fb6d43bf
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-30 13:48:05 -0400
Commit message:

 update Leonardo, Dockstore service md5 sums
 
Package: AnVIL
Commit: 053bccb2a915d9acfa8421d8839c106e8a25f80b
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-30 12:41:12 -0400
Commit message:

 add avfiles_* functionality for accessing workspace bucket
 
Package: AnVIL
Commit: f1ada1f75c02dc94d856d9466636c479bdeb85dc
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-30 12:35:30 -0400
Commit message:

 clean return value of gsutil_ls()

- seems like this is a capture of a directory listing, including
  formatting; strip the formatting and blank lines
 
Package: scMerge
Commit: bb12ae602e47161cf871fc139af6c62313a3fd2f
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-30 13:40:07 +1000
Commit message:

 upd GHA workflow
 
Package: scMerge
Commit: e0755222cad575d6354f43ba83c54dbb357b4acc
Author: Kevin Wang GCP <kevin.wang09@gmail.com>
Date: 2020-05-30 03:29:09 +0000
Commit message:

 separate out check inputs function
 
Package: scMerge
Commit: 5cf4d7f5721adac70804fb50feafb3c8b9b2439d
Author: Kevin Wang GCP <kevin.wang09@gmail.com>
Date: 2020-05-30 02:33:04 +0000
Commit message:

 add section on other array in vignette
 
Package: scMerge
Commit: d8dd6ce9b88fedce553b640138a87113c5833421
Author: Kevin Wang GCP <kevin.wang09@gmail.com>
Date: 2020-05-30 01:29:12 +0000
Commit message:

 rm BACKEND arg
 
Package: scMerge
Commit: 98cd7c6fdfe1dc3ae513d16a70bc2386f9448ca8
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-19 18:19:41 +1000
Commit message:

 remove travis
 
Package: scMerge
Commit: c19599345cc30c0381fa06cca59559766ee0fcdc
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-19 15:32:22 +1000
Commit message:

 use github actions
 
Package: scMerge
Commit: be28cd47b8cc6d6ba8d1a11c6d299133267ee6c6
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-19 12:54:43 +1000
Commit message:

 upd travis
 
Package: scMerge
Commit: f80978d83760b54049ecea79e0abb85ab1bfc381
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-18 11:43:38 +1000
Commit message:

 travis devel bioc
 
Package: scMerge
Commit: 26a32b317d83e115952ba1e7bf9c2f4cfdc476c4
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-17 22:05:22 +1000
Commit message:

 Resolve branch merge conflicts
Merge commit '5ff5363f94f5d9073dc1d78c990903e5080d8350'
 
Package: scMerge
Commit: 200f7583e0232c6f681df8dd88a3f711534d6cb9
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-17 08:43:57 +0000
Commit message:

 consolidate tests for matrix in R4.0
 
Package: scMerge
Commit: 5ff5363f94f5d9073dc1d78c990903e5080d8350
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-17 20:12:28 +1000
Commit message:

 Pull from origin after fixes via docker
Merge commit '7af3878e1f59c55a73c50c32bbdca650d41fcfd6'
 
Package: scMerge
Commit: 70652761e6d0f45a73e24da419dcd407416a6aed
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-17 20:11:39 +1000
Commit message:

 Pull from BioC after version bump
Merge commit '875b51724c5f099864ba0bdc750a7be491df0013'
 
Package: scMerge
Commit: 7af3878e1f59c55a73c50c32bbdca650d41fcfd6
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-17 10:02:47 +0000
Commit message:

 rm C++ codes
 
Package: scMerge
Commit: dca1660a669500aa2c59aaca7bef0107e72f7dce
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-05-17 08:43:57 +0000
Commit message:

 consolidate tests for matrix in R4.0
 
Package: scMerge
Commit: 9947cd94eb7e5f0993bd31d70e8fdcd727751271
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-03-25 18:34:02 +1100
Commit message:

 change travis set up
 
Package: scMerge
Commit: b30ae501de4d7650bd7f818f89f32fde1eccb7fb
Author: Kevin Wang <kevin.wang@sydney.edu.au>
Date: 2020-03-24 09:50:22 +1100
Commit message:

 rm dplyr dependency
 
Package: phantasus
Commit: 24584c83d82ac18653d1382b61fa43632a85425e
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-30 15:33:15 +0300
Commit message:

 version bump
 
Package: phantasus
Commit: 42f1e4748e3a8024b33f0ee48c994852a1b6b090
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-25 11:51:51 +0300
Commit message:

 version bump
 
Package: phantasus
Commit: 75e9b767d8c57add414619174966f20d83bd2a4f
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-25 11:50:37 +0300
Commit message:

 Merge branch 'master' of github.com:ctlab/phantasus
 
Package: phantasus
Commit: 2e41a62130e0c651cb18c3befd2ccbd7ab01e88c
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-23 13:05:33 +0300
Commit message:

 checking number of selected rows on row profile start
 
Package: phantasus
Commit: 8023a5f6aced9abad56d7686dec85bb16a054895
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 20:56:06 +0300
Commit message:

 Travis fix 1 (#154)

* Update .travis.yml 
Package: phantasus
Commit: 5ae6e3d86f7a0bd3804f99f4c1c6854f152b5dbf
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 15:31:17 +0300
Commit message:

 Update appveyor.yml 
Package: phantasus
Commit: 65ff2d0b4a43756ff036c5f74b38112032b0a1e1
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 15:15:39 +0300
Commit message:

 Update appveyor.yml 
Package: phantasus
Commit: 75e278903330216e334d3fc006f73d84b5b18e75
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 15:11:46 +0300
Commit message:

 Update README.md 
Package: phantasus
Commit: 59194a61442976e7e9748a425021561bfb211cf4
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 15:06:35 +0300
Commit message:

 remove osx bioc-devl from travis matrix
 
Package: phantasus
Commit: 62b87fd2bc7dac6bf4658d0af88e473518725126
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 15:00:52 +0300
Commit message:

 Update README.md 
Package: phantasus
Commit: c40cd66456d78d7645b184b6b727f2e74a6afe7b
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 14:04:52 +0300
Commit message:

 Even more proper image
 
Package: phantasus
Commit: ed604290ec0ded42322226593729bcdf5a21c8c7
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 14:03:57 +0300
Commit message:

 Proper image link
 
Package: phantasus
Commit: bcd9d807055b490961edbebb49afb0f967249245
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 14:00:43 +0300
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/phantasus
 
Package: phantasus
Commit: 5dfce1de888e20004b83e8dfce26c42f342a6276
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-05-13 14:00:21 +0300
Commit message:

 update README
 
Package: ATACseqQC
Commit: 2996d20e9b39825b38d580b2c38636199975d29e
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-05-29 21:55:02 -0400
Commit message:

 fix a bug the after shift, the index is not changed.
 
Package: sojourner
Commit: 813134af390bdd85fc62108690da90e9a5d176e1
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-29 17:28:29 -0700
Commit message:

 version bump to 1.3.1 for Bioc.
 
Package: sojourner
Commit: 7a968025fe1cfe42b2e63448854fe1462a8783ed
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-29 16:25:43 -0700
Commit message:

 updated package bioc url.
 
Package: CSSQ
Commit: afb08c818cd6fb869519f086adc9e08924775654
Author: Ashwath <akumar301@gatech.edu>
Date: 2020-05-29 19:49:50 -0400
Commit message:

 Updated Description
 
Package: CSSQ
Commit: 880212af21fb7489e6913df066cc325935098d1a
Author: Ashwath <akumar301@gatech.edu>
Date: 2020-05-29 19:37:17 -0400
Commit message:

 Edited Description
 
Package: sojourner
Commit: 786d397a96eec7a2608e35b12f627ac8595d99f5
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-29 15:50:04 -0700
Commit message:

 Merge updates from the Bioconductor (release 3.11), version number to 1.3.0 for Bioconductor sojourner develop branch.

Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
 
Package: sojourner
Commit: 0a613fed6292811e9da3e91a719277ebb09a316a
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-29 15:00:47 -0700
Commit message:

 - tested functions and fixed bugs caused by merging;
- R CMD check and BiocCheck;
- version bump to 1.1.5.
 
Package: sojourner
Commit: c24becfca8656ac98b64ecdd7320416cd8dea35d
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-29 12:27:43 -0700
Commit message:

 diff, merged and tested Dcoef.Helpers.R. The commented out functions was clapsed in the master branch.
 
Package: sojourner
Commit: a1a69793824da8170f7bf9121912d295e6a1cee2
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-28 16:32:02 -0700
Commit message:

 - tested remerged functions and fixed bugs caused by merging;
- regenerated package vignette.
 
Package: sojourner
Commit: 6982675cb95e5ed20d7fb5079b13285773099c0c
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-27 17:09:40 -0700
Commit message:

 (re)merged helperFunctions()
 
Package: sojourner
Commit: 0156e756029853a1aa11248bc6fd71d32a275957
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-27 16:43:16 -0700
Commit message:

 (re)merged exportTrackll;
tested and updated namespace, help doc.
 
Package: sojourner
Commit: 1a100a392922a78fe4e2c6e1ec5488df7b9890ff
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-27 00:12:21 -0700
Commit message:

 - moved plotComponentTrackOverlay() to selComponentTracks() in sojourner.pro;
- tested and further modifications on msd() and plotTrack()
 
Package: sojourner
Commit: 67d126f3c815296422b0ea4be85ffa71876d5b0e
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-26 19:07:49 -0700
Commit message:

 - merged plotTrack();exported .plotNucTrackOverlay vs plotTrackOverlayTrackl;
- re-merged msd(); msd.track vs. msd_track;
 
Package: sojourner
Commit: d39f82b84c7c4d8391f338675d2977295f33bc33
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-26 13:07:25 -0700
Commit message:

 diff and merged msd() function (for exporting msd.track vs msd_track etc).
 
Package: sojourner
Commit: eed6a6c520ef8dc2d2af7864a174ac2cd21145d0
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-25 02:38:34 -0700
Commit message:

 updated namespace and documentation after removal of pro functions.
 
Package: sojourner
Commit: 9d51d428621d529fa3b74c1947734794364bae5b
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-25 02:22:10 -0700
Commit message:

 (re)move merging added pro functions
 
Package: sojourner
Commit: 0313e553bc0bbcff32f758a3b508d7baebe9c2cc
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-25 02:11:28 -0700
Commit message:

 Merge branch 'origin/develop' to master

 
Package: sojourner
Commit: 575bfd1718d2d8d04ad64610f4ac81d35ed3416c
Author: Sheng Liu <sheng.liu@live.ca>
Date: 2020-05-25 00:50:04 -0700
Commit message:

 Prepared files for merging:
- renamed Dcoef_Helpers, Plotting_Helpers so it gets diff with the develop when merging.
- renamed plotIndividualTracks so it won't get compared when merging.
- kept compare_RT_CDF.R, plotLocalizations.Density.R, plotTrackOverlay.Dcoef.R unchanged so it won't get compared when merging.
- updated help docs and namespace
 
Package: sojourner
Commit: 1ba118a98cc87b744e33d90ed892040864985f4b
Author: sheng-liu <shengliumailbox@gmail.com>
Date: 2020-05-24 17:11:10 -0700
Commit message:

 updated namespace and help docs.
 
Package: sojourner
Commit: d7535a26df55ac3f61b35b2faf20fac0fe6f8c84
Author: sheng-liu <shengliumailbox@gmail.com>
Date: 2020-05-24 17:06:23 -0700
Commit message:

 (re)moved bootstrap, fitCDF, getCI, hmmTrackll, and selComponentTracks to sojourner.pro.
 
Package: sojourner
Commit: e2bb1dc9e286bf621af79011552f1350bf39ae56
Author: Xiaona Tang <xtang19@darwin>
Date: 2020-05-12 01:24:16 -0400
Commit message:

 Merge branch 'develop' of https://github.com/sheng-liu/sojourner into develop
 
Package: sojourner
Commit: 5766385862284ccf765adb1b1c6328d830608b8b
Author: Xiaona Tang <xtang19@darwin>
Date: 2020-05-12 01:24:10 -0400
Commit message:

 fixed plotLocalizations.Density(), plotTrackOverlay.Dcoef()
 
Package: sojourner
Commit: c1175902aa736dcdda31528950dc1781d7ca8392
Author: Xiaona Tang <xiaonastang@gmail.com>
Date: 2020-05-12 01:14:26 -0400
Commit message:

 fixed plotTrackOverlay.Dcoef()
 
Package: sojourner
Commit: 0e85e419510fa1aeb9746e2c6ecb6ac110e3c44b
Author: sheng-liu <shengliumailbox@gmail.com>
Date: 2020-05-09 23:08:39 -0700
Commit message:

 updated sojourner GitPages website
 
Package: sojourner
Commit: 0d96d7455d57c193dd077e8d25d03ea7c7415297
Author: sheng-liu <shengliumailbox@gmail.com>
Date: 2020-04-30 19:34:27 -0700
Commit message:

 Updated description and readme for proper citation.
 
Package: sojourner
Commit: c48763c7b5185a859fa256bfeb9cf91503519d12
Author: sheng-liu <shengliumailbox@gmail.com>
Date: 2020-04-23 18:27:18 -0700
Commit message:

 Add readTrackMate() function
 
Package: sojourner
Commit: c50e2a33231524b57adfae22eeb408f83a41581a
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-31 18:38:13 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: a6d073f6f088c8394b516ca1bd9e9deb7d1290b8
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-31 18:20:11 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: ae98cae0778adb9f740733ae4f8cae0c547b582e
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-31 18:20:11 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: a87cbd1c438f624028b75692f3654b0260b8769e
Author: Xiaona Tang <xtang19@darwin>
Date: 2020-01-31 17:00:51 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: a5b084f6c334367eef96b9b63df6ef69356c0e26
Author: Xiaona Tang <xtang19@darwin>
Date: 2020-01-31 17:00:51 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: 8c5cb62fed8e134dfe11f443996e6914654289a6
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-29 20:55:54 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: 1052ab30d60e9f2b7fcca9be8e3d52c4b726db7a
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-29 20:55:54 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: 06e59eae0bead9e61269b2ebe890a57cdd84bd32
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-29 20:48:40 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: 5a664a913682f1cfc44cfb4fb063d243999ec294
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-29 20:48:40 -0500
Commit message:

 resolved Merge conflicts
 
Package: sojourner
Commit: 0f212f663e43424c0dc130786124913fb947794d
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-29 20:31:07 -0500
Commit message:

 Update Bootstrap_fitRT.R
 
Package: sojourner
Commit: fa7aae40ba3f790e01337a2a369d8ebc4d897311
Author: Xiaona Tang <xtang19@galapagos>
Date: 2020-01-29 20:31:07 -0500
Commit message:

 Update Bootstrap_fitRT.R
 
Package: sojourner
Commit: e0c4a020a5468320ac35f0c0136630e587241bae
Author: Xiaona Tang <xtang19@galapagos>
Date: 2019-11-25 14:39:22 -0500
Commit message:

 Merge conflicts
 
Package: sojourner
Commit: 326b7e3c371de41bc7ae68a7ec9707ac3a0ab03d
Author: Xiaona Tang <xtang19@galapagos>
Date: 2019-11-22 19:31:07 -0500
Commit message:

 Merge conflicts of Boot_fitRT.R

Merge branch 'develop' of https://github.com/sheng-liu/sojourner into develop

# Conflicts:
#	R/Bootstrap_fitRT.R
 
Package: sojourner
Commit: 6722b4dd3c5ffcb7c8d9b3eb91e74d3e3168ce61
Author: snjy9182 <snjy9182@gmail.com>
Date: 2019-11-25 13:15:59 -0500
Commit message:

 Namespace and Bootstrap_fitRT.R export fixed.
 
Package: sojourner
Commit: 94ecb59c25d45762f8d373e43ba8bd95e55fccce
Author: Xiaona Tang <xtang19@galapagos>
Date: 2019-11-22 19:31:07 -0500
Commit message:

 Merge conflicts of Boot_fitRT.R

Merge branch 'develop' of https://github.com/sheng-liu/sojourner into develop

# Conflicts:
#	R/Bootstrap_fitRT.R
 
Package: sojourner
Commit: c00a9cd49795543b324bb2e2146f5b0a0757cd1d
Author: Xiaona Tang <xtang19@galapagos>
Date: 2019-11-22 18:51:59 -0500
Commit message:

 Fixed Bootstrap_fitRT.R to export multiple functions.
 
Package: sojourner
Commit: 8573e8b38c45a987e78f1a7717ab363ad0e2a041
Author: Xiaona Tang <xtang19@galapagos>
Date: 2019-11-22 18:51:59 -0500
Commit message:

 Fixed Bootstrap_fitRT.R to export multiple functions.
 
Package: sojourner
Commit: 36569f69fee965f2ab0f30e5742b7ac3ae804709
Author: Xiaona Tang <xtang19@galapagos>
Date: 2019-11-22 15:58:57 -0500
Commit message:

 Merge conflicts of plotIndividualMSD().

Merge branch 'develop' of https://github.com/sheng-liu/smt-beta-0.3.9.1 into develop

# Conflicts:
#	R/plotIndividualMSD.R
 
Package: sojourner
Commit: 42d2e3ea84bc940e004f972bd3c7cb65d3210b51
Author: Xiaona Tang <xtang19@galapagos>
Date: 2019-11-22 15:35:56 -0500
Commit message:

 plotTrackOverlay.Dcoef();plotLocalizations.Density();plotIndividualTracks();plotIndifidualMSD()

Fixed a bug of plotTrackOverlay.Dcoef() when there is no track left for certain images after R sqaure filtration.

Modified plotLocalizations.Density() to plot 2 kinds of localization plots for each image stack, one with square-shaped bins colored based on number of molecules in each bin, the other with each molecule as a dot colored base on local density of molecules. Also added an option to customize color for the dot plot.

Modified plotIndividualTracks(), with options to sort tracks by dwell time, diffusion coefficient, or R square of MSD fit, also with options to add or not add legend on each panel.

New function plotIndifidualMSD() to visualize correlation of MSD regression error (R square) and the corresponding diffusion coefficient. This function can also plot all the individual MSD fits for visualization and diagnosis purpose.
 
Package: sojourner
Commit: 7eed5f00217ed9d3eef7443e5cabe9a81912ff6a
Author: Xiaona Tang <xtang19@galapagos>
Date: 2019-11-22 15:21:35 -0500
Commit message:

 A series of functions to calculate 1-CDF of trajectory dwell times, boostrap the data (resample) and fit all the boostrapped data sets with multi-component exponential decay model to calculate averaged residence time and the standard deviate.
 
Package: sojourner
Commit: c6ebf88af1722fb7770ba579fac1fcf9bd5905cd
Author: Shannon Town <xiaonastang@gmail.com>
Date: 2019-11-22 12:38:51 -0500
Commit message:

 A series of functions to calculate 1-CDF of trajectory dwell times, boostrap the data (resample) and fit all the boostrapped data sets with multi-component exponential decay model to calculate averaged residence time and the standard deviate.
 
Package: sojourner
Commit: 807732c378a5c1f2002fccc9b67252b9c8e65411
Author: Shannon Town <xiaonastang@gmail.com>
Date: 2019-11-22 12:31:36 -0500
Commit message:

 Fixed a bug of plotTrackOverlay.Dcoef() when there is no track left for certain images after R sqaure filtration.

Modified plotLocalizations.Density() to plot 2 kinds of localization plots for each image stack, one with square-shaped bins colored based on number of molecules in each bin, the other with each molecule as a dot colored base on local density of molecules. Also added an option to customize color for the dot plot.

Modified plotIndividualTracks(), with options to sort tracks by dwell time, diffusion coefficient, or R square of MSD fit, also with options to add or not add legend on each panel.

New function plotIndifidualMSD() to visualize correlation of MSD regression error (R square) and the corresponding diffusion coefficient. This function can also plot all the individual MSD fits for visualization and diagnosis purpose.
 
Package: sojourner
Commit: 328b340108bcbd58a37e5b6f92b031a2e48e48a2
Author: Shannon Town <xiaonastang@gmail.com>
Date: 2019-05-24 12:52:58 -0400
Commit message:

 Merge branch 'develop' of https://github.com/sheng-liu/smt-beta-0.3.9.1 into develop
 
Package: sojourner
Commit: 4d82cee608b5c281b236933f8b1ec16863bd991d
Author: Shannon Town <xiaonastang@gmail.com>
Date: 2019-05-24 12:36:15 -0400
Commit message:

 Merge branch 'develop' of https://github.com/sheng-liu/smt-beta-0.3.9.1 into develop
 
Package: sojourner
Commit: bbd4109629b703fee131f9c59be5e13dce38d8b2
Author: Shannon Town <xiaonastang@gmail.com>
Date: 2019-05-24 12:36:15 -0400
Commit message:

 Merge branch 'develop' of https://github.com/sheng-liu/smt-beta-0.3.9.1 into develop
 
Package: sojourner
Commit: 8f87e1c52a4e2578a4d795a2d2360af10f08a030
Author: Shannon Town <xiaonastang@gmail.com>
Date: 2019-05-24 12:23:51 -0400
Commit message:

 plotTrackOverlay.Dcoef() fixed "argument to 'which' is not logical" error; nuclei background pixelated.
 
Package: sojourner
Commit: c38d6fd36ac8f7692af87e57d6553eb0d587223b
Author: Shannon Town <xiaonastang@gmail.com>
Date: 2019-05-24 12:23:51 -0400
Commit message:

 plotTrackOverlay.Dcoef() fixed "argument to 'which' is not logical" error; nuclei background pixelated.
 
Package: sojourner
Commit: 8d5c265f747b2144535a92b41f8a339d4af15cf1
Author: Xiaona Tang <xiaonastang@gmail.com>
Date: 2019-03-17 00:41:04 -0400
Commit message:

 plotTrackOverlay.Dcoef() fixed "subscript out of bound" error when there is no track left for a data file after filtration
 
Package: sojourner
Commit: 48c4563f53c50741f336ff301b40e208eabac432
Author: Sun Jay Yoo <snjy9182@gmail.com>
Date: 2019-02-12 17:02:47 -0500
Commit message:

 Fixed document() errors and addressed build errors. Purged non-ASCII characters.
 
Package: sojourner
Commit: 49e9e4f49acd53c28495c3dd0239321a3a395ac1
Author: Sun Jay Yoo <snjy9182@gmail.com>
Date: 2019-02-12 14:33:53 -0500
Commit message:

 fixed import command
 
Package: sojourner
Commit: ddfe073506c8f1288fc6359914f262ff11fb0559
Author: Sun Jay Yoo <snjy9182@gmail.com>
Date: 2019-02-12 14:32:01 -0500
Commit message:

 Lines added for roxygen2.
 
Package: sojourner
Commit: 75654c97775734068fbb73dc31f88b99300b53a4
Author: Sun Jay Yoo <snjy9182@gmail.com>
Date: 2019-02-12 14:23:56 -0500
Commit message:

 Diffusion map analysis support added: diffusionMap.R. Could not document() with roxygen2 and could not build package.
 
Package: sojourner
Commit: 3128b90a3702929181f451cce33142f13903ee69
Author: Sun Jay Yoo <snjy9182@gmail.com>
Date: 2019-02-01 13:23:35 -0500
Commit message:

 Dmap test file created.
 
Package: sojourner
Commit: 6932ccefbcfae8794bee986e4531094c49bf23cb
Author: sheng-liu <“sheng.liu@live.ca”>
Date: 2018-09-29 22:10:59 -0400
Commit message:

 set .plotNucTrackOverlay() to condition on the input data to adjust for "color" statement differences.
 
Package: sojourner
Commit: 125352f18dd9bdd8cb9f16c6aae4aa3d7c07685a
Author: sheng-liu <“sheng.liu@live.ca”>
Date: 2018-09-29 16:05:38 -0400
Commit message:

 V0.5.3.2
Added feature segmentTrackll() and rebuildTrack() for hmm fitting (Youngsoo Sung)
Fixed bug for exportTrackll() frame number no change (Sun Jay).
Fixed aes to aes_string() change bug in plotTrack() associated functions (Sheng)
 
Package: sojourner
Commit: 2d0e59e5119497f7d434e31e8d79f297e40c8ca8
Author: Youngsoo Sung <ysung6@jhu.edu>
Date: 2018-09-28 00:10:10 -0400
Commit message:

 rebuildTrack reconnects segments along with statistics.
 
Package: sojourner
Commit: d3ac8d8baecea174f31d51e19aabef759574b393
Author: sheng-liu <“sheng.liu@live.ca”>
Date: 2018-09-12 11:07:17 -0400
Commit message:

 Fix exportTrackll() frame number no change (from Sun Jay).
 
Package: sojourner
Commit: eff770c6c7fa47a9a5f86731be8fcd31bef3ace1
Author: Youngsoo Sung <ysung6@jhu.edu>
Date: 2018-08-16 17:51:20 -0400
Commit message:

 Adding functions used for segment generation that will be used for hmm in the future.
A single function (convert.abtrackll) is added for helper functions
 
Package: sojourner
Commit: 8632069000fef5295052ef4f2fa5a00430714bc2
Author: Xiaona Tang <30399381+ShannonTown@users.noreply.github.com>
Date: 2018-08-16 17:40:24 -0400
Commit message:

 Merge pull request #1 from sheng-liu/master

Master 
Package: CSSQ
Commit: 1376210953d3b1e141b50945038c3baa29d3f0bd
Author: Ashwath <akumar301@gatech.edu>
Date: 2020-05-29 18:16:46 -0400
Commit message:

 Description update
 
Package: IRanges
Commit: a7b01212d21191c1ae21f6e6d1ee0e424eb05fd1
Author: Michael Lawrence <michafla@gene.com>
Date: 2020-05-29 13:59:31 -0700
Commit message:

 add some tests, fixes #23
 
Package: IRanges
Commit: 8bea5065ca9494e757e0406e65b8b9de41ceb67a
Author: Michael Lawrence <michafla@gene.com>
Date: 2020-05-29 13:59:17 -0700
Commit message:

 fix %% by 0 error
 
Package: IRanges
Commit: 0932f8525078cb0031cc85f34685744ecaad31ec
Author: Michael Lawrence <michafla@gene.com>
Date: 2020-05-29 10:47:57 -0700
Commit message:

 initial work on list element recycling
 
Package: CSSQ
Commit: 3094509a4641da918eb021d218a8d40b72441814
Author: Ashwath <akumar301@gatech.edu>
Date: 2020-05-29 16:58:05 -0400
Commit message:

 Description update
 
Package: CSSQ
Commit: 0735dac27c9e0ec4cb9789de3d5e34f90727d111
Author: Ashwath <akumar301@gatech.edu>
Date: 2020-05-29 16:48:00 -0400
Commit message:

 Updated Description
 
Package: BiocCheck
Commit: e4993b24b1fd5d41d9fece1535a3e4729661a3f7
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-05-29 11:49:03 -0400
Commit message:

 Fixes #57

   - version bump for Leonardo's PR
 
Package: BiocCheck
Commit: 664ae1a3e6d0cab9cc6088320cd38a357fdacdbf
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-05-29 11:44:09 -0400
Commit message:

 Merge branch 'lcolladotor-suggest_styler_over_formatR'
 
Package: BiocCheck
Commit: d9454a08343b94a5b0473960bf1438b5a686c3de
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-05-29 11:38:48 -0400
Commit message:

 Merge branch 'suggest_styler_over_formatR' of https://github.com/lcolladotor/BiocCheck into lcolladotor-suggest_styler_over_formatR

Conflicts:
	NEWS
 
Package: BiocCheck
Commit: e78b6734555f98d05d1873094c46f2daee74a349
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-26 10:13:57 -0400
Commit message:

 Merge branch 'lcolladotor-add_pr_template'
 
Package: BiocCheck
Commit: 56c91b736958b9d6b6c09c850534ace52249b8a6
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-26 10:06:19 -0400
Commit message:

 Merge branch 'add_pr_template' of git://github.com/lcolladotor/BiocCheck into lcolladotor-add_pr_template
 
Package: BiocCheck
Commit: 2382d67384dd0b76e13c268983d99088ee94a4c5
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-22 14:03:45 -0400
Commit message:

 Merge branch 'master' of github.com:Bioconductor/BiocCheck
 
Package: BiocCheck
Commit: 2ce371861bbcc1ff1deadaf2e4f3fb630410a2a8
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-22 14:00:57 -0400
Commit message:

 Merge branch 'grimbough-dontrun'
 
Package: BiocCheck
Commit: 092a21993cdf2c5b7e538fe48264b75d67f8e8dc
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-22 13:59:47 -0400
Commit message:

 add testpkg1.o to .Rbuildignore
 
Package: BiocCheck
Commit: 79550046a3f4319038b643e6732e02109caa5c06
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-22 13:44:02 -0400
Commit message:

 minor changes to avoid merge conflicts
 
Package: BiocCheck
Commit: 996291466a8f2a704ab1da08fe975d919dec6bb3
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-19 12:32:04 -0400
Commit message:

 Respond to the pull request review comments

This commit responds to the pull request review comments from https://github.com/Bioconductor/BiocCheck/pull/87#pullrequestreview-414581029. In particular, it:

* Removes a checkbox that was too specific.
* Fixes the spelling of 'vignette'.

Furthermore, this commit:

* Updates the NEWS file
* Adds a short entry to the vignette file.
 
Package: BiocCheck
Commit: 4bd0bcc528070cb1c1e1421c2bc171e0e4f31e68
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-19 12:18:44 -0400
Commit message:

 Respond to the PR review

This commit does the things outlined at https://github.com/Bioconductor/BiocCheck/pull/88#issuecomment-630921073. That is:

* Removes any `biocthis` mentions.
* Uses CRAN links for `styler`.
* Fixes a typo.
* No longer bumps the version number to avoid merge conflicts with other BiocCheck-a-thon pull requests as suggested on Slack.
 
Package: BiocCheck
Commit: 0c27a73e3c3e64a84732b12231997b2db384dbf9
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-05-19 18:12:05 +0200
Commit message:

 Remove NOTE from dontrun in internal function man page

- Updated checkUsageOfDont() to look for keyword 'internal' and suppress NOTE if found
- Added unit tests to confirm NOTE appears if required, and is suppressed if keyword found.
 
Package: BiocCheck
Commit: 5604071638d3328bba9a2ea5c49a5c7702057400
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-18 20:56:47 -0400
Commit message:

 v1.25.1 -- Resolve https://github.com/Bioconductor/BiocCheck/issues/57

This commit resolves https://github.com/Bioconductor/BiocCheck/issues/57
by updating the `handleMessage()` calls after the formatting check
fails. Instead of mentioning `formatR`, these messages now refer to:

* `styler`,
* `biocthis`,
* the `BiocCheck` vignette.

Furthermore, the `BiocCheck` vignette section on formatting still
mentions `formatR`, but it now also mentions in more detail:

* `styler`: how to install and run it
* `biocthis`: as a companion to `styler` with code how to run it
(but not install it since it's optional and the install instructions
will hopefully change soon once this package is submitted/reviewed).
* a quick overview of the differences between `formatR` and `styler`,
though this is mostly done by highlighting current limitations of
`formatR`.
* how RStudio Desktop's `Reformat code` button (under the magic wand)
can help break long lines which is something that `styler` cannot do
as discussed in more detail at
https://github.com/r-lib/styler/issues/247. `formatR` can do this,
but personally, the fact that it broke valid R code in some of my
packages made me trust its output less.

The NEWS and DESCRIPTION files have been updated accordingly.
 
Package: BiocCheck
Commit: a61e96fac6a4998cd340337c2df26e3c338f15d6
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-18 20:18:58 -0400
Commit message:

 Add a GitHub pull request template

This commit is related to https://github.com/Bioconductor/BiocCheck/issues/86.
As part of the commit, a new file `.github/pull_request_template.md` was created
that contains a template file based on the instructions at
https://help.github.com/en/github/building-a-strong-community/creating-a-pull-request-template-for-your-repository
and the top lines at https://github.com/lcolladotor/biocthis/blob/master/.github/ISSUE_TEMPLATE/issue_template.md

Ideally, this should be properly recognized by GitHub.

The contents of the md file rely heavily on the presentation by Lori Shepard
for the BiocCheck-a-thon from May 18th 2020. The contents on the presentation
are available at
https://docs.google.com/presentation/d/1DkN2WVPOMVGqUtlSSrWbx6IMjtGP_cEHoE3nfOEnD68/edit#slide=id.p
 
Package: GSVA
Commit: 09cf73d45e6f067ea5edacbe89ef2842631d9f61
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2020-05-29 17:47:09 +0200
Commit message:

 Bugfix when input data is a SummarizedExperiment. Corresponding unit test added.
 
Package: curatedMetagenomicData
Commit: 5fc77ae3c53110881ce7a9c98115548e4f5d8a32
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2020-05-29 15:38:18 +0000
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: curatedMetagenomicData
Commit: 277fa592afa7f68fac0b64461ccd0d99efd459e1
Author: Kelly Eckenrode <kbeckenrode@gmail.com>
Date: 2020-05-08 11:22:08 -0400
Commit message:

 Delete file

Moving to bug sig 
Package: curatedMetagenomicData
Commit: 47f00258155100953a4788d9daef763dd79245fd
Author: Kelly Eckenrode <kbeckenrode@gmail.com>
Date: 2020-05-08 10:55:09 -0400
Commit message:

 Added uploaded file

Microbe directory spreadsheet with edited ontologies. Edited ontologies are located in the second tab. 
Package: cBioPortalData
Commit: 7acd355f99c4458c5c0b7e8c9d5ca42ce7476513
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 11:40:31 -0400
Commit message:

 version bump
 
Package: cBioPortalData
Commit: 9e9961a6e385f4a11e5bad2b2e2727af193efab7
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 11:40:17 -0400
Commit message:

 update unit test
 
Package: cBioPortalData
Commit: f5b370d7f03c82809d623e5417e0282ce2821ef2
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 11:07:18 -0400
Commit message:

 version bump
 
Package: cBioPortalData
Commit: fa83fef95ca2ef70d9277d30c92ab19a0ce790e0
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 11:06:52 -0400
Commit message:

 include tests
 
Package: cBioPortalData
Commit: 7cd24e1ab948044e23fe7e53507de76bc37d320d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 10:57:01 -0400
Commit message:

 update NEWS file
 
Package: cBioPortalData
Commit: 4d7c60a9c3b673794e75a7a8af4663ec8ed7eea3
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 10:56:49 -0400
Commit message:

 version bump
 
Package: cBioPortalData
Commit: ccd8ba1ef29da2df579d72c8378009e3cecda635
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 10:48:22 -0400
Commit message:

 add testthat to Suggests
 
Package: cBioPortalData
Commit: d02d10224e136c214611cbb64cdd07d09fed333e
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 10:47:44 -0400
Commit message:

 add hostname and api. arguments, document
 
Package: cBioPortalData
Commit: 82f6b55c3eee8fabd4493e3e1f83650f9c898db5
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 09:55:36 -0400
Commit message:

 version bump
 
Package: cBioPortalData
Commit: 9b95f2e7b111a9de977577f225d7c8b6d584bde4
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-29 09:51:30 -0400
Commit message:

 allow different subdomain and protocol
 
Package: cBioPortalData
Commit: 768cbd33070770e56f01553b63fdf9d0269d7a1c
Author: Ino de Bruijn <ino@ino.bio>
Date: 2020-05-29 09:12:48 -0400
Commit message:

 Allow pointing to different API 
Package: GenomicRanges
Commit: 78d3f5f60d28092bb526539224383edcb4c74372
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-29 09:09:59 -0400
Commit message:

 Merge pull request #40 from Bioconductor/findKNN

Add FindKnn funcitonality 
Package: GenomicRanges
Commit: bd23e075a82e35ad05eedc79bdfe98e3bf272e63
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-27 15:41:34 -0400
Commit message:

 Fix typo and remove uneeded tests
 
Package: GenomicRanges
Commit: 1bd48bec34e4a37752aca39d7ea693ca0fa5e301
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-26 13:30:59 -0400
Commit message:

 Updated documentation for nearest methods in man pages and vignettes
 
Package: GenomicRanges
Commit: f1532180ae8108e3e98b941478f7ed29b4df7c27
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-24 11:45:43 -0400
Commit message:

 findKNN, select = "all" preceed / follows width on subject, not x
 
Package: GenomicRanges
Commit: e8cf8fc3659fcc619fae8e5a48737ec7a894ca0d
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-24 10:26:22 -0400
Commit message:

 remove unnecessary conditional; minor cleanup
 
Package: GenomicRanges
Commit: 1599e125fa8d13c6914531c94cd7692cf052c5d6
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-24 10:20:55 -0400
Commit message:

 helper and unit tests for findKNN select = "all"
 
Package: GenomicRanges
Commit: 462e13fca6cd984668b1ed1e88b007f696fdb0c1
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-24 10:11:05 -0400
Commit message:

 code clean-up

- nearest-methods.R
  - helpers then interface for findKNN
  - remove dead (commented) code
  - whitespace cleanup
- test_nearest-methods.R
  - remove dead tests
  - use IntegerList coercion for nearest() comparisons
  - separate unit test for issue 76
  - avoid attaching packages
 
Package: GenomicRanges
Commit: 6b28fd4771b77c3b0b8749317672ddb0f8fdceab
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-19 14:52:55 -0400
Commit message:

 Documentation changes for findKNN and assorted fixes
 
Package: GenomicRanges
Commit: df4d8a7589f3a19903ec2d113147c45a9c93d0bd
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-18 13:37:21 -0400
Commit message:

 Further changes to nearest.R and tests to facilitate findKNN
 
Package: GenomicRanges
Commit: 353403b549c0b4b6d14e920cb0b7efc55711e381
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-13 15:37:51 -0400
Commit message:

 Merged with master branch
 
Package: GenomicRanges
Commit: d92adb3b7f62aed4f849a0d74a9ce875d0d2d8d0
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-13 15:01:06 -0400
Commit message:

 Initial findKNN changes
 
Package: GenomicRanges
Commit: f07a964ee85f967439a19e5012d2da7b7315589f
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-01 16:31:45 -0400
Commit message:

 Changes to findKNN() + unit tests
 
Package: GenomicRanges
Commit: 7411250628a57f8c1e28e268b226ec77dd4100cd
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-04-30 17:08:51 -0400
Commit message:

 Initial changes for findKNN to consider overlaps
 
Package: GenomicRanges
Commit: 36833a21d05ee4f1a27ee8abaa4d2ff775cafde1
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-03-12 12:07:27 -0400
Commit message:

 simple unit tests and debugging 0-length cases
 
Package: GenomicRanges
Commit: e78ccab3974fdc23fe0283f41e8357a295004bb4
Author: Kayla-Morrell <Kayla.Morrell@roswellpark.org>
Date: 2020-03-11 11:40:02 -0400
Commit message:

 More tests for findKNN
 
Package: GenomicRanges
Commit: 13ba432bb628a9fe75d6c3ce61ea424f8ba7264d
Author: Kayla-Morrell <Kayla.Morrell@roswellpark.org>
Date: 2020-03-11 10:17:09 -0400
Commit message:

 Change to defaults

- in findKNN, changed from k=5L to k=1L
 
Package: GenomicRanges
Commit: 1f56dac1c94b9e781fb45644a7c5b0b12d28186d
Author: Kayla-Morrell <Kayla.Morrell@roswellpark.org>
Date: 2020-03-09 12:47:04 -0400
Commit message:

 Starting to build tests for `findKNN()`
 
Package: ChIPpeakAnno
Commit: f031de4f4691e4dc0e5b97d7c59c724ee1808c4c
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-05-29 08:11:58 -0400
Commit message:

 fix the issue for new paste output.
 
Package: PhyloProfile
Commit: 5358f5c179677980a125341dc823c32f363e38a2
Author: trvinh <trvinh@gmail.com>
Date: 2020-05-29 12:54:31 +0200
Commit message:

 Update R version
 
Package: GSEABase
Commit: cf64dea52ece4409091c033368f439878e365262
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-29 05:42:09 -0400
Commit message:

 Merge branch 'RELEASE_3_11'
 
Package: GSEABase
Commit: 8498f38b6cb5570276bc4595d000de209cc758a8
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-29 05:40:52 -0400
Commit message:

 update unit tests for new GO.db
 
Package: simpleSingleCell
Commit: 3954b336d3a6c9328052fe5de03e654e10567957
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-28 23:40:27 -0700
Commit message:

 Fixed package name replacement in Makefile.
 
Package: mitch
Commit: 3238a2038b943931387982c097ee9f8e69c1c9ce
Author: markziemann <mark.ziemann@gmail.com>
Date: 2020-05-29 16:10:24 +1000
Commit message:

 bump
 
Package: mitch
Commit: c7b0d77e44fb2a80465c58d6a96b124652566a2b
Author: markziemann <mark.ziemann@gmail.com>
Date: 2020-05-29 16:07:10 +1000
Commit message:

 bump and news
 
Package: mitch
Commit: b636a9ac24257a94ba4b6a574f4965191f07043a
Author: markziemann <mark.ziemann@gmail.com>
Date: 2020-05-28 11:10:01 +1000
Commit message:

 fixed issue with mitch_report absolute path output
 
Package: mitch
Commit: a922ec20d04418734e941f43e59bbaece59509fd
Author: markziemann <mark.ziemann@gmail.com>
Date: 2020-05-21 00:41:38 +1000
Commit message:

 fix vers num
 
Package: SingleR
Commit: 67558c1ef4b4046afc2f4c02b01d3bb66e5aea75
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-24 15:13:10 -0700
Commit message:

 Fixed ontology mapping typo.
 
Package: SingleR
Commit: 19e273fefdf913d69334a2c73cdbd6d3cbf25fe1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-24 00:41:25 -0700
Commit message:

 Avoid memory explosion from storing all pairwise log-FCs.
 
Package: SingleR
Commit: bd29ffc458aea04b0944b5b788c83034e7359542
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 22:36:44 -0700
Commit message:

 Fixes to plotting documentation, reoxygenated.
 
Package: SingleR
Commit: 875b3fba7127c34dd787f3dc30ba28090bf75a98
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 21:42:39 -0700
Commit message:

 Simplified plot*Distribution functions to use matching calls,
as mismatches between scores/deltas and calls makes little sense.
Renamed scores/deltas.use= into references=.
 
Package: SingleR
Commit: e01bccb802dd635ce4e1c737e3e280a30cd25199
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 12:43:00 -0700
Commit message:

 Reoxygenated.
 
Package: SingleR
Commit: e989fbda44054e76c31a4007546837f889437442
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 12:40:04 -0700
Commit message:

 Fixed coloring of pruned calls in delta plot.
 
Package: SingleR
Commit: 50bc885272eab39689dcdacbf50e7817b3b139ed
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 12:28:59 -0700
Commit message:

 Cleaned up documentation for all plotting functions.
 
Package: SingleR
Commit: 65663e05c602510e673eed1c0bbfcfb670025c62
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 12:06:23 -0700
Commit message:

 Organized plotting tests into those for scores and deltas.
 
Package: SingleR
Commit: 32c4a42778e67a43588c2dc72dccfb714426cd8f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 11:34:01 -0700
Commit message:

 Minor aesthetic change to default violin fill.
 
Package: SingleR
Commit: dd48be8377d8e933e60a256f732c9ba5f8d3dc15
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 01:07:43 -0700
Commit message:

 Streamlined delta distribution plots by removing cut-offs,
instead plotting the pruned labels in a different color.
 
Package: SingleR
Commit: 69fefd0822c86a2bcd0d2a8af57683cefb7e8fa2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 00:36:57 -0700
Commit message:

 Synchronize pruned labels with unpruned labels in plotScoreDist.
 
Package: SingleR
Commit: a2729174d7085f6379688a2d1c12c7393d9e7456
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-23 00:26:43 -0700
Commit message:

 Added separate, streamlined function to plot the deltas.
 
Package: SingleR
Commit: 0ea81032f6a148487c16f7dc0a48598a955b1a15
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-22 22:36:05 -0700
Commit message:

 Greatly streamlined the score distribution plotter.
 
Package: SingleR
Commit: 420c793078d51c7e014a25ca9516fc3ec597c2a8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-22 15:01:23 -0700
Commit message:

 Reoxygenated for example.
 
Package: SingleR
Commit: ccf35e9934b447af29e81dc8d02aeaf694ff1816
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-22 10:06:05 -0700
Commit message:

 Reoxygenated.
 
Package: SingleR
Commit: 944f85c28a66f0dd20f14e3d33bc427b473c6a5f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-22 09:21:58 -0700
Commit message:

 Patch over odd matrix zero-subsetting behavior.
Fix to classic markers example.
 
Package: SingleR
Commit: 0e35b19683529d2d30d57adab74e0d1108d2abda
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-22 00:37:53 -0700
Commit message:

 Docfix for pruneScores.
 
Package: SingleR
Commit: a97b6a71959d63f6ae94406e84981353fc908041
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-22 00:37:35 -0700
Commit message:

 Added tests for getClassicMarkers, minor arg fix.
 
Package: SingleR
Commit: 27d06e8818d32285bf0bea6edb4f5ee3ee91b3e7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-21 23:32:23 -0700
Commit message:

 Rolled out classic marker detection into an exported function.
Added support for blocked marker detection.
 
Package: SingleR
Commit: 7b5d47c612a57e1f1e119f26d345018cf508461f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-15 14:30:28 -0700
Commit message:

 Reoxygenated.
 
Package: SingleR
Commit: 5c8b29946896b8446f370971bd86072ca137d753
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-15 14:07:35 -0700
Commit message:

 Updated tests for new metadata in combined output.
 
Package: SingleR
Commit: ee00517aadd8acb7923d3be262b81957d9465b34
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-15 11:01:56 -0700
Commit message:

 Switch examples to use .mock*Data functions for brevity.
 
Package: SingleR
Commit: 404aa4eed497c255f46d4e25f518300eba660280
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-15 10:51:32 -0700
Commit message:

 Avoid redundant documentation of combined metadata.
 
Package: SingleR
Commit: 7ee85da39e31e13cd673c12b201ade4bfab74339
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-15 10:40:24 -0700
Commit message:

 Report the reference of origin for each column of a combined 'scores'.
Remove unnecessary code to merge the marker lists.
Cleaned up combining documentation.
 
Package: SingleR
Commit: caf5e8a3f06322f70d3f4afd3db7b00cd1df0035
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-15 10:28:33 -0700
Commit message:

 More rational organization of source code.
 
Package: SingleR
Commit: 76bcdb454e736ea3c13fa9624c183f2f01e73190
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-14 21:29:34 -0700
Commit message:

 Bumped version and date.
 
Package: SingleR
Commit: 7c55bd5f010949b59ca32ec23066d35143e8591a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-14 21:17:59 -0700
Commit message:

 Docfixes for output of combining functions.
 
Package: BioNetStat
Commit: 993b37b937b908103813a0215ae92e6eaae9828f
Author: jardimViniciusC <viniciusjc@gmail.com>
Date: 2020-05-28 18:16:38 -0300
Commit message:

 changing NAMESPACE file
 
Package: PharmacoGx
Commit: 4079c1824c4d3d9df95ab8edb9292d9075843b3c
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2020-05-22 13:52:53 -0400
Commit message:

 fixing an edge case where incomplete data caused full factor levels to be dropped
 
Package: PharmacoGx
Commit: 7f268d95b5da4d94e620066efe81b70bd2fc4f0d
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2020-05-15 13:23:53 -0400
Commit message:

 bump version number
 
Package: PharmacoGx
Commit: 192add6c23ef9a092fc51ac94b4e48b75671fe84
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2020-05-15 11:37:11 -0400
Commit message:

 Merge branch 'master' of https://github.com/bhklab/PharmacoGx
 
Package: PharmacoGx
Commit: 6691d19302940e74a4ad6b251776b15636b17ff6
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2020-05-15 11:36:26 -0400
Commit message:

 added version update to pset conversion, otherwise already converted psets loaded by downloadPSet would be converted again (and fail)
 
Package: PharmacoGx
Commit: 69b411d1d0d73f20803acc317e6addfbb9824cb2
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2020-04-29 11:38:50 -0400
Commit message:

 Trigger 
Package: cBioPortalData
Commit: b3ddd88ea111b3ac390128e15eb519b1c1fe17cf
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-28 15:52:17 -0400
Commit message:

 version bump
 
Package: cBioPortalData
Commit: 94decfc1be775a212d3297f54cfe955664b7376f
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-05-28 15:50:42 -0400
Commit message:

 bug fix: update checkIdValidity

- replace instances of spread with pivot_wider
- name arguments
- reorganize helpers
 
Package: Rcwl
Commit: 65638780c9ce3a9e6172af7ef09af99714224f22
Author: Qiang Hu <qiang.hu@roswellpark.org>
Date: 2020-05-28 14:27:16 -0400
Commit message:

 fix version check warning
 
Package: oligoClasses
Commit: 156758518f2ca61048cb7e8b2892478098139803
Author: Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu>
Date: 2020-05-28 11:24:26 -0700
Commit message:

 Removed defunct RangedData functions.
 
Package: oligoClasses
Commit: 0202691ed41e0d9c3faee5481c6e832b4fdb0066
Author: Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu>
Date: 2020-05-27 11:05:48 -0700
Commit message:

 Removed RangedData functions as they are now gone from IRanges.
 
Package: Organism.dplyr
Commit: 516225004365e4ef236b2bedcde6b259042b88d3
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-05-28 12:15:01 -0400
Commit message:

 Changes to avoid race condition involving finalizer removing tables
 
Package: BioMM
Commit: de6c71536dfd2de040547796a5ea9a56241289b0
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2020-05-28 16:38:53 +0200
Commit message:

 update version
 
Package: BioMM
Commit: 7879f373e6e52968330ff223c4c1e81760c27add
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2020-05-28 16:37:58 +0200
Commit message:

 debug the code in the function getDataByFilter(), cor.test().
 
Package: ChAMP
Commit: d5241390d2a257833a2bb3a9a218865942695822
Author: Yuan Tian <tianyuan1991hit@gmail.com>
Date: 2020-05-28 12:35:49 +0100
Commit message:

 Fixed boundary issue for champ.refbase.
 
Package: BgeeDB
Commit: 6ee7a5a62b6351533e3ccce7055d338175f13fb4
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-28 12:09:49 +0200
Commit message:

 bump version
 
Package: MsCoreUtils
Commit: cd9b1c52bda6f5ebbfe585f6ef8021eb89c246ab
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2020-05-28 11:56:20 +0200
Commit message:

 Merge pull request #54 from lgatto/master

feat: new countFeatures aggregation function 
Package: MsCoreUtils
Commit: f75afc38451f3945d8f2dfcc181ed75eb0398e33
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-05-28 09:30:55 +0200
Commit message:

 remove countFeatures man page
 
Package: MsCoreUtils
Commit: c8ba998c21b9ce60b65e1167d62098a4491cd57a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-05-28 09:30:39 +0200
Commit message:

 test: add colCounts() unit tests
 
Package: MsCoreUtils
Commit: 5dbe2fbb853eb4120009047e6630aa6dc3fab58e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-05-28 09:30:07 +0200
Commit message:

 refact: rename countFeatures() as colCounts()
 
Package: MsCoreUtils
Commit: c6c592ff4e8fa70c178ad329052aa8cc11071088
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-05-27 18:52:23 +0200
Commit message:

 feat: new countFeatures aggregation function
 
Package: plyranges
Commit: 0cf2e40071004ab0926f075f4196e28ad7a17889
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2020-05-28 17:05:42 +1000
Commit message:

 minor vignette fixes
 
Package: plyranges
Commit: 25ed1ae558f7c9cf7b57a4f66df14012f22bf0f8
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2020-05-27 12:34:12 +1000
Commit message:

 Merge pull request #83 from PeteHaitch/master

Fix table in vignette 
Package: plyranges
Commit: f22e06468ae9ccf328f7e253e0104eafaf9e5e45
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2020-05-27 11:38:37 +1000
Commit message:

 Fix table in vignette
 
Package: plyranges
Commit: 4a3df0115e2c37fe79331b585a2944b2594f39d3
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2020-05-22 09:50:58 +1000
Commit message:

 Merge pull request #82 from snystrom/nearest_distance_doc_edit

Quick fix to join_nearest_distance docs 
Package: plyranges
Commit: 3da97b2402499461feadb1e6cebf2cb9e864b934
Author: snystrom <snystrom@ad.unc.edu>
Date: 2020-05-21 10:02:49 -0400
Commit message:

 updating docs for join_nearest to remove outdated information about the "distance" argument.
 
Package: SingleCellExperiment
Commit: 755684ac359ad54044a2deee44fea202d1fe9ba3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-27 22:08:02 -0700
Commit message:

 Mention rowSubset usage in vignette.
 
Package: SingleCellExperiment
Commit: 440028387c0cc5e6a4d80c4648d3cb64c646ca3c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-27 21:48:18 -0700
Commit message:

 Generalized rowSubset to get/set to any rowData field.
 
Package: SingleCellExperiment
Commit: a28218adc42cc7579a5d09f9db2b2f8062b377d0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-27 21:34:41 -0700
Commit message:

 Bumped version and date, updated NEWS.
 
Package: SingleCellExperiment
Commit: 064ee909d80569b6a154e6c67bd7f438ae908555
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-27 21:31:33 -0700
Commit message:

 Expand on colLabels docs.
 
Package: SingleCellExperiment
Commit: d92290774537b4335be4b9793a49a36cb53a7095
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-27 21:30:45 -0700
Commit message:

 Added the rowSubset utility for storing row subsets.
 
Package: SharedObject
Commit: 044bf50d7e00306bf4edcfd173f9ab4551751b83
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2020-05-28 12:44:25 +0800
Commit message:

 add unshare function
 
Package: SharedObject
Commit: 353baa1c4d9ad398132e1db8666a5fe4dfde6e9f
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2020-05-22 20:53:45 +0800
Commit message:

 add automatic conversion method
Make the generic function more generic.
add document.
 
Package: sangeranalyseR
Commit: a616212811fc2ed42315284ba8208afa4d8bf767
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-28 13:06:05 +1000
Commit message:

 Add user manual & How to page header
 
Package: sangeranalyseR
Commit: d3d7d53b54ca446e3fe303d08ce5a374b189bd5d
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-28 12:28:51 +1000
Commit message:

 Update version bump
 
Package: CytoML
Commit: a9cddf6962b44943ca539352fa50da0b79ea466e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-27 16:25:58 -0700
Commit message:

 bump
 
Package: CytoML
Commit: f926a1e2521924598bd37139baee6885d9cdf875
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-27 16:05:57 -0700
Commit message:

 prepend extra meta info to wsp file generated by gs-to-flowjo
 
Package: CytoML
Commit: 505964eec2151a6019aa171209ea7efaad0c3a06
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-26 15:33:11 -0700
Commit message:

 #99: Implement subset by filtering expression in flowjo_to_gatingset
 
Package: CytoML
Commit: fb291aa9a2e3cdc9352dd023fbb16b5cccdd1d6a
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-22 18:37:21 -0700
Commit message:

 Handle spaces in paths in gatingset_to_flowjo
 
Package: CytoML
Commit: 55546ed500388d7b52266f8681c53577497f88ef
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-22 17:36:33 -0700
Commit message:

 bump
 
Package: CytoML
Commit: 0e8d35ccae0ae32f587e6040c5a086b5d5540b9f
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-22 17:36:15 -0700
Commit message:

 Add docker image version match to gatingset_to_flowjo
 
Package: CytoML
Commit: fbe4290be5abddf88eebc067e577994fc1344ce7
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-21 18:01:32 -0700
Commit message:

 Update docs
 
Package: CytoML
Commit: 834fa76fa3c64ecd38ae1900c2c31d9519886c7d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-21 14:53:53 -0700
Commit message:

 Let gatingset_to_flowjo use binary or docker
 
Package: CytoML
Commit: fb38b242010a6ccd6c1af40de0cb28eca42dd00a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 17:31:53 -0700
Commit message:

 bump
 
Package: CytoML
Commit: 284bf8aedb71561227c3c343e19ff31cfe0ac597
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 17:30:51 -0700
Commit message:

 add skip_faulty_gate arugment to flowJo parser. #96
 
Package: CytoML
Commit: f0271dd8820c8f2db17ea9cc00cfa469b998b2eb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 15:58:36 -0700
Commit message:

 add test case for redefined_error xml
 
Package: CytoML
Commit: 042bd62bd55babe2c3445dc55620c8e36f1ef5e6
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-01 09:56:29 -0700
Commit message:

 Make docker availability check work with Windows
 
Package: DSS
Commit: 41caaa8fa36caf1c44c29308378512ab381df09d
Author: hwu30 <hwu30@Haos-MBP-16.attlocal.net>
Date: 2020-05-27 15:43:02 -0400
Commit message:

 update DMLtest
 
Package: DSS
Commit: e0a125547e540facada459f314ddc12e584e9835
Author: hwu30 <hwu30@Haos-MBP-16.attlocal.net>
Date: 2020-05-27 15:39:33 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/DSS
 
Package: DSS
Commit: 903a23068b5ba4005ee0cd6337e5568657454c78
Author: hwu30 <hwu30@Haos-MBP-16.attlocal.net>
Date: 2020-05-27 15:37:41 -0400
Commit message:

 update DMLtest
 
Package: IRanges
Commit: 4abc194c78adc88dac8a39bceb94af7078249942
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-05-27 12:00:49 -0700
Commit message:

 Move coercions from Hits to DataFrame and data.frame to S4Vectors package
 
Package: S4Vectors
Commit: 897714233e6a317b87acfca7298f517e7a9eec14
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-05-27 11:59:21 -0700
Commit message:

 Move coercions from Hits to DataFrame and data.frame from IRanges package
 
Package: fishpond
Commit: 41ba79069767cbbee9d8b31f89034cbfaaed4067
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-05-27 14:13:06 -0400
Commit message:

 alter computeInfRV function for mean and var
 
Package: graph
Commit: e51cc0347d4bc64fd2b5447b4fa20a985d06c50f
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-05-27 09:46:59 -0700
Commit message:

 Set signature of edges() and degree() generics to "object"

This restricts dispatch to their first argument ("object").
 
Package: GSVA
Commit: 7be5de0aba777b167a79a075cd4bd287546d53ff
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2020-05-27 18:47:38 +0200
Commit message:

 Bump version.
 
Package: GSVA
Commit: ef86e17fd5282ab8db9250f9faef8da9dba45ee8
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2020-05-27 18:45:04 +0200
Commit message:

 Merge branch 'pablo-rodr-bio2-shiny-updates'
 
Package: GSVA
Commit: afd832e3553856ff471e3fc558df4cf2b915aa1c
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2020-05-27 10:25:21 +0200
Commit message:

 Merge branch 'shiny-updates' of https://github.com/pablo-rodr-bio2/GSVA into pablo-rodr-bio2-shiny-updates
 
Package: GSVA
Commit: 630c31e3e3e2b1d9c3d5bfe9f3b1543aaffb4311
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2020-05-26 18:32:08 +0200
Commit message:

 Adding shiny app features
 
Package: BgeeDB
Commit: 27b5d5b711dfe422e7590edb0137aa415f56e582
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-27 13:02:26 +0200
Commit message:

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 
Package: BgeeDB
Commit: 647ad66a4e2297ce1fb358e6aed16ef8578725aa
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-27 13:01:44 +0200
Commit message:

 update VignetteIndexEntry with package title
 
Package: BgeeDB
Commit: 5f3b24ecb104d6f786c95925d37e14d221946da8
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-27 12:39:01 +0200
Commit message:

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 
Package: BgeeDB
Commit: a6a9cdd67e25dc1eda8cbf3ab5c71d545d44bd60
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-27 11:32:55 +0200
Commit message:

 increase timeout limit
 
Package: BgeeDB
Commit: 6825dd01806696500552a53a2379eadd3091983a
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-27 11:20:35 +0200
Commit message:

 update vignette and add message asking to look at the doc if curl not installed on Windows
 
Package: BgeeDB
Commit: 17725a4b8874059a01b2c45990e78cc5e0740704
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-27 10:22:48 +0200
Commit message:

 add curl as dependency
 
Package: ShortRead
Commit: 187835ac1080de771fc123563a69e89449fdd7bc
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-27 05:24:05 -0400
Commit message:

 missing header file for countFastq
 
Package: VariantAnnotation
Commit: 61ecbd8e019cd3e15013506fc5ec6a4495829f7c
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-27 04:46:28 -0400
Commit message:

 allow length recylcing in ref<-, alt<-, qual<-, filt<-

- closes #41
 
Package: regutools
Commit: 7a67896cf7511538261b90f2e6584a530255517a
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:10:37 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: brainflowprobes
Commit: 8556164735017a5a31454f56e9d56c6bf057489d
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:09:22 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: recountWorkflow
Commit: c1c205caa74fb7d8476c95e79508f82e6c4e0af6
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:08:27 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: spatialLIBD
Commit: b6d65b8ab58a0ce9714a9ae0de0b6811a017be39
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:06:58 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: derfinderData
Commit: 615161559b1da6ef1d43864d2a24da7347e2a238
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:05:45 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: regionReport
Commit: 9c4d1bb40c6f31e7a68b37ca19c874c2c7144a31
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:03:36 -0400
Commit message:

 Update dev/ files
 
Package: recount
Commit: a78728b35ad4df9611eadfd26430bb19d47c468d
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:02:48 -0400
Commit message:

 Update dev/ files
 
Package: derfinderPlot
Commit: 175c81b5748f0c29e2881823b5317facd11760d2
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:02:03 -0400
Commit message:

 Update dev/ files
 
Package: derfinderHelper
Commit: af1f0d71d0c9165613cb3ce6f872d3eb2afefa60
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:01:22 -0400
Commit message:

 Update dev/ files
 
Package: derfinder
Commit: 19b02e177b9da8351bb25e8beb65399ea7e8b2c0
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 01:00:32 -0400
Commit message:

 Update dev/ files
 
Package: GenomicState
Commit: e5d07a1b0ab1ab561875ba351ad633974acb69d3
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 00:59:22 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: regionReport
Commit: da1076877a017dbfbe4a2f7b4734e39add422eca
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 00:56:15 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: recount
Commit: 5d98a84d85e7dc19f407f2b32b63ad1e2c1d4fb7
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 00:54:49 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: derfinderPlot
Commit: 6ea343c2d7a3adfb825d687d70bff873f27c71b6
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 00:53:14 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: derfinderHelper
Commit: 1d5eacb3f64b86ad930f149c7de5bbad87df9b7b
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 00:51:55 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: derfinder
Commit: 40d7481bbd68c945a6902590de9429d7bfbd96f6
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-05-27 00:50:59 -0400
Commit message:

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 
Package: scRNAseq
Commit: 254b298e92f075864b4efe2aa517699b2ebc8dd6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-26 21:47:35 -0700
Commit message:

 Bumped version and date, added extra contributors.
 
Package: scRNAseq
Commit: d229565dd92e1d07167e91993ccd040625ae7b09
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-26 21:47:07 -0700
Commit message:

 Added metadata CSV for Zilionis.
 
Package: scRNAseq
Commit: b96d733f4551551c30210e6fa90a01b58584f480
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 12:57:14 -0700
Commit message:

 Cleaned up Zilionis-related scripts:

- Moved them into the right subdirectory.
- Use more appropriate functions for data loading.
- Retain more of the published metadata, where sensible.
 
Package: scRNAseq
Commit: 67f67124c37654be1679e9f50f458530708db06a
Author: Jens Preußner <jenzopr@users.noreply.github.com>
Date: 2020-05-25 20:10:00 +0200
Commit message:

 Added Zilionis dataset and associated getter.

 
Package: tradeSeq
Commit: 2eaab691e068eda2e7b2ff21c5986b5739f60cab
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-26 20:00:07 -0700
Commit message:

 removing monocle and igraph dependencies
 
Package: tradeSeq
Commit: be852228a15a5023e287fc761bcd295ee09b0bad
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-26 17:11:29 -0700
Commit message:

 update vignette to accommodate new tidy output of `predictSmooth`
 
Package: tradeSeq
Commit: 77bebb2d817a8381741783f9653497150d1122e4
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-26 17:06:07 -0700
Commit message:

 set tidy=TRUE as default in predictSmooth, #51
 
Package: tradeSeq
Commit: 25c72e2d48da4387c2c58ca1961ba19ba17a3e17
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-26 17:02:10 -0700
Commit message:

 add test for tidy predictSmooth output
 
Package: tradeSeq
Commit: 25f9846ac626ae07a232f28758b24cbec10e59a1
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-26 16:57:07 -0700
Commit message:

 add tidy argument for predictSmooth, #51
 
Package: ChIPpeakAnno
Commit: bfeccca9afecbb9444a5bd8508b474bcaa432654
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-05-26 17:04:26 -0400
Commit message:

 remove dependence of Rfast
 
Package: affycoretools
Commit: 2f77a7be11edfcd446e0e3cad97971ad6e3f2023
Author: Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu>
Date: 2020-05-26 12:52:12 -0700
Commit message:

 Added travis build badge
 
Package: affycoretools
Commit: a7aee71c32faed303f0ed90bf49d47fe85cce572
Author: Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu>
Date: 2020-05-26 12:49:48 -0700
Commit message:

 Added .travis.yml.
 
Package: multiMiR
Commit: 5e1c0c218ffe4f0300e9f9d55d1ffae2642ba7c2
Author: Matt Mulvahill <mmulvahi@amazon.com>
Date: 2020-05-26 12:41:50 -0700
Commit message:

 sycning w/ bioconductor Merge branch 'master' of git.bioconductor.org:packages/multiMiR
 
Package: multiMiR
Commit: db87e9ab4977108fbe9332adf1e9f30797580c9c
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2020-05-26 11:31:12 -0600
Commit message:

 Add warning message about target IDs 
Package: multiMiR
Commit: 6d075cce34edcc9f1f7bd42a8f9300322e8c99cb
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2020-05-26 11:17:38 -0600
Commit message:

 Add warning message about target IDs 
Package: isomiRs
Commit: fc442b3e82d7dce392ea31cdb37d1a7e752f39bf
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2020-05-26 15:12:40 -0400
Commit message:

 bump version
 
Package: isomiRs
Commit: b1c95feff9008e408f069b08984d13ce86fc3dba
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2020-05-26 15:11:11 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/isomiRs into gitdev
 
Package: isomiRs
Commit: 18fa73d8036ac45a3a6b81328551a86694892b45
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2020-05-26 15:10:52 -0400
Commit message:

 fix tibble column selection error

now it needs unlist to get a vector
 
Package: ReactomeGSA
Commit: 576563292612ada24615d060d9b2836770a42320
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2020-05-26 20:45:03 +0200
Commit message:

 Updated documentation
 
Package: PSICQUIC
Commit: 53f215720b97a7734c58b68a751774290b8447dc
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2020-05-26 10:34:16 -0700
Commit message:

 disabling tests for now
 
Package: ATACseqQC
Commit: 2e3bbaae16c4897bfd50c6372bb99090c3a154fe
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-05-26 12:34:00 -0400
Commit message:

 change the normalization method by library size for factorFootprints for user defined group samples.
 
Package: structToolbox
Commit: 443bf793bc45b473f2fb6f8fd0b27a9adbe2d287
Author: Gavin Rhys Lloyd <g.r.lloyd@bham.ac.uk>
Date: 2020-05-26 13:46:56 +0100
Commit message:

 version bump

bug fix issue #7
 
Package: structToolbox
Commit: 740bac77b6be218218c6db8a1e29cb89b63cb3af
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2020-05-26 13:31:57 +0100
Commit message:

 Merge pull request #12 from computational-metabolomics/bug_fix_1_0_1

bug fix issue #7 
Package: structToolbox
Commit: ed76d50e00016476c5d9480ff65bb00812db9625
Author: Gavin Rhys Lloyd <g.r.lloyd@bham.ac.uk>
Date: 2020-05-26 13:27:38 +0100
Commit message:

 bug fix issue #7

Correctly re-order the sample_meta column for colouring samples in the dendrogram plot
 
Package: iSEE
Commit: cbb512906e88437dcd7aefcb18b50fdd35e49a5e
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-05-26 12:22:56 +0100
Commit message:

 version bump
 
Package: iSEE
Commit: d6d8121aacd6184f353ce3b710f63e488a0b81d8
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-05-26 11:37:45 +0100
Commit message:

 missing importFrom
 
Package: iSEE
Commit: df2425dca5ba76fdc222aa237d29ef3cae792d8e
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-05-26 11:31:38 +0100
Commit message:

 start adding items to NEWS file
 
Package: iSEE
Commit: 54dc5522261279dc5b8f438cc8ddeedfa93c6c15
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-05-26 11:17:18 +0100
Commit message:

 Fix section of createLandingPage() man page
 
Package: iSEE
Commit: 93263d80a180d8475132dbddc1035e1e08f56527
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-05-26 11:09:09 +0100
Commit message:

 progress bar when generating plots for ZIP download
 
Package: iSEE
Commit: 29c4a1fd4124ed45457ec5ae6a38f1f2ec715ef2
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2020-05-18 16:26:53 -0700
Commit message:

 Updated tour to use correct variable names.

* Reorganized tour observers to use the assembled tour.
* Allow the landing page function to control the tour.
* Added a defaultTour() function to show the default tour,
  erase unnecessary (and outdated) first steps file in extdata.
* Added test coverage for default test construction.
* Updated heatmap section for new functionality.

Co-authored-by: Kevin Rue-Albrecht <kevinrue67@gmail.com> 
Package: ReactomeGSA
Commit: 0b911e2cab0fc88b5f6b8f7560aae1e780f1385c
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2020-05-26 11:47:36 +0200
Commit message:

 Merge branch 'RELEASE_3_11'
 
Package: ReactomeGSA
Commit: 9e23d001b1a0e43e630839e1b30eb8ad29e79bcf
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2020-05-26 11:44:54 +0200
Commit message:

 Added workaround for SEC_E_ILLEGAL_MESSAGE error
 
Package: ReactomeGSA
Commit: 8105d12efa7fef4ba8e53997a8f12d7a64eae345
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2020-04-29 15:58:13 +0200
Commit message:

 Fixed colour assignment
 
Package: ReactomeGSA
Commit: b2cd66f20a335baebdf3cc469fd1ebe63708090f
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2020-04-29 15:54:43 +0200
Commit message:

 Fixed type
 
Package: ReactomeGSA
Commit: 1f49afdfd94d54fea1b2f5da6a0270207bcce12b
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2020-04-29 15:50:49 +0200
Commit message:

 Added option to hide non-sig pathways in plot_correlations
 
Package: BgeeDB
Commit: e4f2d1090a74e5c7e88ee580607bb4ef31da9b37
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-26 10:22:33 +0200
Commit message:

 bump version
 
Package: seqLogo
Commit: 405756e194109757e471901407474c9d29122c6d
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-05-26 09:59:23 +0200
Commit message:

 bumbed version
 
Package: seqLogo
Commit: 0a422f7ad0fb5c2a53cc520c6d5266f1677c35a0
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-05-22 12:09:59 +0200
Commit message:

 updated the logo
 
Package: BgeeDB
Commit: 30ace1854ed992e2608dd7be69db729be51df2ca
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-26 09:56:52 +0200
Commit message:

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 
Package: BgeeDB
Commit: a11cdd72e5894cb73cb7de5642696b8e22cfa172
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-26 09:54:08 +0200
Commit message:

 update NEWS section
 
Package: tradeSeq
Commit: 531be4e979354212d04d99e08a3e1b2701ae2b2d
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-25 20:39:50 -0700
Commit message:

 version bump
 
Package: tradeSeq
Commit: 223fb00c99dbc92795fa6c87edb41bc3c1ce4526
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-25 17:38:03 -0700
Commit message:

 define rowMedians from matrixStats
 
Package: tradeSeq
Commit: 9d8a47269456ecbc96fa00bb3d12d7e6f110c999
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-25 17:17:29 -0700
Commit message:

 rm importFrom clusterExperiment
 
Package: tradeSeq
Commit: e0b550a9b1bb0e7c8e17575a1c2fff95bbd996a0
Author: koenvandenberge <koen.vandenberge@ugent.be>
Date: 2020-05-25 17:16:04 -0700
Commit message:

 try moving clusterExperiment from Imports to Suggests
 
Package: sangeranalyseR
Commit: 7d2bd4c82b0e0e87b60f56a3d6ad576fe8956aba
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-26 11:54:43 +1000
Commit message:

 Update documentation (R > 4.0.0; Installation from Bioconductor)
 
Package: sangeranalyseR
Commit: 775da8f1582e8e07ca138e71873143cd324172f3
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-26 06:36:20 +1000
Commit message:

 Update testthat tests for reverse reads
 
Package: sangeranalyseR
Commit: 64fa96f7d9d15adf71ffb356e551791796d88345
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-26 06:23:39 +1000
Commit message:

 Update SangerAlignment reverse read testthat error
 
Package: sangeranalyseR
Commit: 79f1d893f2af6950b4b211ac36ec6a5ec0e6be67
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-26 06:03:27 +1000
Commit message:

 Update SangerRead & SangerContig reverse read error
 
Package: sangeranalyseR
Commit: 5ca7ee0d17f70d4f0441a73c9232a30b4aa6fc4b
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-26 04:34:08 +1000
Commit message:

 Fix sangerRead testthat error
 
Package: sangeranalyseR
Commit: e081d1377e72dc681468b3d0bd742f23d38fe078
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-26 04:15:17 +1000
Commit message:

 Update reverse sequence error
 
Package: sangeranalyseR
Commit: 6e30af06666c4171196c5443358739c946ec547b
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-26 00:57:52 +1000
Commit message:

 Fix primary seq reverse trimming start & end point error
 
Package: sangeranalyseR
Commit: f4a47f18ad4cd39dba21313b4ec711a8225a2ddc
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-25 23:50:00 +1000
Commit message:

 Fix SangerRead not chromatogram revserse
 
Package: sangeranalyseR
Commit: cb24c34da5700e80b5c1d6c751fcc95a21b41a8b
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-25 13:26:15 +1000
Commit message:

 Fixing secondary peaks (reverse raw data)
 
Package: sangeranalyseR
Commit: 0088ef5569e537e84a1175ab08fee7a4003b25bc
Author: HowardChao <ntueeb05howard@gmail.com>
Date: 2020-05-22 13:32:50 +1000
Commit message:

 Merge master to develop branch
 
Package: sangeranalyseR
Commit: 5a5806ed765bd1d7d225edb075148c11066131b6
Author: Kuan-Hao, Chao <ntueeb05howard@gmail.com>
Date: 2020-05-18 11:53:56 +1000
Commit message:

 Update readme.md 
Package: ideal
Commit: 6c1ff5307c9ac241d2505430a9e9e04f62941556
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-26 01:40:12 +0200
Commit message:

 Version bump - 1.13.1
 
Package: ideal
Commit: 2b51a590f038e43fb8a9dfacf9de61bcc318906c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-25 23:18:23 +0200
Commit message:

 updating call for interactive heatmap in the template report
 
Package: ideal
Commit: 67bf07e8a26b6874617af4acd43cd5637cb42048
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-25 23:18:02 +0200
Commit message:

 Fixing namespace imports
 
Package: ideal
Commit: 7e9d5901203a5fd8af1e70141ec5f6bf4294df6e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-25 23:17:35 +0200
Commit message:

 Replacing the archived d3heatmap with heatmaply and plotly - work as drop-in replacement
 
Package: ideal
Commit: b4ce31e0c327b90bd1a880bdabc3c7066b250b68
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-25 23:16:22 +0200
Commit message:

 explicitly specifying the lfc shrinkage method to normal
 
Package: ideal
Commit: dbe255374a205f463cc360f5767f732b79d713bf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-25 22:19:25 +0200
Commit message:

 updated content for pkgdown setup
 
Package: ideal
Commit: d540439dcdad6585eb8efa5627230db8a9e9ea92
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-25 22:18:51 +0200
Commit message:

 rerendered pkgdown website
 
Package: ideal
Commit: 55a2c97390f98f8e3d1a47e57104b4a1acb7e95f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-10 23:34:39 +0200
Commit message:

 added badge for GH actions, looks all good on all OSs ;)
 
Package: ideal
Commit: d8891610ffb05ecb109976e7dc047f551b075703
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-10 22:50:33 +0200
Commit message:

 adjusting gh actions a la iSEE
 
Package: ideal
Commit: 1ff68ae8ca59052da8ce2c4c98b0dac4868cbc21
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-10 22:37:14 +0200
Commit message:

 trying httr and covr as binary
 
Package: ideal
Commit: 9290256ffcf7690eabf54763760c80282fc04375
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-10 22:32:30 +0200
Commit message:

 triggering travis for new build
 
Package: ideal
Commit: be5bcc429e7e57828005bc369bfbaca1cd0c678c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-04-30 00:41:06 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
 
Package: ideal
Commit: 05411230be48dbba16c39f4b071f38541e12bfa0
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-18 11:39:11 +0100
Commit message:

 Version 1.11.3 - post-revision
 
Package: ideal
Commit: 3ff55d9bc91a4a018ac60a83bfcf682dc9472f2a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-18 11:33:58 +0100
Commit message:

 Updated the news - after revision suggestions
 
Package: ideal
Commit: 7ae92d9043e649772adc1d6b278d1020957c8b43
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-15 23:26:28 +0100
Commit message:

 Updated Roxygen version
 
Package: ideal
Commit: 8d84555673ebea4f178c53d25d9bb872a220b44a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-15 23:26:12 +0100
Commit message:

 Highlighting syntax for R blocks in README
 
Package: ideal
Commit: c89e069386dd0a258a682e794b4ae50ebce3a9df
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-04 17:50:16 +0100
Commit message:

 Fixing GH actions - added GO.db
 
Package: ideal
Commit: aab5df31efeab526016438b86564dcf071f6965e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-04 17:03:18 +0100
Commit message:

 Installing also dependencies in Suggests with extra parameter specified
 
Package: ideal
Commit: 2b5d4756c47562ce3386f1d64b025cacd8ad331b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-04 16:08:47 +0100
Commit message:

 Added md-formatted content for the collapsible element on EDA-before-DE
 
Package: ideal
Commit: 9758c7497148e04d65baff3bfe48320d0acd33e6
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-04 16:08:05 +0100
Commit message:

 Added collapsible element to remind to perform proper EDA before testing for DE in Data Setup panel
 
Package: ideal
Commit: f5d9ca94ab13cd9f02a496215d887c8709d1bb44
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-04 15:09:26 +0100
Commit message:

 Replaced rlog with vst also in the vignette, explaining rationale behind this
 
Package: ideal
Commit: 46004b8e46d78a2cab8102ee21a83baf93d882de
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-03 22:25:39 +0100
Commit message:

 Added subsection for addressing the point of which version to use, with respect to the user profile.
 
Package: ideal
Commit: 51f4b195e4935a9810cdeae36e911928b54caac4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-03 18:39:29 +0100
Commit message:

 Added extra information on installation troubleshooting
 
Package: ideal
Commit: 32644ddcc4828704f18f9fca159381cf3db3be43
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-03 12:52:50 +0100
Commit message:

 fixing deps in gh actions
 
Package: ideal
Commit: 97dc0aa7fe3cf1de4037cfcafb1df034e8212dbf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-03 12:40:54 +0100
Commit message:

 setting up github actions
 
Package: ideal
Commit: 4e003bd953ce9cee5c84a0ebe062545b114763f6
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-03 12:29:40 +0100
Commit message:

 Set and explain dependencies = TRUE in the devel install procedure
 
Package: ideal
Commit: 65b59fa1a0b518f5111605781924a43d77136a03
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-02 12:34:14 +0100
Commit message:

 Updating related code after switch from vst to rlog
 
Package: ideal
Commit: f55cfb93be7f5de1485290ea6aa748e109cdca7b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-02 12:33:48 +0100
Commit message:

 Handling alternative normalization/transformation via vst instead of rlog
 
Package: pcaExplorer
Commit: db193719c3036043b671444af9f224b8038954df
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-26 01:03:32 +0200
Commit message:

 Version bump - 2.15.1, edited news
 
Package: pcaExplorer
Commit: 91d4ced5becaa2ede180940f30116ef4b0f8542b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-26 00:46:59 +0200
Commit message:

 Replacing d3heatmap, bringing in heatmaply
 
Package: pcaExplorer
Commit: c6c3bd17df07a7bca48aed4bc7d1d43c0dd6f2b9
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-26 00:46:13 +0200
Commit message:

 updated rendered pkgdown
 
Package: pcaExplorer
Commit: 93b72799acf7087ecf7bb12bc780ce46d51b6536
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-10 23:44:50 +0200
Commit message:

 added badge to README
 
Package: pcaExplorer
Commit: 5bfbd450c0f4c5bb2e7088c95feb9120e5bba4d1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-05-10 23:44:03 +0200
Commit message:

 Adding integration with GH actions
 
Package: pcaExplorer
Commit: 050376ffe05f5bd7e227e5dd2947b208e3c61a78
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-04-30 00:36:53 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: pcaExplorer
Commit: c8e1ca8cf467f9810c2308c4916b9d05b482e130
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-15 23:26:39 +0100
Commit message:

 Updated Roxygen version
 
Package: pcaExplorer
Commit: 187daeb4050dd903eb41f0c7d0247355da5490aa
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-03-15 23:25:55 +0100
Commit message:

 Highlighting syntax for R blocks in README
 
Package: pcaExplorer
Commit: 0c5033bcc1a67ffdd23aefa83dc2c0ddd1540505
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-27 21:48:10 +0100
Commit message:

 fixing travis...
 
Package: pcaExplorer
Commit: 0169403b6cdf4a98b8b987bbe738619e1c55a1f4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-21 00:47:18 +0100
Commit message:

 Updated roxygen version
 
Package: pcaExplorer
Commit: a8777479b2ce43e1df23765d3d12d31839b6deb4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-21 00:47:04 +0100
Commit message:

 Refreshing the indentation
 
Package: pcaExplorer
Commit: 2964608d68a80291ac749e08df11424a76567e32
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-21 00:39:51 +0100
Commit message:

 Linting main function
 
Package: pcaExplorer
Commit: c8e298cb798a3a65ffd2533175a808f122146b77
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-21 00:05:29 +0100
Commit message:

 Updated man after linting
 
Package: pcaExplorer
Commit: b8a3e4dfa593d98cd2887f885ecd32aa28fe27c8
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-21 00:05:00 +0100
Commit message:

 Linting tests
 
Package: pcaExplorer
Commit: c784462a8d26548ebb7614744aea8eaf599a4cde
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-20 22:58:12 +0100
Commit message:

 lint lint lint
 
Package: pcaExplorer
Commit: a55ff9ff791b08140290fb8a7b9fbca9103f4e5d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-20 22:53:02 +0100
Commit message:

 More linting :)
 
Package: pcaExplorer
Commit: 1f1366146985ac96acffb0b12cd89aa65f34e50f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-20 22:43:44 +0100
Commit message:

 Further round of linting
 
Package: pcaExplorer
Commit: e6492abec5695d5f7c904c4e374602ced681f4bc
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-20 22:39:19 +0100
Commit message:

 Linting round, correlatePCs, distro_expr, and genespca
 
Package: pcaExplorer
Commit: eb2613367d9ced9987ddd64f17dffaed24a251f4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-01-18 14:29:36 +0100
Commit message:

 Trying to solve fail in vignette build - ideas from https://github.com/yihui/knitr/issues/1796
 
Package: pcaExplorer
Commit: 8fa4a88af7033a4a776877c6eedc10d75f50b118
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2019-11-18 14:17:27 +0100
Commit message:

 updated to newer roxygen version
 
Package: BioNetStat
Commit: c738595f759d60a3f1a6124c0297d0a8904df4b1
Author: jardimViniciusC <viniciusjc@gmail.com>
Date: 2020-05-25 18:40:30 -0300
Commit message:

 fixing help files and adding citation file
 
Package: DEScan2
Commit: a8bae30244febaefc7d514df6c040da5588435ec
Author: drighelli <d.righelli@gmail.com>
Date: 2020-05-25 22:30:55 +0200
Commit message:

 bumping version 1.9.1

Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
 
Package: DEScan2
Commit: 93158ebf949263290ffa9bd8f4e018ee58ae8c99
Author: drighelli <d.righelli@gmail.com>
Date: 2020-05-25 22:26:48 +0200
Commit message:

 bumping version 1.3.3
 
Package: DEScan2
Commit: 3cfc308d0fa129b50b72aed881b04ac7f1cb36c5
Author: drighelli <d.righelli@gmail.com>
Date: 2020-05-13 20:29:27 +0200
Commit message:

 removing chr name check on peak caller and keepRelevantChrs
 
Package: MSstatsQCgui
Commit: 8fd43a0fdfc2bd8fa779961d2d6e7b508ab168f8
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2020-05-25 23:11:34 +0300
Commit message:

 Conflicts resolved
 
Package: MSstatsQCgui
Commit: d3687a0d660d4b97e61824e48b186ef90a6e6308
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2020-05-25 23:05:10 +0300
Commit message:

 Version bump
 
Package: MSstatsQCgui
Commit: 0f14f1a92ed4d569ba86aef28782876054b0ce00
Author: Eralp DOGU <eralp.dogu@gmail.com>
Date: 2020-05-25 18:27:38 +0300
Commit message:

 Conflict markers removed and Rproj removed
 
Package: fishpond
Commit: b6083fad1f10f65c86a78dd126c5b9cc8d817b40
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-05-25 15:47:59 -0400
Commit message:

 adding more legend args
 
Package: BgeeDB
Commit: 0474edb08ab15e67439faa1adfdce2c1a80414c8
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-25 20:23:42 +0200
Commit message:

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 
Package: BgeeDB
Commit: e874e1657eeee1502a8be0d54a51b1082b3340e3
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-25 20:23:08 +0200
Commit message:

 manage error message
 
Package: BgeeDB
Commit: 0513213fccd3b8db5651894d7e120d2f3ad898a6
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-25 19:21:09 +0200
Commit message:

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 
Package: BgeeDB
Commit: 769e1783a16a87f0e7bfbac4d00c4e3a0d83e05a
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-25 19:13:05 +0200
Commit message:

 hotfix to allow download on windows
 
Package: ribosomeProfilingQC
Commit: ab5474cc1703f00a90e17ead29070305f0f8086c
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-05-25 14:19:52 -0400
Commit message:

 update vignette to fix the typos.
 
Package: netDx
Commit: 90010dceeadc1564d845e1c10f939da01f1c76e3
Author: Shraddha Pai <shraddha.pai@utoronto.ca>
Date: 2020-05-25 17:00:55 +0000
Commit message:

 fixed broken link from biomart with own copy of gene defs
 
Package: ATACseqQC
Commit: b63a696463c686372f3279966ec0d5f899be581b
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-05-25 13:03:52 -0400
Commit message:

 Add documentation to decribe the format of bindingSites for factorFootprints.
 
Package: glmGamPoi
Commit: 6eaf620fed7f5bb3ea8081b8a4576e21bc405101
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-25 18:51:56 +0200
Commit message:

 Bump version
 
Package: glmGamPoi
Commit: 22114a54b129376113a292a0204afd473ab22c9e
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-25 18:51:38 +0200
Commit message:

 Update NEWS
 
Package: glmGamPoi
Commit: 7e39ac9a0359c542b51ec85ebb9d40d9f2858b5b
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-25 18:43:38 +0200
Commit message:

 Add upper and lower bounds for nlminb of 1e16 to handle extreme cases
 
Package: glmGamPoi
Commit: 9cc29f342c3242906b81a35a1da66642fd7b1243
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-25 18:00:41 +0200
Commit message:

 Update comments
 
Package: glmGamPoi
Commit: f7b5eda8eb55101be71ebf4ab3957df29916b703
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 21:42:13 +0200
Commit message:

 Fix potential bug by explicitly calling std::abs() in C++
 
Package: metaseqR2
Commit: 0826a9190750649cdf0277a7ba6229e14f4ab261
Author: Panagiotis Moulos <moulos@fleming.gr>
Date: 2020-05-25 18:30:12 +0300
Commit message:

 Added harmonic mean p-value combination, fixed serious bug in statDss, added a p-value dataset
 
Package: metaseqR2
Commit: 5e0b38e645ad791b7587552ad6325bfc5c2cfe1d
Author: Panagiotis Moulos <moulos@fleming.gr>
Date: 2020-04-29 09:14:43 +0300
Commit message:

 More leftovers from "1:"
 
Package: rnaseqGene
Commit: 2c138e9511faa47d8bce2b0544a1f9d4957d4e52
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-05-25 08:54:12 -0400
Commit message:

 update re shrinkage
 
Package: fishpond
Commit: 852bae5d947a9931f2408497c3a3b918aee3631a
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-05-25 07:58:52 -0400
Commit message:

 swap red and green in plot
 
Package: PhyloProfile
Commit: 6335c9260bf65d44d8c4ddd44c1b442c72299de0
Author: trvinh <trvinh@gmail.com>
Date: 2020-05-25 13:47:45 +0200
Commit message:

 Fixed bug unkTaxaId not found
 
Package: MsCoreUtils
Commit: 399a9cf8beff8aa53466092405c367c876323b77
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2020-05-25 12:48:53 +0200
Commit message:

 Merge pull request #53 from lgatto/master

fix: deprecate doproduct signature 
Package: MsCoreUtils
Commit: b58e0c77f6b763eead15194faa166b928b5a3bde
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-05-22 20:03:52 +0200
Commit message:

 fix: deprecate doproduct signature
 
Package: MsCoreUtils
Commit: 144b34eb5954149632f4b31975b65c48e460706d
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-05-22 20:03:30 +0200
Commit message:

 test: add dotproduct deprecation test
 
Package: MsCoreUtils
Commit: cce3b0972dbcd3dbe73af2c25048366083c4c14d
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-05-22 19:52:08 +0200
Commit message:

 fix: deprevate doproduct
 
Package: MsCoreUtils
Commit: a6ca19b0b5cb043b81f1b4dce3c871148a33393d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-05-08 14:45:24 +0200
Commit message:

 chore: bump version number
 
Package: MsCoreUtils
Commit: 1156bc663cad787f61b3046cee831677378f440f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-05-08 14:45:14 +0200
Commit message:

 doc: news about distance metrices
 
Package: MsCoreUtils
Commit: 1215fb3c1f14a0687dfb1aa77acc6a54a20f9755
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-05-08 14:41:25 +0200
Commit message:

 chore: rerun roxygenise
 
Package: MsCoreUtils
Commit: 01864f079ec1de1ac16e9a009a298c24a4fe4bcc
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-03-30 12:46:34 +0200
Commit message:

 docs: emphasize that sim/dist calculations are normalised
 
Package: MsCoreUtils
Commit: 44c38056afbeeedf638f81ecad1b852aa8960b9a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-03-05 12:58:45 +0100
Commit message:

 docs: add note about missing reference implementation as suggested by @jorainer
 
Package: MsCoreUtils
Commit: efb5ff79c64a867795132663b4fa1b151f41bfb3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-03-05 12:58:21 +0100
Commit message:

 docs: remove duplicated author entries
 
Package: MsCoreUtils
Commit: 920a7f880a504e064615b08042c44df74d0fa05f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-12-13 20:31:00 +0100
Commit message:

 docs: add 'see details section' for m and n argument
 
Package: MsCoreUtils
Commit: bc22ef61325e6d80bde67a8419d3462e0c4d7d27
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-12-12 09:38:50 +0100
Commit message:

 docs: fix typo
 
Package: MsCoreUtils
Commit: ee2d5ee50cf4f878b4a77fb0ffe6f90ab847fc65
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-12-12 09:35:18 +0100
Commit message:

 docs: add some newlines as suggested by @jorainer
 
Package: MsCoreUtils
Commit: 202f9d50bd57978c62069f5eeadd80f8d644d31c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-05-08 14:30:28 +0200
Commit message:

 docs: add distance functions to pkgdown site
 
Package: MsCoreUtils
Commit: c79af98f86d80def34c0e49d848d2d14a2a45c97
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-12-11 22:52:52 +0100
Commit message:

 feat: add navdist
 
Package: MsCoreUtils
Commit: d9cf17a938cbee9976e9c692b61d61fc32ea741d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-05-08 14:29:21 +0200
Commit message:

 feat: add nspectraangle
 
Package: MsCoreUtils
Commit: bca23aadf8c9c5b4ef9f1417617243e54008504e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-12-11 22:14:15 +0100
Commit message:

 feat: add neuclidean
 
Package: MsCoreUtils
Commit: cb2be9ffb2014e7cfcc95aecffc5498d7feb71c6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-05-08 14:29:04 +0200
Commit message:

 feat: add ndotproduct
 
Package: MsCoreUtils
Commit: 3e824931bc97f985673c8e8d7b8837182f4f4593
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-12-11 20:41:51 +0100
Commit message:

 refactor: remove old dotproduct
 
Package: MsCoreUtils
Commit: bd497fb0bb5382313e0d1b300eab303a9f1106d0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-12-11 12:03:20 +0100
Commit message:

 feat: add .weightxy
 
Package: MsCoreUtils
Commit: 72f97bd58c442ea7449cf34927c00965b5e9b6a4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-12-11 11:52:24 +0100
Commit message:

 feat: add .calibrate
 
Package: MsCoreUtils
Commit: 7df83733f3a707cc5f9da48f14454dc7ba041268
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-05-08 14:25:45 +0200
Commit message:

 chore: update NEWS.md after bioc version bump
 
Package: basilisk
Commit: eed185af50549086b8790637ec6c57cf4aa4a4ed
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 01:41:40 -0700
Commit message:

 Avoid check on windows as it does not throw an error.
 
Package: basilisk
Commit: 8c1efa1cfdedbf82b789d2abd70779355c3a244c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 00:56:38 -0700
Commit message:

 Reoxygenated.
 
Package: basilisk
Commit: 2a6a039804dc1cdaaed787f8e0788d3afb789d0d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 00:27:58 -0700
Commit message:

 Generalized package listing functionality for environments.
Updated tests that use freezing internals.
 
Package: basilisk
Commit: 3d5f60073c51e7bb4a4608b90aebcf1e2054ecf6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 00:25:47 -0700
Commit message:

 Further streamlining of useBasiliskEnv to remove required=.
Shift the logic into basiliskStart for greater clarity.
 
Package: basilisk
Commit: bf4b264c0d199b69282e4ca9be69c37aea329253
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-24 23:53:27 -0700
Commit message:

 Don't bother to deactivate the conda environment.
Removed dry run code from useBasiliskEnv.
 
Package: basilisk
Commit: 3a834f34001c38d1c790a592bda5662684946ec8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-24 22:42:56 -0700
Commit message:

 Migrated activation code to basilisk.utils,
updated all affected functions.
 
Package: basilisk
Commit: 0c086f1543f4dd13058104c6407632cb4cb47531
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-24 21:39:23 -0700
Commit message:

 Updated DESCRIPTION.
 
Package: basilisk.utils
Commit: e87edf5f9c3ff20f5f89cec499f0eda92c46e0e9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-24 23:54:20 -0700
Commit message:

 Migrated conda activation utilities from basilisk.
 
Package: CAGEr
Commit: 165f5bf86f5c562fa5e6f5018712824d288bd7be
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2020-05-25 09:58:35 +0900
Commit message:

 Merge remote-tracking branch 'bioc/master'
 
Package: CAGEr
Commit: 3eff005cec36a323f8302fcfa14e25c8262476bf
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2020-05-25 00:49:24 +0000
Commit message:

 Changes in version 1.31.1:

BUG FIXES

    o Allow empty `CTSS.chr` objects.
    o Correct `plotInterquantileWidth()` to really use consensus clusters
      when passed the argument `clusters = "consensusClusters".
    o Fix failures on `CAGEexp` objects containing only one sample.
 
Package: CAGEr
Commit: f0ffa61b8f6d9e582a8fb32843f4973617be4fcd
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2020-05-25 00:43:42 +0000
Commit message:

 Really get quantile information of consensus clusters when requested.

(instead of silently using the tag clusters by mistake)
 
Package: CAGEr
Commit: d9b98613d0c35dcb729fec01282b8e5321ae2da0
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2020-05-25 00:41:00 +0000
Commit message:

 Allow empty `CTSS.chr` objects.

These empty objects happen when looping on seqlevels of CTSS positions
in samples where expression is null.

See Issue #25 for details.
 
Package: CAGEr
Commit: 7d61e3a8ce5ff5639b867a21b40718fd4f125488
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2020-04-29 19:26:01 +0000
Commit message:

 Fix failures on CAGEexp objects containing a single sample.
 
Package: fishpond
Commit: 71a1ef4a13bc89aa5be3c2eaf7a1bf72e5ddbbb9
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-05-24 20:12:22 -0400
Commit message:

 fix colors
 
Package: BgeeDB
Commit: 57416f541e0322a71608eacc780e8a37a2085164
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-25 01:19:34 +0200
Commit message:

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 
Package: BgeeDB
Commit: 69b8eaa5c1f58e85b8974eb47a2e3aa3f48b2ce1
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-25 01:17:59 +0200
Commit message:

 correct anat entity ID
 
Package: PureCN
Commit: a32080d01602f207a2c0a44b6c3c65682bcd286a
Author: lima1 <mriester@gmx.de>
Date: 2020-05-24 19:03:49 -0400
Commit message:

 roxgen2 update.
 
Package: PureCN
Commit: 84e51dd57e69fc34ecb6082b0cb0a02e4c0cafb8
Author: lima1 <mriester@gmx.de>
Date: 2020-05-24 12:30:25 -0400
Commit message:

 Fixed build error of previous commit.
 
Package: BioNetStat
Commit: df3f1169c616eeacaf3e2211e7cee6754d5a00e7
Author: jardimViniciusC <viniciusjc@gmail.com>
Date: 2020-05-17 21:07:30 -0300
Commit message:

 fixing table bugs and tutorials
 
Package: simpleSingleCell
Commit: 9f09af047363e36eea092c5a9dcfd9169f4ca540
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-17 22:13:55 -0700
Commit message:

 Bumped version and date.
 
Package: simpleSingleCell
Commit: 28c702308a343fbe23fff44d378f90a64a6888b5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-17 22:13:30 -0700
Commit message:

 Remove all of the bookdown intermediate output.
 
Package: simpleSingleCell
Commit: 8f398280aee0bfc9a494d9e4cc87b93f238fa9f8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-17 17:26:18 -0700
Commit message:

 Added Makefile to trick the system into building the book.
 
Package: simpleSingleCell
Commit: bb71076b87fe24ca8d64e9413c7b650cf8536b27
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-17 17:20:27 -0700
Commit message:

 Transplanted the contents of rebook here for testing purposes.
 
Package: hypeR
Commit: 44bade5fce4c2914cb8cca76c9b151b6311fb506
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-05-24 15:38:08 -0400
Commit message:

 Update NEWS.md
 
Package: hypeR
Commit: 43552890664115991bc8e3766f2f294f40da5504
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-05-24 15:37:58 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: hypeR
Commit: 55ff4725dd6f27601bc7cad61f928506b118a91f
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-05-24 15:09:29 -0400
Commit message:

 Update NEWS.md
 
Package: hypeR
Commit: 856166db2c2b80ff85b236c79e4a9123009a4dcd
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-05-24 15:08:28 -0400
Commit message:

 Improved markdown reporting
 
Package: hypeR
Commit: e24839e98ef69b21c287b5236eb4ce0c9a0fc5f4
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-05-20 12:48:26 -0400
Commit message:

 Ability to clean geneset names

- Remove of the longest leading common substring
- Replace underscores with spaces
- Capitalize terms
 
Package: hypeR
Commit: 7683a6c23a70976d65701b1eaff6f4b96b5baba7
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-05-20 12:20:45 -0400
Commit message:

 Update README.md
 
Package: hypeR
Commit: 930df94200e3dc2d95e038854e29f9e09fe2d952
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-05-20 12:19:39 -0400
Commit message:

 Update docs
 
Package: hypeR
Commit: 8aa045c5c5c36f2599e089f9fb781d93f1eae4c5
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-04-28 13:47:29 -0400
Commit message:

 Add travis badge
 
Package: hypeR
Commit: 5d159875ce7e0ab76cced08670d4cbbd8198fefe
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-04-24 19:55:50 -0400
Commit message:

 Create .travis.yml
 
Package: hypeR
Commit: cf7eb006058b4a2315d3e739d36b0c7930912c55
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-02-04 06:29:12 -0500
Commit message:

 Update DESCRIPTION
 
Package: hypeR
Commit: 6fb91dd3ebd963f2952ea6e0fbc10407fe73325d
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2020-01-30 22:28:43 -0500
Commit message:

 Improved reproducibility methods
 
Package: hypeR
Commit: a5d7b04274b846f6c36ba53e228d468e6c5a7a59
Author: anfederico <anfederico@users.noreply.github.com>
Date: 2019-12-31 00:43:31 -0500
Commit message:

 Update NEWS.md 
Package: hypeR
Commit: 1707ec02599eb129c9a3b1f2e233ad965482e9dc
Author: anfederico <anfederico@users.noreply.github.com>
Date: 2019-12-31 00:42:46 -0500
Commit message:

 Update NEWS.md 
Package: hypeR
Commit: d3b972cf69e2c6a45c7cffead5e7b32e19aaac31
Author: anfederico <anfederico@users.noreply.github.com>
Date: 2019-12-29 11:44:45 -0500
Commit message:

 Update DESCRIPTION 
Package: hypeR
Commit: a7e809c697f5a45d9b969b29615f16696298337b
Author: Anthony Federico <anfederico@users.noreply.github.com>
Date: 2019-12-29 11:38:07 -0500
Commit message:

 Update DESCRIPTION
 
Package: trackViewer
Commit: f5e75e273bffb9b938b07d8e764fa3b33f4dee8e
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-05-24 14:30:31 -0400
Commit message:

 Provide more clearly warning or error message if the input is not sorted or contain NA values.
 
Package: glmGamPoi
Commit: f665fe1fcedbc343c5b479ef10199d877a60984c
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 19:40:12 +0200
Commit message:

 Bump version
 
Package: glmGamPoi
Commit: 9496cc42b3478770803df9f66b0d6984cd8843ed
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 19:40:00 +0200
Commit message:

 Return iterations = 0 instead of NA if dispersion estimate is instant
 
Package: BLMA
Commit: 7567bb997331b8a92ebe3bb0373381bd0e7926f2
Author: Phi <hungnp@nevada.unr.edu>
Date: 2020-05-24 10:35:12 -0700
Commit message:

 version bump
 
Package: BLMA
Commit: 5950bf22b9cd28c15f8155845638d73da231206d
Author: Phi <hungnp@nevada.unr.edu>
Date: 2020-05-24 10:29:16 -0700
Commit message:

 add getStatistics to export
 
Package: glmGamPoi
Commit: ad7c05f086c6c6d9122415efa12dafedee8d6b4d
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 19:16:58 +0200
Commit message:

 Bump version
 
Package: glmGamPoi
Commit: 615a27c174336b809864ba4250a2eb5492b12812
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 19:15:05 +0200
Commit message:

 Update README
 
Package: glmGamPoi
Commit: e2aa4b357e0187fcc2d0205d38a0c4f74f8f3d81
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 19:14:49 +0200
Commit message:

 Make conventional_score_function_fast() more robust to extreme values
 
Package: glmGamPoi
Commit: 2387bc4a3f56c5fdef16796449808fdfa5c8ed74
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-21 15:39:02 +0200
Commit message:

 Update new GitHub action script from kevinrue

https://github.com/iSEE/iSEE/blob/master/.github/workflows/R-CMD-check.yaml
 
Package: fishpond
Commit: 498f062cce24d12f15f7282ce826b5eec32b4205
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-05-24 13:02:47 -0400
Commit message:

 add to vignette
 
Package: fishpond
Commit: f185617f2251bc66a1a16ac290e1443ba5fe10fe
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-05-24 08:20:32 -0400
Commit message:

 more work on plotting w numeric x
 
Package: sparseMatrixStats
Commit: f825865393f853db76c0e13765671d65d42b4b09
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 13:15:03 +0200
Commit message:

 Bump version
 
Package: sparseMatrixStats
Commit: 6d6fb75ea82d48d11e1ee81455517957e74e097d
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 13:14:49 +0200
Commit message:

 Update NEWS
 
Package: sparseMatrixStats
Commit: f36e78fdf9297b8153b2df0f7d752ba779016781
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 13:13:24 +0200
Commit message:

 Fix link in colProds due to some bad linking by @inherit
 
Package: sparseMatrixStats
Commit: 1c68b80ea305ab5a8407c5d10a9572c448de3fca
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-05-24 13:09:17 +0200
Commit message:

 Update documentation to latest version (1.1.2) of MatrixGenerics
 
Package: ontoProc
Commit: fcd3c51e13dfd8d35bdbd41586bc849d554b3b98
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2020-05-24 06:38:31 -0400
Commit message:

 adding cache discipline for getCellOnto
 
Package: chimeraviz
Commit: 82f67ebbcd823ba8afdb54710f7a4fd0984dd683
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2020-05-24 12:06:11 +0200
Commit message:

 Add citation
 
Package: fishpond
Commit: dbcb495ad04918459f4bfec6cf209e6dca99fdb6
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-05-23 21:20:41 -0400
Commit message:

 new plot functionality for numeric x
 
Package: MatrixGenerics
Commit: 9e2e67b1086e69df59b2785b12d0b1b78577ff17
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2020-05-24 10:44:06 +1000
Commit message:

 Version bump
 
Package: MatrixGenerics
Commit: 580e1006938ff27a51fbf6f80988ad15657029b4
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2020-05-24 10:43:50 +1000
Commit message:

 Fix remaining docuemntation link warning on Windows
 
Package: S4Vectors
Commit: ccbde78beeaa21d47d3781bc98628a12445c6e3d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-05-23 17:04:51 -0700
Commit message:

 showAsCell() now trims strings that are > 22 characters
 
Package: ShortRead
Commit: 3616077f9f6f551cf031a3cff8dcfe17f02f7e2f
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-23 17:40:33 -0400
Commit message:

 Merge remote-tracking branch 'refs/remotes/upstream/master'
 
Package: ShortRead
Commit: 3e7a6c069583e868be39afabb643d7b496e6a446
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-23 17:37:00 -0400
Commit message:

 remove coercion to defunct RangedData
 
Package: ShortRead
Commit: 2fc1782a774fd59ebb185238f2d9e776212e4fa1
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-05-23 17:27:06 -0400
Commit message:

 add countFastq for fast counting of fastq records
 
Package: tradeSeq
Commit: 9dd7f4d95885d92bf7aa65c6e36dd6e79a0aa6e1
Author: Hector <hector.rouxdebezieux@berkeley.edu>
Date: 2020-05-20 15:55:12 +0200
Commit message:

 Fixed issue from #4
 
Package: tradeSeq
Commit: c7a6450de9e3eb1bbdecdc5b198b9c93d23d241c
Author: Hector <hector.rouxdebezieux@berkeley.edu>
Date: 2020-05-16 19:52:31 +0200
Commit message:

 fixed #46

New evaluateK functions to mirror fitGAM
New function to extract_monocle_info
 
Package: S4Vectors
Commit: 1bb90866a66894e33f51dbcbcf6b046488704689
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-05-23 13:26:48 -0700
Commit message:

 Fix showAsCell() on ordinary data frames
 
Package: ComplexHeatmap
Commit: c1485e374a84f3cd9451f30db22391e1bb70d23d
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-21 23:13:54 +0200
Commit message:

 anno_image(): fixed a bug that images are not reordered
 
Package: ComplexHeatmap
Commit: 515946b494c0f99a8b9fdd47344940381b60efff
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-19 11:31:32 +0200
Commit message:

 discrete_legend_body(): adjust ncol and nrow if there are empty rows and columns in the layout.
 
Package: ComplexHeatmap
Commit: 019330c50a66b01b88fd6a04bdf09ed0ae797783
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-18 22:10:51 +0200
Commit message:

 default_col():print messages if there are outliers
 
Package: ComplexHeatmap
Commit: d8dd42d76e4dbea0cdd2c8457c4b2c0f5421207a
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-18 14:45:03 +0200
Commit message:

 fixed typo
 
Package: ComplexHeatmap
Commit: a5d512e6fdb1e79fe2c3cee48df53ab4baed6cd6
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-18 13:21:34 +0200
Commit message:

 Merge branch 'master' of https://github.com/jokergoo/ComplexHeatmap
 
Package: ComplexHeatmap
Commit: 003c6791b3f0d4f1ade9237a50f9bec8bbe4e6c9
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-18 13:21:25 +0200
Commit message:

 add instrument in the app
 
Package: ComplexHeatmap
Commit: 6c9b8718ef5f9afe2ace2c09517cc640aa1aff76
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-17 22:45:08 +0200
Commit message:

 Update README.md 
Package: ComplexHeatmap
Commit: bd6ac6e65265266a39efbdc2e8a79454fb4e2e93
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-17 22:44:21 +0200
Commit message:

 Update README.md 
Package: ComplexHeatmap
Commit: f9834abfff97fd9b17ae3240e720dd44b2336d03
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-17 22:32:10 +0200
Commit message:

 js and css locally
 
Package: ComplexHeatmap
Commit: 6f5e41a3faadc2eb5b3394848a465935b145c4c9
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-17 21:08:25 +0200
Commit message:

 change from http to https
 
Package: ComplexHeatmap
Commit: a8e7d4433619ce0656f7cd046203f4fe8c3dc6a2
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-17 20:26:17 +0200
Commit message:

 update
 
Package: ComplexHeatmap
Commit: e1120d38ed8b1cd61af97aaf398b41b3327ffe1a
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-17 16:14:19 +0200
Commit message:

 add comments
 
Package: ComplexHeatmap
Commit: 395426e568964f340e0a6d0b63138a66975d6489
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-17 15:40:19 +0200
Commit message:

 remove quotes
 
Package: ComplexHeatmap
Commit: 049449b1ecd4f9b1aa142dc24997a589cfbe7b9f
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-17 15:20:00 +0200
Commit message:

 export heatmaps as a shiny app
 
Package: ComplexHeatmap
Commit: 3502258ea720e248d8185f5abdb7703d7d4f826d
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-14 13:57:45 +0200
Commit message:

 add title
 
Package: ComplexHeatmap
Commit: d5bb3034c1517d8d874558e90f49cbb945a45043
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-14 13:48:03 +0200
Commit message:

 ht_list is saved into an environment
 
Package: ComplexHeatmap
Commit: 7033e43c781eea53fbca5ed4377153a6166cd036
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-14 09:00:55 +0200
Commit message:

 update docs
 
Package: ComplexHeatmap
Commit: b62323e4e3e96f7003a39b46367ff61c8f2322d9
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-14 08:36:17 +0200
Commit message:

 add selectArea()
 
Package: ComplexHeatmap
Commit: ea8dcf7732b4f208af56730c9eb9ebded348e95b
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2020-05-13 10:47:06 +0200
Commit message:

 update docs
 

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