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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: GenProSeq
Commit: c2d14a597c41cee4cb9a8708921ea87414c2f905
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2022-01-21 10:30:17 +0900
Commit message:

 update
 
Package: GenomicDistributions
Commit: 37e8c306537db84a6c7283004b56f3ae97964e70
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:36:49 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: GenomicDistributions
Commit: 68e6acac8b08608568786e39b161d67afe42bd46
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:33:47 -0500
Commit message:

 Merge pull request #186 from databio/dev

increase version number - correct 
Package: GenomicDistributions
Commit: 142461ec29dc53101ab774282d08bcb32d80b967
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:33:25 -0500
Commit message:

 increase version number - correct
 
Package: GenomicDistributions
Commit: 4e9b7a76481d790e54547e9bc243d913eafcd19f
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:24:22 -0500
Commit message:

 Merge pull request #185 from databio/dev

Update full-power.Rmd 
Package: GenomicDistributions
Commit: eb336615b570a2e49e63904d86d4a0c229d1d9b4
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:23:36 -0500
Commit message:

 Update full-power.Rmd
 
Package: GenomicDistributions
Commit: 67664d997cc6245c5c52a04d910973d7426449e6
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:00:32 -0500
Commit message:

 Merge pull request #184 from databio/dev

1.3.1 update NEWS 
Package: GenomicDistributions
Commit: 304e7b4b93cbcd6bee1cf11c114e758fa3b84f59
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:59:44 -0500
Commit message:

 Update NEWS
 
Package: GenomicDistributions
Commit: 000a81f23d88b819ecaac9a94619eb69b7e657ca
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:58:51 -0500
Commit message:

 Update NEWS
 
Package: GenomicDistributions
Commit: 496d06b9c093fc8bb2a16f125c3c206de6f9f29a
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:57:32 -0500
Commit message:

 Merge pull request #183 from databio/dev

Version 1.3.1 
Package: GenomicDistributions
Commit: dd07ad9e1a89fb3ee6b202a7cdd7ed5759f9ace9
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:56:00 -0500
Commit message:

 Update DESCRIPTION
 
Package: GenomicDistributions
Commit: e03f1005b60c24d3e9765bb8735dffea0741419a
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:55:15 -0500
Commit message:

 biocheck notes fix
 
Package: GenomicDistributions
Commit: fa332328e6996bdd5138bcfe7847cf10c1bd46bf
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:37:35 -0500
Commit message:

 edits to pass check
 
Package: GenomicDistributions
Commit: 15f9b17fbd20d1260d4eda0c8eb3f62b9865c371
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 17:51:29 -0500
Commit message:

 Updated example datasets for building gene models from custom genomes
 
Package: GenomicDistributions
Commit: 2b875d8d2b5e9e99a6751bfeae37af2ef0eca9ce
Author: Jose E. Verdezoto Mosquera <j.esiempreliga@hotmail.com>
Date: 2022-01-19 16:29:46 -0500
Commit message:

 Merge pull request #182 from databio/dev_jose

Dev jose 
Package: GenomicDistributions
Commit: 23e61fb48cda086b7f5db4e2a9fb7740fcdf8a54
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2022-01-19 16:12:34 -0500
Commit message:

 updated NEWS
 
Package: GenomicDistributions
Commit: 66df18ae5079dccfea0e694e43c0451835e2df49
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2022-01-18 12:26:53 -0500
Commit message:

 fixed arg in plotQThist, added pvals plot, updated descript
 
Package: GenomicDistributions
Commit: 46542ff91277ddbc073985bf4e1e42baa8700664
Author: Jose E. Verdezoto Mosquera <j.esiempreliga@hotmail.com>
Date: 2022-01-18 10:33:01 -0500
Commit message:

 Merge pull request #181 from databio/dev_jose

Dev jose 
Package: GenomicDistributions
Commit: b58bf8880539931b696d7eb4578acfc8d5de5787
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-14 16:35:33 -0500
Commit message:

 biocheck guidelines
 
Package: GenomicDistributions
Commit: 3166946c917fe388d1dc78c747fccc670f89704d
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-13 20:44:40 -0500
Commit message:

 paramater description update
 
Package: GenomicDistributions
Commit: c9037e3d9bec03bed55ef714dcf064fb5eb0a9a2
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-13 20:23:24 -0500
Commit message:

 #178 parameter quantile replaced with quantThresh

examples relevant to quantile function (function had dist to TSS example)
 
Package: GenomicDistributions
Commit: b2af9848d731f2cc3876273923006025f189e3c0
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-13 19:47:36 -0500
Commit message:

 #176 fixed guides(fill = "none")
 
Package: GenomicDistributions
Commit: 56d969a6a473f16d449ac3ca991b89cfbc484d24
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-13 19:38:43 -0500
Commit message:

 #174 <- removed where possible
 
Package: GenomicDistributions
Commit: d3d85fb96289c657ae4d1bc5d693b466c6ef101c
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-08 14:29:27 -0500
Commit message:

 Merge branch 'dev' of github.com:databio/GenomicDistributions into dev
 
Package: GenomicDistributions
Commit: f04e6b27b8f273f3831ceb358ad2d09d41b9a302
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-08 14:28:37 -0500
Commit message:

 Make QTHist consistent

now QThist will show percentages, rather then frequencies,
for single distributions as well as multi-distributions.
Also, the numbers param now works in both cases. Fix #179
 
Package: GenomicDistributions
Commit: 12b5090e0844d6900adbfd99ed11cc74d80d6e7f
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-08 14:28:37 -0500
Commit message:

 Make QTHist consistent

now QThist will show percentages, rather then frequencies,
for single distributions as well as multi-distributions.
Also, the numbers param now works in both cases. Fix #176
 
Package: GenomicDistributions
Commit: 3f4129954ca0415d31737e0f22caf0aeb3f375dc
Author: Nathan Sheffield <nsheff@users.noreply.github.com>
Date: 2022-01-08 10:20:40 -0500
Commit message:

 Merge pull request #171 from tgstoecker/master

plotChromBins - option to change limit of y-axes 
Package: GenomicDistributions
Commit: 9b34a6c49f5a0d176deb150de412f0660ae51ced
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-08 10:09:48 -0500
Commit message:

 Update chrom bins plots
 
Package: GenomicDistributions
Commit: e0a113a7163cc3c6e6508422d0fa0f4beb07efc1
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-07 17:54:00 -0500
Commit message:

 Merge branch 'dev' of github.com:databio/GenomicDistributions into dev
 
Package: GenomicDistributions
Commit: cf49252085a5813b41af4e84e947cb9a44523857
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-07 17:53:56 -0500
Commit message:

 Add new, faster implementation of calcCChromBinsRef
 
Package: GenomicDistributions
Commit: 5abe04ceacdc3457c2bd639bd8f459a4195b927e
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2022-01-07 11:01:05 -0500
Commit message:

 add stars for p vals instead of numbers
 
Package: GenomicDistributions
Commit: 9cdfada1e6f01a2c0bcd8f5ab3c023ad02920f22
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-05 15:52:52 -0500
Commit message:

 fix partition overlap frequency count - multi input
 
Package: GenomicDistributions
Commit: a7f0bd119f6a81b38e715b698422fe91f1497ded
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-03 13:29:24 -0500
Commit message:

 updated cell specificity function to more flexible use
 
Package: GenomicDistributions
Commit: b510a0b1984acd660f52b69983dc2f9304c5177c
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2022-01-03 12:54:11 -0500
Commit message:

 change size/position of pval labels
 
Package: GenomicDistributions
Commit: e36563ef357fb091a28060c08cf3807c7ef6f94d
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2021-12-28 14:08:05 -0500
Commit message:

 update pval sig figs, make exp plot pvals optional, update doc
 
Package: GenomicDistributions
Commit: 9655c7da154b1c95c0733f2a49415bf143a2c43d
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2021-12-28 10:50:34 -0500
Commit message:

 use tidy directly from broom
 
Package: GenomicDistributions
Commit: fde1bd4d43ca0c4db9797a337079579cd82c0ef7
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2021-12-28 10:43:03 -0500
Commit message:

 add p-vals for exp part calc, import broom, update doc
 
Package: GenomicDistributions
Commit: c3b2d03b6d3dec00ed8ccb6f64b7a516cae0d23b
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2021-11-30 18:39:06 -0500
Commit message:

 today date
 
Package: GenomicDistributions
Commit: d2707a01761124a2b7538df95d561b4f9e0e39a9
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2021-11-30 18:19:22 -0500
Commit message:

 Update DESCRIPTION
 
Package: GenomicDistributions
Commit: db9ada5c1c4351efc7ab33ddcabc160c8f3dd33b
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2021-11-30 18:14:34 -0500
Commit message:

 update version for next release
 
Package: GenomicDistributions
Commit: b9ef8c399903651cc7bba1191e56d4708e7b7e86
Author: Tyll Stöcker <53227400+tgstoecker@users.noreply.github.com>
Date: 2021-11-24 21:06:54 +0100
Commit message:

 Merge pull request #1 from tgstoecker/tgstoecker-contribs

Added option to set ylim in plotChromBins 
Package: GenomicDistributions
Commit: 54e25ddff0313aa365fa495afa91c52aec786ad1
Author: Tyll Stöcker <53227400+tgstoecker@users.noreply.github.com>
Date: 2021-11-24 21:06:34 +0100
Commit message:

 Added option to set ylim in plotChromBins

- even one extreme bin size makes the plotChromBins output less usable
  - e.g. if most bins N ~10-100 and one is 8000 everything is scaled for this one bar (ran into this twice now in my work)
- instead of having to manually remove data one can simply set the ylim manually using the new ylim option 
Package: GenomicDistributions
Commit: d279427a5e58355f0af31b46a4e4792518870a55
Author: Jose E. Verdezoto Mosquera <j.esiempreliga@hotmail.com>
Date: 2021-09-28 13:13:51 -0400
Commit message:

 Merge pull request #169 from databio/jose_dev

Add corrected neighbor dist, nearestNeighbors, doc changes 
Package: GenomicDistributions
Commit: 60e2cd09abdc97e5d7abdf789f788883e2e88dc2
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2021-06-04 19:53:14 -0400
Commit message:

 Add corrected neighbor dist, nearestNeighbors, doc changes
 
Package: octad.db
Commit: 59b1f7a0e12d8acb436760877d06a002be68cd99
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:30:23 -0500
Commit message:

 0.21 partial responce to review
 
Package: octad.db
Commit: b78c1c93927de3a3ba28e7dbdc3cb768509ba818
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:21:06 -0500
Commit message:

 0.20 partial responce to review
 
Package: octad.db
Commit: 7ce5a494ca60756607f997fa39b6f74b3dc46f8b
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:15:40 -0500
Commit message:

 0.19 partial responce to review
 
Package: octad.db
Commit: 8b880d7872515cff97adb31468ceace19061d9e2
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:13:19 -0500
Commit message:

 0.19 partial responce to review
 
Package: octad.db
Commit: 0ed03daaf2feb1242a5290c0a41d035064f26236
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:03:28 -0500
Commit message:

 0.19 partial responce to review
 
Package: octad.db
Commit: 45578a92179292eb65d9defcc22afa54cdb8addd
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:03:03 -0500
Commit message:

 0.19 partial responce to review
 
Package: octad.db
Commit: 9404a74fa61a815e80093ce2c7e2ef9e69677cd2
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:01:06 -0500
Commit message:

 0.18 partial responce to review
 
Package: octad.db
Commit: dcd3016c0bfdbc3c01ebacfd22aff5aa8d788c88
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:59:02 -0500
Commit message:

 0.18 partial responce to review
 
Package: octad.db
Commit: 032c8f077c133dc2bc035884f7dd2c42ba4e4604
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:55:50 -0500
Commit message:

 0.41 partial responce to review
 
Package: octad.db
Commit: 74a70b62a811a67f0d569b41cf971164345c23dc
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:38:02 -0500
Commit message:

 0.40 partial responce to review
 
Package: octad.db
Commit: 8c1e42a0461524ffba073110ed04c09b8aaff3df
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-17 13:57:25 -0500
Commit message:

 0.39 author list update
 
Package: octad.db
Commit: f2e89c4a2e91c3c5bc517ed03e4d77e0dd0c7ddc
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-12 13:17:15 -0500
Commit message:

 0.38 tidy up
 
Package: octad.db
Commit: f0cd38ae27fe79c4afc8e20704b0f482a5328e04
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-12 12:51:43 -0500
Commit message:

 0.37 tidy up
 
Package: octad.db
Commit: bf5867abb9ff5e25e043daa8a15a2ef64c6b462d
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-12 12:28:05 -0500
Commit message:

 0.36 tidy up
 
Package: octad.db
Commit: 5014a58576fb6c10f87cf2aa15b680208b66b6c8
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-12 00:46:36 -0500
Commit message:

 removed 32-bit support 0.35
 
Package: octad.db
Commit: 5072bb896a671e3a1165a6622a70190762c66525
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 17:00:49 -0500
Commit message:

 looking for the bottleneck 0.34
 
Package: octad.db
Commit: 8008680b901e250ae0610ea03f06b3f52db83b64
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 14:27:17 -0500
Commit message:

 looking for the bottleneck
 
Package: octad.db
Commit: 6a5943f7d9c4b474d8fde25b5bbecfd23b253d0f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 13:59:58 -0500
Commit message:

 v0.99.32
 
Package: octad.db
Commit: ed6b7e409add11db2f04ffddb4462afd2f02542f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 13:14:40 -0500
Commit message:

 v0.99.31
 
Package: octad.db
Commit: d7ee8bd03af9bd9591860d08e9159c9ac42d9199
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 12:44:48 -0500
Commit message:

 v0.99.30
 
Package: octad.db
Commit: b274c4fe9db428eaf62006c49f5b1d0da150ea1a
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 12:44:12 -0500
Commit message:

 v0.99.30
 
Package: octad.db
Commit: 7360f8d93836602b3e6ccba5b88f60629e5fd03c
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 14:28:47 -0500
Commit message:

 v0.99.29
 
Package: octad.db
Commit: 8179437270ae2bc02b98c27ee2e581b8aeed1364
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 14:07:30 -0500
Commit message:

 v0.99.30
 
Package: octad.db
Commit: cd5198365ee719c18dd14cad50bec69733d94960
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 13:11:14 -0500
Commit message:

 v0.99.29
 
Package: octad.db
Commit: d27e509fac730b752c793044e186cd75ea1b8063
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 13:10:25 -0500
Commit message:

 v0.99.29
 
Package: octad.db
Commit: e9a1a9e819f509d81636a9295fc61d51b776eb84
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 13:05:17 -0500
Commit message:

 v0.99.29
 
Package: octad.db
Commit: 8674abaeba928d40096aa188866532cac391353f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 11:38:25 -0500
Commit message:

 v0.99.28
 
Package: octad.db
Commit: 390311db4fa122bdfe3dce8da078c9fc7b6c2779
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 11:30:27 -0500
Commit message:

 v0.99.27
 
Package: octad.db
Commit: 20111439399516806c98238763c019e3b2cb75cb
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 19:58:41 -0500
Commit message:

 v0.99.26
 
Package: octad.db
Commit: 944778d670d4465a1207ed336f403b60855f39cd
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 18:59:01 -0500
Commit message:

 v0.99.25
 
Package: octad.db
Commit: 87d3333051f972a26c0b262e6685fb79b52034eb
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 18:10:44 -0500
Commit message:

 v0.99.24
 
Package: octad.db
Commit: 330a4c6db5cf7c58aecb10ce1ff9f98808ab3e9c
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 16:44:26 -0500
Commit message:

 v0.99.23
 
Package: octad.db
Commit: 97e9337a643cda7eade8f15d7b721bc2240193de
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 16:33:43 -0500
Commit message:

 v0.99.24
 
Package: octad.db
Commit: 5ce3487710ea38e55039416b850675adc6d978b0
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 16:32:12 -0500
Commit message:

 v0.99.23
 
Package: octad.db
Commit: e547c1f4a83ab898fad4c018e3188ab63ab3e730
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 12:34:15 -0500
Commit message:

 v0.99.22
 
Package: octad.db
Commit: 1bcd66bd36d4017c68fda9678ac28ea862ae5a60
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 12:07:03 -0500
Commit message:

 v0.99.21
 
Package: octad.db
Commit: 4e54b1d916421ea096cc9495b2b7af64ce2657d2
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 12:06:08 -0500
Commit message:

 v0.99.20
 
Package: octad.db
Commit: 449e5e9df47c9e288ee2a3fe072a16d1dc897b06
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-07 12:01:57 -0500
Commit message:

 v0.99.19
 
Package: octad.db
Commit: 13fc02fb0d84ad9ab3ce26977ca874295b382102
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-07 11:42:26 -0500
Commit message:

 v0.99.18
 
Package: octad.db
Commit: e3f193f3cacefd578902602ad81b00faf26de19c
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-07 10:51:24 -0500
Commit message:

 v0.99.17
 
Package: octad.db
Commit: 1e217fc18c1b85270f8f1eabe75ca7d08004f9e1
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 23:48:05 -0400
Commit message:

 v0.99.16
 
Package: octad.db
Commit: fc66fbfd0c224c2b6ab2b5fee811d47b39e3e0a8
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 23:10:53 -0400
Commit message:

 v0.99.15
 
Package: octad.db
Commit: b1f80f983c4e7eaa8a3019ac6bd44cba31a3e040
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 22:37:13 -0400
Commit message:

 v0.99.14
 
Package: octad.db
Commit: 8ee7d2abc4925ea4d8b4bf2c686465c600bf42c5
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 22:01:01 -0400
Commit message:

 v0.99.13
 
Package: octad.db
Commit: 91deceed5df932bfd9344fad37ef6827cc4c336a
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 14:41:54 -0400
Commit message:

 v0.99.9
 
Package: octad.db
Commit: 328519c0f23bb5f74f3d9db2a1444a86a58d6ce8
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 13:16:15 -0400
Commit message:

 v0.99.9
 
Package: octad.db
Commit: 1df358a73c316ed90fb55bd880b03b1c2954e252
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 13:01:39 -0400
Commit message:

 v0.99.9
 
Package: octad.db
Commit: 2a81ac2615073c26fab1385348eb305779d8a10a
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 11:27:15 -0400
Commit message:

 v0.99.9
 
Package: octad.db
Commit: a1747daf41078c46ab099a7f7eb6452e2e13f7e2
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 09:17:35 -0400
Commit message:

 v0.99.8
 
Package: octad.db
Commit: e640a1b3e2645587d28773fed5d62aa6e846ab3f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-05 21:43:35 -0400
Commit message:

 v0.99.7
 
Package: octad.db
Commit: 1581553f22a738c8203c8cd3f5abaf60f307cf9e
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-05 17:29:50 -0400
Commit message:

 v0.99.6
 
Package: octad.db
Commit: 3728e08dcd1928fb7803f4b224e717a3f8b29f43
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-05 17:11:54 -0400
Commit message:

 v0.99.5
 
Package: octad.db
Commit: 3e84b07f8c02ce9450a4d5c7671aa1dcfcd7e679
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-05 15:54:52 -0400
Commit message:

 v0.99.4
 
Package: octad.db
Commit: 9fc8f3c8f86e460fc00be6ecfaf8b68d2d51efd5
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:56:00 -0400
Commit message:

 v0.99.3
 
Package: octad.db
Commit: c6ff8aa750e89704d88142522a81fde48ff17baa
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:41:49 -0400
Commit message:

 v0.99.2
 
Package: octad.db
Commit: 8731193c05c9a1c59fa00c357a35cf63bc7fa54d
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:40:17 -0400
Commit message:

 v0.99.1
 
Package: octad.db
Commit: ce42d281724c5c1789c53e99b249769e224a9d5f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:37:39 -0400
Commit message:

 v0.99.1
 
Package: octad.db
Commit: 0f9e8f4685e0a9a9d608878cb41456b94afbf253
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:33:34 -0400
Commit message:

 v0.99.1
 
Package: octad.db
Commit: a74aa78ddadb23ab4b51f107f16ed68318ba0c67
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:13:07 -0400
Commit message:

 v0.99.1
 
Package: octad.db
Commit: 68d115523f3a5bbb28d155358ac704b3b9e2583a
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-10-25 14:50:30 -0400
Commit message:

 v0.99.0
 
Package: octad.db
Commit: 20ba2200b6b3bc230c6f10498965e345b2f92822
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-10-25 14:49:18 -0400
Commit message:

 v0.99.0
 
Package: octad.db
Commit: 3b860e2cd4910ac6807ab924b1f2b16a77a6b701
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-10-25 14:30:39 -0400
Commit message:

 v0.99.0
 
Package: octad.db
Commit: 050695223f278250e4b42090b8d05c60ac1cd161
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-10-25 14:25:19 -0400
Commit message:

 v0.99.0
 
Package: octad.db
Commit: 1e2994a38ae41dfab4abb72468d626f20cc8dbd7
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-10-19 18:10:36 -0400
Commit message:

 Delete Bootcamp_octad_setup.R 
Package: octad.db
Commit: e5d7e4fb15330a7598908c537b718acca76b9dcb
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-10-19 18:10:31 -0400
Commit message:

 Delete Bootcamp_octad_example_small.r 
Package: octad.db
Commit: c13c51ab2bbf5d997788b54f5727b14229d12ef0
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-10-19 18:10:25 -0400
Commit message:

 Delete Bootcamp_octad_example.R 
Package: octad.db
Commit: 63dc5c7ed0d68dad0fcf05cecfea50cbe5985869
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-08-19 12:45:20 -0400
Commit message:

 Add files via upload 
Package: octad.db
Commit: b6d553c531f57f1edf679f0c8df7a4bad9ffdbc5
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-07-19 17:41:45 -0400
Commit message:

 Update README.md 
Package: octad.db
Commit: 7fe5994e596887e19d5e2e998106be6339b46ddf
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-02-20 14:26:30 -0500
Commit message:

 Update README.md 
Package: octad.db
Commit: 95e58d772b280745c515741d2e93aedc3abaa6da
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-02-18 13:33:20 -0500
Commit message:

 Update README.md 
Package: octad.db
Commit: 8557986400ffbda60d68994653bca14c184b852e
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-02-03 17:23:13 -0500
Commit message:

 Update README.md 
Package: octad.db
Commit: 6e09463054c6610b2e02895dc0e4aed127db76ec
Author: Lionir <39910199+Lionir@users.noreply.github.com>
Date: 2021-02-02 20:59:12 -0500
Commit message:

 Update README.md 
Package: octad.db
Commit: 1952230b666cd1d85a8a73a9f6674188a592074c
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-10-29 10:50:27 -0400
Commit message:

 octad.db
 
Package: octad.db
Commit: 824ca0591d809aa5599e5f7b8ba3f7d07c3bf190
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-10-27 13:09:25 -0400
Commit message:

 Paper link
 
Package: octad.db
Commit: 7f3858dab5a85f3e5d19f431b26ff9f01201d8e3
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-10-26 11:19:08 -0400
Commit message:

 Example link
 
Package: octad.db
Commit: 3b1782526a3119e849bcf04ca64c80b1de4b8b8b
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-10-26 11:18:42 -0400
Commit message:

 Example link
 
Package: octad.db
Commit: e688f9ac3614bcb72299bed4c4193175f7733ad0
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-10-09 11:12:11 -0400
Commit message:

 Readme update
 
Package: octad.db
Commit: 12e32962f21d76302c3bad1bcc978efc5000b12f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-10-01 22:05:53 -0400
Commit message:

 stable 0.99
 
Package: octad.db
Commit: cd2b2eeb4a5d95a8d2db20419f5f878405fb2837
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-10-01 18:41:16 -0400
Commit message:

 0.99.0
 
Package: octad.db
Commit: 463000436d81ed21e1e51ccb1aab9c1af0a5f061
Author: Bin Chen Lab @ MSU <binchenindiana@gmail.com>
Date: 2020-10-01 15:25:54 -0400
Commit message:

 Update octad.Rmd

edited rmd 
Package: octad.db
Commit: 1e64f570e02641f760d33bd0541a5eb3a7088259
Author: Bin Chen Lab @ MSU <binchenindiana@gmail.com>
Date: 2020-10-01 15:09:27 -0400
Commit message:

 Update octad.Rmd

edited rmd 
Package: octad.db
Commit: 24d7c307dbc76e47eb42a10de25253f77755d322
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-09-30 11:19:26 -0400
Commit message:

 Octad_99
 
Package: octad.db
Commit: 44285275e69e8c7667def2c70f51610abade1f90
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-09-30 10:00:21 -0400
Commit message:

 octad 0.99.0
 
Package: octad.db
Commit: cc6c6fc2af6f90f4cfc1a02faf3869d576a1be82
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-09-30 09:48:22 -0400
Commit message:

 octad 0.99.0
 
Package: octad.db
Commit: 0bfa737fc92cb975a119ca902da5f066e33856d8
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-09-30 09:47:41 -0400
Commit message:

 octad 0.99.0
 
Package: octad.db
Commit: f27c0d43d542779d12ef03c0f499c4fe081b3a81
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-09-30 09:40:51 -0400
Commit message:

 octad 0.99.0
 
Package: octad.db
Commit: 72be8f2744df182e4fb4675de751003b8c845028
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2020-09-30 09:39:58 -0400
Commit message:

 octad 0.99.0
 
Package: octad.db
Commit: 456514aa84223ea89e7f270d8509a24c528de669
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-06-24 15:50:04 -0400
Commit message:

 updated drugs rges

updated drugs rges
 
Package: octad.db
Commit: 57200d4d784fe4a5619187c06c940e60290f1475
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-04-22 18:01:32 -0700
Commit message:

 Updated Diff_Exp to incorporate Limma

Updated Diff_Exp to incorporate Limma
 
Package: octad.db
Commit: 08957bfdf491cb0e85609f0d110c1d03f02a13e1
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-04-06 21:22:06 -0700
Commit message:

 Diff_Exp.R

Given
case_id and control_id from dz_expr counts df
parameters from set_parameters.R
runs DE using edgeR
 
Package: octad.db
Commit: e19d3740947ef747c2bb8e70c6c46fbee4ff6a92
Author: bzengUCSF <30878321+bzengUCSF@users.noreply.github.com>
Date: 2018-04-06 20:46:37 -0700
Commit message:

 new folder

new folder 
Package: octad.db
Commit: e32ea4c255bdd1cc16538b37666fee1a0d079324
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-02-05 08:43:42 -0800
Commit message:

 Updated Core functions and create dz sig

Updated Core functions and create dz sig
 
Package: octad.db
Commit: 776068b26141098e416f6058e10bd3a283744a9f
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-01-16 22:35:11 -0800
Commit message:

 Changed flow for create dz sig

-Lowly expressed genes are now removed prior to normalization
-ruvseq normalization is embedded to edgeR via the design matrix
e.g. design = condition + W_1
-gdc query change to allow for querying of only the tumor and not just tumor and mutant gene
 
Package: octad.db
Commit: c3ca530e858026ece9fd66f07ed92dea3ac26578
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-01-09 20:58:27 -0800
Commit message:

 Fixed some syntax errors

Fixed some syntax errors
 
Package: octad.db
Commit: 2698080739fb2942b0ef56f479c72138db964925
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-01-09 10:38:40 -0800
Commit message:

 Create Disease Sig update

allows for contrast mutants within edgeR only
 
Package: octad.db
Commit: 9192f2711e249dfa7325da1634615b93f120c8b4
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-01-09 10:09:12 -0800
Commit message:

 Fixed typo in contrast mutants

Fixed typo in contrast mutants results
 
Package: octad.db
Commit: f17eb9ff04d3d8c2bca73dc355eb63f03e8122f8
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-01-09 09:59:56 -0800
Commit message:

 Updated Create_dz_sig to allow contrast for mutants

-create_dz_sig now allow mutant tumor contrast e.g.
 IDH1 vs non-IDH1 tumor vs ref tissues
 
Package: octad.db
Commit: 007b514a05126c8758a81ee8942d157670a549ff
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-01-06 04:03:39 -0800
Commit message:

 Fixed Merging issue from Mapping

-Replace merging issue from mapping w/ left_join via dplyr
-This prevents the issue of missing hits while merging

-added create_dz_signature_geneMut.R
script helps to calculate gene mutation vs. non-mutant tumor and normal tissue of a specified gene
 
Package: octad.db
Commit: a76fe395e20e993d8529341dea58f756b5ca4982
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-01-05 17:10:04 -0800
Commit message:

 updated directories

updated directory for dz, drug, and target code folders to refer to the set code, dataFolder, and output folder from workflow
 
Package: octad.db
Commit: 3b4b2e7448cb9faf4a7bb450d91124eec7e319f0
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2018-01-03 23:44:16 -0800
Commit message:

 updated dir paths

workflow.R now requires directory to point to:
1. code folder (where all codes stored)
2. output folder (default folder for output)
3. data folder (folder required for loading raw data files to run code)

workflow will also create a subdirectory output folder for cancers ran. The subdir will have title : cancer_genemutant_dataran_methodused e.g glioma_idh1_180101_edgeR/
 
Package: octad.db
Commit: c54f7364b8703c5fd12bae120d6e9ba3cea6a2e2
Author: Ubuntu <ubuntu@ip-172-31-30-74.us-west-2.compute.internal>
Date: 2018-01-02 00:33:05 +0000
Commit message:

 fix small gene set
 
Package: octad.db
Commit: 5347e103cb9c4d0eb974f4f12442957821c12b63
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2018-01-01 16:01:26 -0800
Commit message:

 compute all cancers
 
Package: octad.db
Commit: ff23fe0798be4c9587ab9c1cadf32908fe1b6535
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-29 13:04:12 -0800
Commit message:

 for parameter optimization
 
Package: octad.db
Commit: a2076ac8e21fb93c12094e14e8e160d1a7c66aa6
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-29 12:51:52 -0800
Commit message:

 for parameter optimization
 
Package: octad.db
Commit: a4a165abab8e0dc300b11c017f63afab272ece35
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-29 12:39:36 -0800
Commit message:

 add to find optimized parameters
 
Package: octad.db
Commit: ca99b995b8f850c7acee50af3dff959f87695154
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-29 12:37:39 -0800
Commit message:

 update
 
Package: octad.db
Commit: 5a66f632904f8e781a651e243a103be61f521b1c
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-28 21:03:40 -0800
Commit message:

 add outlier removal option
 
Package: octad.db
Commit: 28f472d1dc92172ec948ff4392edc06b9c737a7e
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-28 21:02:54 -0800
Commit message:

 add outlier removal option
 
Package: octad.db
Commit: 59d59734c8764e61f4a7c7df4bb5a0e84c7bc493
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-27 15:46:55 -0800
Commit message:

 add weighting LINCS cell lines
 
Package: octad.db
Commit: af1b5f32e6ec3d107fbeed0dc3b80db0c0f698a9
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-27 14:24:20 -0800
Commit message:

 add drug hits visualization
 
Package: octad.db
Commit: 0b28c65ab888bd46d7bb6d63c94c6a92de8f3234
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-27 14:23:56 -0800
Commit message:

 add evaluation of HCC hits
 
Package: octad.db
Commit: ce22c9a4cb455945a0dccafa865ed89b3c23cd70
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-27 14:23:00 -0800
Commit message:

 add drug hits evaluation and visualization
 
Package: octad.db
Commit: efeba28a1aed72ef9c9e24a73db03212030f18a0
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-27 14:22:32 -0800
Commit message:

 clean up, add sig visualization
 
Package: octad.db
Commit: 449cb22710ab2c5d728e0cf8da7ba9ede77e4994
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-27 14:21:46 -0800
Commit message:

 reformat
 
Package: octad.db
Commit: 750f8d5b7eb2166f1f848be21b9e801325cbffd1
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-26 17:36:14 -0800
Commit message:

 visualize correlation with reference tissues and cell lines
 
Package: octad.db
Commit: 46995af010318e40504000e27d792f68d3638d55
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-26 17:35:28 -0800
Commit message:

 add cell line correlation
 
Package: octad.db
Commit: 5510c0ebb5844e557eaedc21719a78d01e8c6a8c
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-26 17:34:53 -0800
Commit message:

 add enrichment plot of the top target
 
Package: octad.db
Commit: 50e0b29e2d7437a777cf6beaa5ba13b40453d37a
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-26 09:58:03 -0800
Commit message:

 update DS_store
 
Package: octad.db
Commit: f66e74874a72227c9862e7392c56c635d507b1ad
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-22 22:32:36 -0800
Commit message:

 restore workflow
 
Package: octad.db
Commit: 066106e479c42944704ce5f459d52b594604eeff
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-22 21:08:34 -0800
Commit message:

 integrate
 
Package: octad.db
Commit: f09adaaa30d9708480bb07b4ee0bf0a223cb4fab
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-22 21:06:45 -0800
Commit message:

 add limma and edgeR
 
Package: octad.db
Commit: 1f4e31162dd490e87f2970f2de61f4981269bc7b
Author: Billy Zeng <billy.zeng@ucsf.edu>
Date: 2017-12-22 02:12:17 -0800
Commit message:

 Fixed counts return

Counts should set to normalized counts
 
Package: octad.db
Commit: 950e6aecafe97e3a6415c5fa9871113caa593444
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-19 16:18:07 -0800
Commit message:

 add grade specific sig
 
Package: octad.db
Commit: f6574cdc2f062804c4b07c35bb285d151da8bb65
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-18 16:22:54 -0800
Commit message:

 support inferred genes
 
Package: octad.db
Commit: aae210a4851bf930c2135ce1e98bb552209f4a51
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-18 11:57:14 -0800
Commit message:

 add outlier dedection and rna-seq count normalization
 
Package: octad.db
Commit: 987f9f720520f769575157b60894eaf4982d375e
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-15 10:17:31 -0800
Commit message:

 merge stages and relax thresholds
 
Package: octad.db
Commit: 4527432d44d0e95b6981cf4415347af15176f560
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-14 21:34:55 -0800
Commit message:

 support patient selection & QC
 
Package: octad.db
Commit: 3d29acd85f5c2233e334a3fbca189727a164e181
Author: BenGlicksberg <ben.glicksberg@gmail.com>
Date: 2017-12-14 19:18:06 -0500
Commit message:

 Add files via upload

function to query GDC API via GENE & Project 
Package: octad.db
Commit: 9df87c7359bb7ed5065bbbc7b32c1afff1ac4732
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-11 15:07:23 -0800
Commit message:

 add purity estimation function
 
Package: octad.db
Commit: 5b5bcf66aa2bef013a30e60d88e6397cb9ea2756
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-12-06 15:37:43 -0800
Commit message:

 add stage feature
 
Package: octad.db
Commit: 1f1506f7b967726db6a4ed6ea906fb68b060abe7
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-23 15:03:30 -0700
Commit message:

 add more to do items
 
Package: octad.db
Commit: a0be5132b1d0e75ce72024ae1c5541ec1896bd2a
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-23 14:56:50 -0700
Commit message:

 add batch pathway prediction two sides
 
Package: octad.db
Commit: ee7a9b34e14ce50ac57186be351b4b429b2a583f
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-23 10:55:20 -0700
Commit message:

 add batch pathway prediction two sides
 
Package: octad.db
Commit: f578fa2975758a3fbe7b53d7366b555f423442e5
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-23 10:53:04 -0700
Commit message:

 add batch pathway prediction two sides
 
Package: octad.db
Commit: 967d3e85ee1784d13218b1ed6d56de7ecf103a0d
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-21 21:43:43 -0700
Commit message:

 first
 
Package: octad.db
Commit: 434b6085c927d776f9beb343ff3864607eb1d8cc
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-21 18:15:22 -0700
Commit message:

 first
 
Package: octad.db
Commit: e44af14577e735decc97a66946b282b36ab3debd
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-21 17:40:09 -0700
Commit message:

 first
 
Package: octad.db
Commit: 109bfa63da82670e756f478901b081d3d2e88c71
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-21 17:28:42 -0700
Commit message:

 first
 
Package: octad.db
Commit: e8aa77c7cbe45b41ca9a2380fc4a1a0441d56789
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-21 16:47:05 -0700
Commit message:

 first
 
Package: octad.db
Commit: e887fefb1e4b6723dbd0d982c14bd41ffa4b7959
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-21 16:10:08 -0700
Commit message:

 first
 
Package: octad.db
Commit: e4c5614f863713daa3396872c5b54eb12ccceb8c
Author: Bin Chen <binchenindiana@gmail.com>
Date: 2017-10-21 15:27:37 -0700
Commit message:

 first
 
Package: octad
Commit: 032c8f077c133dc2bc035884f7dd2c42ba4e4604
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:55:50 -0500
Commit message:

 0.41 partial responce to review
 
Package: octad.db
Commit: 55565f72134fc674d6e6f828bf542c7d4eae632d
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:53:15 -0500
Commit message:

 0.17 partial responce to review
 
Package: octad.db
Commit: 3fa6ff5e6230d92be18be7071152fa4aa895aaae
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:44:13 -0500
Commit message:

 0.17 partial responce to review
 
Package: octad
Commit: 74a70b62a811a67f0d569b41cf971164345c23dc
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:38:02 -0500
Commit message:

 0.40 partial responce to review
 
Package: RTopper
Commit: 097ccd18f48da10b7711f4742ee47e6ff21313bc
Author: Claudio Zanettini <clz4002@med.cornell.edu>
Date: 2022-01-20 14:32:32 -0500
Commit message:

 vignettes chunk 21
 
Package: DiffBind
Commit: f30e1d60329c5cd3cd4a382b0c284881225c6bc7
Author: Randall Stark <rory.stark@cruk.cam.ac.uk>
Date: 2022-01-20 19:15:31 +0000
Commit message:

 cleanup Called fixes and add test
 
Package: OmnipathR
Commit: 30364ccacd59d2405e97c24dbb26a2301d5eff36
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-20 19:37:14 +0100
Commit message:

 v3.3.13 - version bump
 
Package: OmnipathR
Commit: b09fb0a1b3c83ab789a0de3a0ff0a4f6406771ac
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-20 19:36:44 +0100
Commit message:

 not loading ConsensusPathDB in NicheNet examples
 
Package: igvR
Commit: 20ba6bed202eb8f99c44ebeadcd263c9e8c5db17
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2022-01-20 10:33:44 -0800
Commit message:

 fixed 3 printf calls
 
Package: Rhdf5lib
Commit: 49e05b7519169e74c52c78872248688c23f46c15
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-20 16:34:59 +0100
Commit message:

 Fix tests on Windows
 
Package: Rhdf5lib
Commit: 81109922619bdfd9e1786ee5a0f514367f25363c
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-20 14:45:26 +0100
Commit message:

 Correct linking directory on linux
 
Package: Rhdf5lib
Commit: c8788162b39cceec3ac34a74c25d3b2f22b4d73f
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-20 13:58:51 +0100
Commit message:

 Merge branch 'master' of github.com:grimbough/Rhdf5lib
 
Package: Rhdf5lib
Commit: 9cff9d05c9dc8aa08200da1d4d15627108f5114b
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-20 13:44:34 +0100
Commit message:

 Update R CMD check workflow
 
Package: Rhdf5lib
Commit: eb00b22438cba3b5659da3cb681af1cb1794e03f
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-20 11:54:41 +0100
Commit message:

 Quieten workflow output
 
Package: Rhdf5lib
Commit: 77e4668fdf594601f8a62afe4b00d794556ccda3
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-20 11:37:04 +0100
Commit message:

 Link to copied files
 
Package: Rhdf5lib
Commit: 59fce7c892a2c0843c58ba620f67fdb446cb0fe2
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-20 11:11:16 +0100
Commit message:

 Compress and bundle libraries
 
Package: Rhdf5lib
Commit: efaf49d4d2c048b5735d795087dbf2b58f8ffa83
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 16:23:57 +0100
Commit message:

 Merge changes

Merge branch 'ucrt-precompiled' of https://github.com/grimbough/Rhdf5lib into ucrt-precompiled

# Conflicts:
#	src/Makevars.win
 
Package: Rhdf5lib
Commit: 79b98a7d39bc0b1a0f23aaa6e8314a7b7c34320d
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 16:20:23 +0100
Commit message:

 Simplify header usage
 
Package: Rhdf5lib
Commit: a9016d3a2d2a6f103878abfcfdfbc174ef97a50e
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 16:03:22 +0100
Commit message:

 Update NEWS
 
Package: Rhdf5lib
Commit: e05fc657cb8d7ac865e69f028c35e29dad3aa67f
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 16:03:14 +0100
Commit message:

 Remove travis file
 
Package: Rhdf5lib
Commit: 14d3e77bb9583f1cbe797a6a79cc4ea86e367231
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 15:17:03 +0100
Commit message:

 Enclose path in quotes
 
Package: Rhdf5lib
Commit: eb94d90f50fe199d8e5f3cc8df7a98b35b94c5ba
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 14:05:48 +0100
Commit message:

 Consistent argument order
 
Package: Rhdf5lib
Commit: 464d04e502ceaa16175b73c1fc76e83a65490647
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 13:58:01 +0100
Commit message:

 Simplify windows building script
 
Package: Rhdf5lib
Commit: 011ecd1570da4b30f592f16fd300f1cb286fc38c
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 13:11:20 +0100
Commit message:

 Version bump
 
Package: Rhdf5lib
Commit: c7385a5ad719ccc2ae8a2ca989af30cb2f2ea38c
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 13:06:47 +0100
Commit message:

 Merge remote-tracking branch 'bioc/master' into ucrt-precompiled
 
Package: Rhdf5lib
Commit: 10943b30b399e9fe5cf09c5bc4f260ffa0417ec4
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 11:46:09 +0100
Commit message:

 Make sure rhdf5 dependencies are installed
 
Package: Rhdf5lib
Commit: 7acc8c7da0e7460b38ee936b4dadea1514d2d354
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 11:15:44 +0100
Commit message:

 Update job name
 
Package: Rhdf5lib
Commit: 78f34770d185b9c849c606a8efeab4d72c7fa758
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 11:07:11 +0100
Commit message:

 Add workflow to test rhdf5
 
Package: Rhdf5lib
Commit: 94731ee27a691a8eeb5e718405472dfc589b9403
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 08:26:27 +0100
Commit message:

 Add ucrt-x64 library versions
 
Package: Rhdf5lib
Commit: dec0699b46627164526d14d315df2739884bd5d9
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-07-14 18:21:30 +0200
Commit message:

 Update logo
 
Package: Rhdf5lib
Commit: 745809b756e71e0e8f785844c0ccd24551463ee0
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-07-14 11:57:55 +0200
Commit message:

 Add pkgdown logo
 
Package: CompoundDb
Commit: 1b0bc42e732ecd5f3a458a008d6f072c1d4e4872
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-20 16:21:29 +0100
Commit message:

 ci: use also R 4.2 for macOS
 
Package: CompoundDb
Commit: 4fc03c2327369920d6a2793ccddff1ac141c1189
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-20 16:19:06 +0100
Commit message:

 refactor: remove paste in stop
 
Package: ExperimentHub
Commit: 1b4beeb52d220fa17c282e47d7013b8d5883a800
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-20 09:38:12 -0500
Commit message:

 Update description and news for documentaiton update
 
Package: ExperimentHub
Commit: 245d6abb255ccb261773736a361f532b7ec3e0b3
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-20 09:36:15 -0500
Commit message:

 Update vignette to include instructions for shared hub location across multiple users
 
Package: AnnotationHub
Commit: 18ea5267da937e07ee8e82aefbdc04ceb9517652
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-20 09:32:14 -0500
Commit message:

 Updated Description and NEWS for documentaiton change
 
Package: AnnotationHub
Commit: 24b85e525667d21b53cd903e75efa717d4364afc
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-20 09:30:16 -0500
Commit message:

 Closes #31

  - add instructions for creating a shared hub across multiple users
 
Package: BiocFileCache
Commit: 24da416acb9dca9896c203e1bc9e694522004c19
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-20 09:19:22 -0500
Commit message:

 version bump and news for shared cache instructions
 
Package: BiocFileCache
Commit: 7b0ba5c9cd7551fed1de982467227eb6e558c08a
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-20 09:18:07 -0500
Commit message:

 Update vignette with shared cache instructions
 
Package: annmap
Commit: 1f8be5eab50e8aa31db8fe6a7698e6b52793762f
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-20 13:54:03 +0000
Commit message:

 Fixing devel version number from previous commit
 
Package: annmap
Commit: 242c90926b31277ba346041999577c607d8b6f74
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-20 13:49:41 +0000
Commit message:

 Merge branch 'RELEASE_3_14'
 
Package: annmap
Commit: 02efb301940fd110bf78950405abc270854490f2
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-20 13:49:39 +0000
Commit message:

 Updating version number in NEWS and correcting URL in DESCRIPTION
 
Package: annmap
Commit: bd06715ff20659b65a51267e86ffd300dbdccf47
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-20 13:46:33 +0000
Commit message:

 Updating version number in NEWS and correcting URL in DESCRIPTION
 
Package: annmap
Commit: 959b765fedc0bd7cb0652e9404525b3239e34093
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-07 12:25:06 +0000
Commit message:

 still trying to change version numbers so devel will ultimately not be ahead of release
 
Package: annmap
Commit: d9f0092a9c836d71a32c6cb74ece8707ff914042
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-07 12:18:28 +0000
Commit message:

 trying to increment version to next allowed number - trying same as devel
 
Package: annmap
Commit: 51afe43361d4035eb4983b1c4dd74ad83f690363
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-07 12:15:01 +0000
Commit message:

 trying to increment version to next allowed number up from devel
 
Package: annmap
Commit: 45abb3450de94bd530a2e14fab85828485995363
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-07 12:13:58 +0000
Commit message:

 trying another time to increment version to next allowed number
 
Package: annmap
Commit: 434076dcdc583d6578711bbfe50e0d210f84ce32
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-07 12:13:13 +0000
Commit message:

 trying again to increment version to next allowed number
 
Package: annmap
Commit: 4f473928c940fdcb798998839a54fe565e1185dc
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-07 12:10:47 +0000
Commit message:

 incrementing version to next allowed number (hopefully)
 
Package: annmap
Commit: 24620257598711edc47ab6f6e4f35c329c5af836
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-07 12:08:12 +0000
Commit message:

 setting version to 1.36.1 in another attempt to avoid illegal bump
 
Package: annmap
Commit: e39854941c319ba10afaa7b491991f144c1fe67d
Author: christopherwirth <christopher.wirth@manchester.ac.uk>
Date: 2022-01-07 12:07:15 +0000
Commit message:

 resetting version to 1.37.0 to avoid illegal bump
 
Package: scanMiRApp
Commit: 6cb642a5a12c5216ab00201bb43ef584787a3e35
Author: plger <pl.germain@gmail.com>
Date: 2022-01-19 08:06:29 +0000
Commit message:

 missing word
 
Package: scanMiRApp
Commit: 06cecde178664fb9daefa001483ba1121d646ca5
Author: plger <pl.germain@gmail.com>
Date: 2022-01-19 08:06:14 +0000
Commit message:

 missing event on stypesHelp2
 
Package: scanMiRApp
Commit: c065ff5bd35b67ffc1bd0f1b135ac10298eddd45
Author: plger <pl.germain@gmail.com>
Date: 2022-01-18 16:37:46 +0000
Commit message:

 version bump
 
Package: scanMiRApp
Commit: efd71717a34456f40f42c168277365ae71f96c64
Author: plger <pl.germain@gmail.com>
Date: 2022-01-18 16:37:36 +0000
Commit message:

 minor reformating
 
Package: scanMiRApp
Commit: 1b73104355fe9735c1ed5a3aafb578dd17c9d29b
Author: plger <pl.germain@gmail.com>
Date: 2022-01-18 16:27:36 +0000
Commit message:

 Merge branch 'main' of github.com:ETHZ-INS/scanMiRApp into main
 
Package: scanMiRApp
Commit: 012dfd210a4142fb5fbcbd4ae3541d68050806d0
Author: plger <pl.germain@gmail.com>
Date: 2022-01-18 16:26:55 +0000
Commit message:

 changed details box
 
Package: scanMiRApp
Commit: c5629e4bcc0e13b0f2062522170f85de511f8758
Author: michasou <michael.soutschek@hest.ethz.ch>
Date: 2022-01-18 15:25:22 +0000
Commit message:

 Update help collections
 
Package: scanMiRApp
Commit: 32dbcb2ab65b7469bc1db3ccbcd715be27f46da9
Author: plger <pl.germain@gmail.com>
Date: 2022-01-17 18:45:45 +0000
Commit message:

 updated help
 
Package: scanMiRApp
Commit: f6bf310c5560cf609936b48443df5a958e686002
Author: plger <pl.germain@gmail.com>
Date: 2022-01-17 18:45:22 +0000
Commit message:

 allow species + specific ensdb
 
Package: scanMiRApp
Commit: 8be68b3be88ce1b99c0cf35c9c2f95428a38b163
Author: plger <pl.germain@gmail.com>
Date: 2022-01-17 18:29:02 +0000
Commit message:

 updated help
 
Package: scanMiRApp
Commit: 33da69960559f9b611acc15fe9775303367bcaee
Author: plger <pl.germain@gmail.com>
Date: 2022-01-17 19:04:04 +0100
Commit message:

 added site types
 
Package: scanMiRApp
Commit: eebb623db3b03acd6dc92a47cb3883af6eff0b96
Author: michasou <michael.soutschek@hest.ethz.ch>
Date: 2022-01-17 17:45:01 +0000
Commit message:

 Help Section Update
 
Package: scanMiRApp
Commit: 63026f39c2f697c33a15093907d9c0a75378334d
Author: plger <pl.germain@gmail.com>
Date: 2022-01-13 13:41:15 +0000
Commit message:

 version bump
 
Package: scanMiRApp
Commit: ab529130b145de7cc911915491ec76c44c9f1300
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2022-01-13 14:40:33 +0100
Commit message:

 add missing dep 
Package: scanMiRApp
Commit: ee7ba94dbc5973def32a41cb3d5d3c79a29a4904
Author: plger <pl.germain@gmail.com>
Date: 2022-01-13 13:30:20 +0000
Commit message:

 jqui_resizable modplot, added help buttons
 
Package: scanMiRApp
Commit: c541e3bc44f901f8c70fb7fc310345f0f2506498
Author: plger <pl.germain@gmail.com>
Date: 2022-01-13 13:10:09 +0000
Commit message:

 Merge branch 'main' of github.com:ETHZ-INS/scanMiRApp into main
 
Package: scanMiRApp
Commit: 1288ef71d5ce50abe54928e2b3349fd7a0346145
Author: plger <pl.germain@gmail.com>
Date: 2022-01-13 13:09:42 +0000
Commit message:

 updated interface and intro
 
Package: scanMiRApp
Commit: 75c6eaa6b3bda000162d4f50cce2b92b952648cd
Author: michasou <michael.soutschek@hest.ethz.ch>
Date: 2021-12-07 08:36:18 +0000
Commit message:

 disable rnor7
 
Package: scanMiRApp
Commit: 7b7acce8d5dc47903e8cd50a1132ed2c7e38d97b
Author: michasou <michael.soutschek@hest.ethz.ch>
Date: 2021-11-26 15:25:38 +0000
Commit message:

 merge
 
Package: scanMiRApp
Commit: a6f27ffb1d9cee68e60c8fd1811ac65a4929764c
Author: michasou <michael.soutschek@hest.ethz.ch>
Date: 2021-11-26 15:25:30 +0000
Commit message:

 merge

Merge branch 'main' of github.com:ETHZ-INS/scanMiRApp into main

# Conflicts:
#	R/scanMiRAnno.R
 
Package: scanMiRApp
Commit: 0337783d04f3b1970ca97b1522819a78f7d5e0eb
Author: michasou <michael.soutschek@hest.ethz.ch>
Date: 2021-11-26 15:20:56 +0000
Commit message:

 Include rn_7 and GRCm39 in ScanMiRAnno (requires Bioconductor 3.14)
 
Package: scanMiRApp
Commit: 2d905319143866ba9129ff6f65fcfdb83a40099b
Author: plger <pl.germain@gmail.com>
Date: 2021-11-02 12:37:14 +0100
Commit message:

 version bump
 
Package: scanMiRApp
Commit: 82f5064c26665c2fcd61f6582770a8669bb5f794
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2021-11-02 12:28:08 +0100
Commit message:

 changed install source to bioc 
Package: uncoverappLib
Commit: 7dc0be1220e54689efd3c219022f988d24f7c079
Author: eiovino <emanuelaiovino.87@gmail.com>
Date: 2022-01-20 12:17:51 +0100
Commit message:

 remove useless package
 
Package: qsea
Commit: 2caabc97f075f90878063580471bff72d4df634f
Author: MatthiasLienard <mali270484@gmail.com>
Date: 2022-01-20 09:48:09 +0100
Commit message:

 version bump
 
Package: qsea
Commit: 6a59c5f6327e157efbf005659f20a3978fb8550b
Author: Matthias Lienhard <mali270484@gmail.com>
Date: 2022-01-20 09:38:46 +0100
Commit message:

 Merge pull request #8 from SPPearce:SPPearce

Fix makeTable when asking for one window 
Package: qsea
Commit: 82b50902ed1dff4e2ca643668dcfe53041a50f9d
Author: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Date: 2022-01-18 12:09:23 +0000
Commit message:

 Fix makeTable when asking for one window
 
Package: sitePath
Commit: 36cd6c63a40bb07e5bc22eb3f3c6ca87e6419327
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-01-20 05:47:19 +0000
Commit message:

 Update NEWS and DESCRIPTION; Bump version
 
Package: sitePath
Commit: 70c5a4bc7bca43552184e49612769ad011dcaf27
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-01-20 01:04:19 +0000
Commit message:

 Update README
 
Package: sitePath
Commit: a276ccd6ee957058e1cac701f93143b04476f1f1
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-01-19 15:40:37 +0000
Commit message:

 Move the simpler vignettes to READMEN
 
Package: sitePath
Commit: f1b2afa2b8d3c964e59890c7bde094bfcb7fd320
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-01-19 15:12:05 +0000
Commit message:

 Add a simpler vignette
 
Package: sitePath
Commit: f1068c9284e884c6d392c3beaa6fad5d4467ec23
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-01-19 13:25:06 +0000
Commit message:

 Add 'plotFixationSites' and 'plotParallelSites'; add print function for 'alignment' object
 
Package: sitePath
Commit: 0d07c6c244291fcd5f5c255c987167dfa36acbae
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-01-19 11:55:29 +0000
Commit message:

 Core number set to 1 will disable multiprocessing
 
Package: sitePath
Commit: 5208932453eed8ea62c759f77859be0a2a35e361
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-01-19 03:20:49 +0000
Commit message:

 'biocthis' version 1.5.0 generated GHA
 
Package: sitePath
Commit: 8a0438f7525e3538ba41a3cfa6fda5c80f4e8cc3
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-01-19 03:16:26 +0000
Commit message:

 Update README and vignettes
 
Package: GenomicFeatures
Commit: dd8aaa67e6f3a936f4439f325512ea358d590848
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-01-19 19:39:14 -0800
Commit message:

 Add warning about status of FeatureDb-releated functionalities
 
Package: AnVIL
Commit: 62bdecab39494b8df5858e5a6d6bb90e5d344861
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-01-19 14:44:37 -0500
Commit message:

 version bump and NEWS entry for improved gcloud token timeout

- closes #45
 
Package: AnVIL
Commit: a9307519a8cac98b8492e1f367098e73a085edc2
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-01-19 14:41:39 -0500
Commit message:

 Merge branch 'master' into token-timeout
 
Package: AnVIL
Commit: 22ef9341a8f465b862bc73937140a7c5c6993461
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-01-13 05:13:55 -0500
Commit message:

 better manage gcloud access token timeout

- token may have been issued (considerably) before first retrieved,
  so respect expires_in token info, rather than hard coded 60' limit
 
Package: AnVIL
Commit: bbbca715d66c2cec619c9d1fec5938497736b0ec
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-01-19 14:40:25 -0500
Commit message:

 version bump and NEWS for avdata() / avdata_import()
 
Package: AnVIL
Commit: 983b60fca9840505f4e28fc6ac0994b99b298a1f
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-01-19 14:37:09 -0500
Commit message:

 implement avdata_import()
 
Package: AnVIL
Commit: 2672f7f08bdf73ef43354744094290ec632e048f
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-01-19 10:46:56 -0500
Commit message:

 refactor avdata()

- use getWorkspace("workspace.attributes") rather than getAttributesTSV
- more carefully exclude non-'DATA' elements
 
Package: tximeta
Commit: 1a18f223ff46840a9f32c3a65103683ac3cfc2e1
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-01-19 12:03:56 -0500
Commit message:

 add note about missing metadata
 
Package: GenomicFeatures
Commit: c2af946e9c1afc2285a69be47c2b90ed097fa4c3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-01-19 09:03:06 -0800
Commit message:

 Make sure internal helper map_SQLtypes_to_Rtypes() handles enum types
 
Package: scPCA
Commit: 3328a6e622fba60c02ff4e278a754580f992efb1
Author: Philippe Boileau <pboileau.swim@gmail.com>
Date: 2022-01-19 10:15:43 -0500
Commit message:

 updating copyright years and citation info in readme
 
Package: MatrixQCvis
Commit: 47d52efdcff9194a75d55ea813d2d91f6d61a5be
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-01-19 15:42:27 +0100
Commit message:

 add new features to NEWS file and change date in DESCRIPTION
 
Package: MatrixQCvis
Commit: 7990e5797d9b12def3082fad07c19aa1a9743141
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-01-19 15:33:14 +0100
Commit message:

 add rounding in mosaic
 
Package: MatrixQCvis
Commit: eea4345228b211c4262c4e40ebb0a447bb07259a
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-01-18 12:01:21 +0100
Commit message:

 fix bug in y labels in dimension reduction plots (use here y_coord)
 
Package: MatrixQCvis
Commit: 1010ff6223b6f43ad6fab8fbfebe1fc08dbc853e
Author: tnaake <thomasnaake@gmx.de>
Date: 2021-12-14 18:39:06 +0100
Commit message:

 update NEWS
 
Package: MatrixQCvis
Commit: c8bd917a52c1ea171068c98834edf7fa8bd05fc0
Author: tnaake <thomasnaake@gmx.de>
Date: 2021-12-13 14:52:50 +0100
Commit message:

 update measured missing tabs, missing means all values are missing
 
Package: MatrixQCvis
Commit: 23c1f5892a2bfa409c61e2356793fb5fc975ed42
Author: tnaake <thomasnaake@gmx.de>
Date: 2021-12-10 14:55:39 +0100
Commit message:

 add unit tests for txt import functionality in maxQuant
 
Package: MatrixQCvis
Commit: a50de749c4fc5f58238145846bcee05e26e6df96
Author: tnaake <thomasnaake@gmx.de>
Date: 2021-12-09 20:09:13 +0100
Commit message:

 update maxQuant function and allow also for txt file import
 
Package: MatrixQCvis
Commit: 4d8e431120a722a8adab87f4d9ca9bc28cee6041
Author: tnaake <thomasnaake@gmx.de>
Date: 2021-12-02 15:05:06 +0100
Commit message:

 add ORCID
 
Package: Spectra
Commit: 627df302d5d8afff98c933ad7d6ae69afe6199cd
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2022-01-19 12:12:06 +0100
Commit message:

 Merge pull request #232 from rformassspectrometry/filterPrecursorMzValue

Add filterPrecursorMzValue to support filtering by multiple m/z values 
Package: Spectra
Commit: bc6d4ea7353418b53864fe1c8372315d50a00ad6
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-19 11:59:20 +0100
Commit message:

 fix: add missing bracket and fix unit test suite
 
Package: Spectra
Commit: a956c3ee64f07caff01a02900b99b5696b26ee2c
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-19 10:51:02 +0100
Commit message:

 refactor: add filterPrecursorMzRange and depracate filterPrecursorMz
 
Package: Spectra
Commit: 6e97171033bdcc528f5332031e97757116475577
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-18 13:26:19 +0100
Commit message:

 refactor: adapt to Sebastian's suggestions
 
Package: Spectra
Commit: b58e240fc84864861e29d668e4735b5702b3fa6b
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-14 11:56:34 +0100
Commit message:

 fix: address Sebastian's comments
 
Package: Spectra
Commit: f165cbd0a52cf1e99a1ac58910a4872a56e48173
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2022-01-14 08:56:49 +0100
Commit message:

 Update R/MsBackend.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 
Package: Spectra
Commit: 3e9b9914ca7e5f55d63b0df4379459f7f33ce2be
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-13 12:39:43 +0100
Commit message:

 Bump version
 
Package: Spectra
Commit: 1e1791e0416512cfc5f34a6c08084bcaed63ca85
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-13 11:59:16 +0100
Commit message:

 Merge branch 'master' into filterPrecursorMzValue
 
Package: Spectra
Commit: 4687a57a73a59c774497f4febf7296bd96b45d83
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-12-10 14:14:52 +0100
Commit message:

 feat: add filterPrecursorMzValues (issue #230)

- Add the `filterPrecursorMzValues` method to enable filtering based on multiple
  target precursor m/z values.
 
Package: GeneTonic
Commit: cd1b0b1150c58e41f958185fdfacf2c0be771d4f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-19 12:01:20 +0100
Commit message:

 Fixing the expectations for the small backbone example - Sometimes returns 2 nodes, adjusting the test
 
Package: GeneTonic
Commit: 445f1a492131996374dbf98da48fda9ed518ba61
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-19 11:56:25 +0100
Commit message:

 updating info in the README
 
Package: GeneTonic
Commit: b02de34a4da6c9082739f66c4bef3119b0bffb97
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-19 11:51:43 +0100
Commit message:

 Version bump, 1.7.2
 
Package: GeneTonic
Commit: afac709ea70f92bb2ba1c15b6997402be87a22aa
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-19 11:50:54 +0100
Commit message:

 updating the news for 1.7.2
 
Package: GeneTonic
Commit: 25e762f0f5bf43a2bb5c593c6b763bec36a90246
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-19 11:47:09 +0100
Commit message:

 Inserting Anka in the footer :)
 
Package: GeneTonic
Commit: 0623acdf2ceefa52d829b6e469511f4f9bc20b6e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2021-12-31 21:26:45 +0100
Commit message:

 updating citation info
 
Package: karyoploteR
Commit: 6fc3dfd2ead966067a01985b4e6e1ff83da56d1a
Author: Bernat <bernatgel@gmail.com>
Date: 2022-01-19 11:33:07 +0100
Commit message:

 Version Bump

 
Package: karyoploteR
Commit: 30eedcea4eb490c62acbe03e6f5ca1d7b5cd0e85
Author: Bernat <bernatgel@gmail.com>
Date: 2022-01-19 11:33:00 +0100
Commit message:

 Updated news

 
Package: karyoploteR
Commit: 9c557f64b0b177c5ef4e3c51b63bd45cd11b1d9e
Author: Bernat <bernatgel@gmail.com>
Date: 2022-01-19 11:32:48 +0100
Commit message:

 Fixed Bug Issue 112 - Zoom and labels on the right side

 
Package: ASSET
Commit: 57f5da6e7ea43621cbd83724cca33eb8dfa1e45f
Author: Samsiddhi Bhattacharjee <sb.statgen@gmail.com>
Date: 2022-01-19 15:42:46 +0530
Commit message:

 Increased the version number from 2.13.1 to 2.13.2 .
 
Package: ASSET
Commit: b4f57170b5cb39e5156384deb7436b59ca23aab6
Author: Samsiddhi Bhattacharjee <sb.statgen@gmail.com>
Date: 2022-01-19 15:16:37 +0530
Commit message:

 Overhauled the h.forest function to be able to plot 1 summary
or 2 summary or 3 summaries as present in the input object. Earlier
it as designed to work only in the case where all 3 summaries had
been pre calculated and filled in the traits.forest or types.forest
functions. Hence fast_asset example which was not doing meta-analysis
was failing to generate forest plot.
 
Package: ASSET
Commit: 73b4fb459332a10091a9451614f2a70dab815211
Author: Samsiddhi Bhattacharjee <sb.statgen@gmail.com>
Date: 2022-01-19 15:09:30 +0530
Commit message:

 Introduced the argument calc.miss=FALSE in h.forestPlot to avoid computing
summaries in traits.forest and types.forest functions unless the user wants
to calculate and fill all 3 summaries (e.g. Meta, 1-sided, 2-sided).
Also fixed minor bug in h.traits which was generating error when
traits.forest was calling h.traits with one SNP.
 
Package: ASSET
Commit: aeafd7fa160505b25fa1cc52d691819ede37640d
Author: Samsiddhi Bhattacharjee <sb.statgen@gmail.com>
Date: 2022-01-19 15:04:04 +0530
Commit message:

 Added a help file for the fast asset example dataset to avoid
warnings about missing object names in namespace. Added a
pointer to the new data as 'see also' from the help pages of the
other two example datasets.
 
Package: atena
Commit: 57953e4ee91181c58e8b0c480cc1405b34bc48dd
Author: Beatriz Calvo Serra <45432116+beacalvo@users.noreply.github.com>
Date: 2022-01-19 09:44:27 +0100
Commit message:

 Merge pull request #4 from functionalgenomics/Telesc_multiovbyaln_minOv

Updating Telescope minimum overlap and implementing approach for alignments overlapping multiple features 
Package: atena
Commit: 838b94befd11b9443fbfe451fbce7c3d60aa4d11
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-18 21:10:42 +0100
Commit message:

 Fixed error
 
Package: atena
Commit: 48b776c832edea2b5afd4d80db2ee5e7e06001d1
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-18 18:05:05 +0100
Commit message:

 Version bump
 
Package: atena
Commit: 70a2f6e1b125822de5d8b79a3b49084c673d729c
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-18 18:04:16 +0100
Commit message:

 Updating branch with commits in master
 
Package: atena
Commit: 6dc53fe987e598154e67b324ec7243c64b81c2a9
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-18 15:15:19 +0100
Commit message:

 Decommented lines in test_TEtranscripts.R
 
Package: atena
Commit: 32b0a3d609ad59310f68bf558590138784a15770
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-18 14:57:54 +0100
Commit message:

 Commented lines in test_TEtranscripts.R
 
Package: atena
Commit: 6fed1193608fde6d81c53035942682993ad792e2
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-18 12:35:55 +0100
Commit message:

 Decommented lines in test_TEtranscripts.R
 
Package: atena
Commit: 6417006f89db68dc506c8520962750dcc341b3f0
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-18 12:34:53 +0100
Commit message:

 Commented lines in test_TEtranscripts.R
 
Package: atena
Commit: 224aa18bf64387cfc44e5da629851ade5b0b7f6e
Author: Beatriz Calvo Serra <45432116+beacalvo@users.noreply.github.com>
Date: 2022-01-18 12:08:44 +0100
Commit message:

 Merge pull request #3 from pablo-rodr-bio2/updateSparse

Update sparse functions. Optimizations on TEtranscripts and Telescope methods. 
Package: atena
Commit: 572d47ec56625b22cdae4af27ece2174e0cdb832
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-04 19:08:39 +0100
Commit message:

 Implemented Telescope approach for when an alignment overlaps multiple features. Implemented Telescope approach for min overlap.
 
Package: atena
Commit: d9f3405061515e71feaf6cc03427fcc1e03bac22
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 21:13:10 +0100
Commit message:

 version Bump
 
Package: atena
Commit: 00970600523180b575648c81713ac7a20c323520
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 20:46:01 +0100
Commit message:

 Telescope new .tsEstep() and .tsMstepPi
 
Package: atena
Commit: c8ab0eccdf01909e4552b85a2b2e0ef4397d4cef
Author: beacalvo <beacalvo96@gmail.com>
Date: 2021-12-17 20:39:28 +0100
Commit message:

 Added if for when minOverlap = 0 and no overlaps are included in 'no_features'
 
Package: atena
Commit: 0bfdee9b6d9a74a3ee559c0696745427026ee9e2
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 19:39:45 +0100
Commit message:

 Telescope new .tsEMstep
 
Package: atena
Commit: 6866b9558c9f7cb252fcd061f678bf531ed71ffe
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 19:18:05 +0100
Commit message:

 Telescope change all rowSums2 and colSums2
 
Package: atena
Commit: 71b32ed045f09cee8872d072fa4d7a9154a6acd2
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 18:43:24 +0100
Commit message:

 added tests for new TEtrasncripts
 
Package: atena
Commit: ff7f7ad33afb1b99d6c822379dfda45dca591a91
Author: beacalvo <beacalvo96@gmail.com>
Date: 2021-12-17 17:24:54 +0100
Commit message:

 Modified Telescope.R so that only alignments mapping to features but where the overlap is < min Overlap are consiedered as no_feature counts
 
Package: atena
Commit: 9ff1f33c8f1abd7e68fe617f6adbb76c8779e36c
Author: beacalvo <beacalvo96@gmail.com>
Date: 2021-12-17 15:46:34 +0100
Commit message:

 Testing modification
 
Package: atena
Commit: f0fd6a98e5e364caae6ad2fa4ead83afc0391733
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 13:04:38 +0100
Commit message:

 TEtranscript new .ttEstep() and .ttMstep()
 
Package: atena
Commit: 527f7e0bf86d6d0d6bb403e651b694ecdaf95432
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 13:02:03 +0100
Commit message:

 TEtranscripts reverting Qmat and cntvecovtx creation
 
Package: atena
Commit: 04c92ecc058e24c8080f7f773bf5cd177e107058
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 12:48:31 +0100
Commit message:

 TEtrasncripts reverting Qmat div, new cntvecovtx
 
Package: atena
Commit: e645e2561425b4ab890dadc8339a6c97a74207ef
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 12:40:08 +0100
Commit message:

 TEtrasncripts reverting Qmat div, new cntvecovtx
 
Package: atena
Commit: 7c4b665cabdc05f050cbf1ca50941d81c47163d8
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 12:25:58 +0100
Commit message:

 TEtranscripts new Qmat div and cntvecovtx creation
 
Package: atena
Commit: 3f3dfc4f57bdc0aabd0e57cdad283b1438c409f4
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 12:22:35 +0100
Commit message:

 TEtranscripts new Qmat creation
 
Package: atena
Commit: e47a75d87eb3de59d6944b28d7594975a2d35cd2
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 12:18:51 +0100
Commit message:

 TEtranscripts new buildOvAlignmentsMatrix
 
Package: atena
Commit: 721b9d3cd236831658e6009c69935e32e7431c64
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 11:55:58 +0100
Commit message:

 TEtranscripts changed all rowSums2 and colSums2
 
Package: atena
Commit: f383ff712cb45d22b88362191347cb552d172e5d
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 11:44:47 +0100
Commit message:

 changed github workflow
 
Package: atena
Commit: 9ee70a14b331176b2a7697bf544b071e66247f66
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-17 11:43:49 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: atena
Commit: 9c4bdecd10c32477b245f1bb26a887ebb9618286
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-12-16 21:43:18 +0100
Commit message:

 version bump
 
Package: MicrobiotaProcess
Commit: 9fb8d2110e5cfa20014dd67dbec04e13d788075e
Author: xiangpin <xshuangbin@163.com>
Date: 2022-01-19 14:29:48 +0800
Commit message:

 bump version
 
Package: MicrobiotaProcess
Commit: 3293692633a788794ae44510d74ee4f8a9044bfd
Author: xiangpin <xshuangbin@163.com>
Date: 2022-01-14 12:00:47 +0800
Commit message:

 update news
 
Package: MicrobiotaProcess
Commit: 15a5a5f727133c034ad7f260bde3ceda0d858f0b
Author: xiangpin <xshuangbin@163.com>
Date: 2022-01-14 12:00:32 +0800
Commit message:

 fix bug for incomplete kingdom annotation
 
Package: MicrobiotaProcess
Commit: 84c494a83d6b60e3d286d78c8e4f9dc968f8ffbe
Author: xiangpin <xshuangbin@163.com>
Date: 2022-01-14 11:59:11 +0800
Commit message:

 add mp_extract_taxatree and mp_extract_otutree, alias of mp_extract_tree
 
Package: MicrobiotaProcess
Commit: c209f910deff306ee13b844bc95791cfddb7a46a
Author: xiangpin <xshuangbin@163.com>
Date: 2022-01-14 11:57:30 +0800
Commit message:

 typo
 
Package: NanoStringNCTools
Commit: c60a712d5378b025197aa98bd73763372e73c42e
Author: Nicole Ortogero <20404635+NicoleEO@users.noreply.github.com>
Date: 2022-01-18 16:21:43 -0800
Commit message:

 Merge pull request #26 from Nanostring-Biostats/dev

Update master to dev 1.3.1 
Package: NanoStringNCTools
Commit: c8ad5e583d67bce7415fdedb1827cc816be89f84
Author: karagorman <38232391+karagorman@users.noreply.github.com>
Date: 2022-01-13 15:33:05 -0800
Commit message:

 Merge pull request #25 from Nanostring-Biostats/iss24

Iss24 
Package: NanoStringNCTools
Commit: d39608d6d3275eed1ef306ee1ed43d82f3e61c35
Author: NicoleEO <Nicole.Ortogero@gmail.com>
Date: 2022-01-12 15:26:22 -0800
Commit message:

 Update news
 
Package: NanoStringNCTools
Commit: c90fb2d9dbedb4d9fc676387ca6d71f26042bb2b
Author: NicoleEO <Nicole.Ortogero@gmail.com>
Date: 2022-01-12 15:22:51 -0800
Commit message:

 match bioc minor
 
Package: NanoStringNCTools
Commit: 2ce56bff5028426492dc6f6dd0807a983634e297
Author: NicoleEO <Nicole.Ortogero@gmail.com>
Date: 2022-01-12 15:15:11 -0800
Commit message:

 Pull in bioc version bumps
 
Package: NanoStringNCTools
Commit: 9ecf2c6b79abba0c68565cb5cd8227b7dba303a5
Author: karagorman <karagorman@yahoo.com>
Date: 2022-01-12 21:38:16 +0000
Commit message:

 #24 update version and news
 
Package: NanoStringNCTools
Commit: ad9a1c6a791bcea3139a4b8b430cce647a320c60
Author: karagorman <karagorman@yahoo.com>
Date: 2022-01-05 19:24:42 +0000
Commit message:

 #24 fix typo
 
Package: NanoStringNCTools
Commit: 134f6343cadf8fe3660e37a41eac66ef2ce00fda
Author: karagorman <karagorman@yahoo.com>
Date: 2022-01-05 19:21:53 +0000
Commit message:

 #24 add E as scanner ID letter option for Gen 2.5 RCCs
 
Package: karyoploteR
Commit: 1fa67811567fd68ffda93644f4d96e68845677d7
Author: Bernat <bernatgel@gmail.com>
Date: 2022-01-19 00:24:15 +0100
Commit message:

 Version Bump

 
Package: karyoploteR
Commit: 6c4dc81e627edce8a6062223a4c5c9957a980e3b
Author: Bernat <bernatgel@gmail.com>
Date: 2022-01-19 00:14:02 +0100
Commit message:

 Fixed error in plotKaryotype chromosome order

In some cases the chromosome order in the karyoplot$chromosome slot ignored the user supplied order. This affected also github issue 114. 
Package: karyoploteR
Commit: c657a2d812101f2693da4771ebcacba1d71eee35
Author: Bernat <bernatgel@gmail.com>
Date: 2022-01-18 16:15:36 +0100
Commit message:

 Fixed github issue 114 - Wrong position of chromosome names

A bug caused the names of the chromosomes to be plotted at the wrong position when the chromosomes  where unordered and a custom genome was used. 
Package: karyoploteR
Commit: 216184c9070f821718e459f11f4d92ddb59cffc7
Author: Bernat <bernatgel@gmail.com>
Date: 2022-01-18 16:13:57 +0100
Commit message:

 Version Bump

 
Package: karyoploteR
Commit: 141b8b82658a13cc710388c32730df7c8103ab8a
Author: Bernat <bernatgel@gmail.com>
Date: 2022-01-18 16:13:47 +0100
Commit message:

 Removed debugging messages

 
Package: sesame
Commit: a6e26e9fddeb224866a7e3c430ab3099284fb671
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-18 17:26:59 -0500
Commit message:

 bump to 1.13.15
 
Package: sesame
Commit: b6c93131eac4c8ffc226aca77ce583d27c8cf213
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-18 14:58:56 -0500
Commit message:

 update reference inference
 
Package: sesame
Commit: 608adda39dd52b75683acf5d84da49bbcfcb191c
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-18 12:03:17 -0500
Commit message:

 minor, message omitted
 
Package: sesame
Commit: d33d24438796f9292913ec738c47df336fe7feab
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-18 10:41:24 -0500
Commit message:

 inferSpecies add species meta info
 
Package: sesame
Commit: e58e3d99985947c1a47950f842bb7a767eb7a403
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-18 10:32:14 -0500
Commit message:

 bug fix to inferSpecies
 
Package: sesame
Commit: 8ea805384ad494d523d9f6c977deedc68df03fc6
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-18 10:04:25 -0500
Commit message:

 update to inferSpecies
 
Package: ggspavis
Commit: 06011b7488f85fb752d72d92cc8df4cd0f2e466e
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-01-18 16:59:22 -0500
Commit message:

 version
 
Package: ggspavis
Commit: 68e9a9ae941cf4565de27a1bbb40ede4dabf8ee7
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-01-18 16:50:12 -0500
Commit message:

 temporary fixes for spatialData deprecation
 
Package: ggspavis
Commit: 5a8de9248b537cad0b276e55e153548cfbfe46c4
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-01-18 16:17:59 -0500
Commit message:

 temporary fix for spatialData deprecation
 
Package: GenomeInfoDb
Commit: 513a854cb990dc6229f86af29f0fbc389bcb2a7f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-01-18 12:27:15 -0800
Commit message:

 Register 3 NCBI assemblies for Acyrthosiphon pisum
 
Package: pRolocGUI
Commit: fb7a8e54eeb76f2daa3f2f2f3de9daec77142296
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2022-01-18 16:57:22 +0000
Commit message:

 Update news and package version to fix conflicts
 
Package: pRolocGUI
Commit: 34dc269ed99e6f344b9e0c3152d239444f35065a
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2022-01-18 13:45:07 +0000
Commit message:

 fixes #109
 
Package: plotgardener
Commit: dceef6e046dd67b49e68a332b47946ab0423810c
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-18 12:39:22 -0500
Commit message:

 Merge updates and bug fixes from release
 
Package: plotgardener
Commit: 6733512248041ea451c8ce567e88de795a86c1f2
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-18 12:38:03 -0500
Commit message:

 News update and version bump
 
Package: plotgardener
Commit: 3bb5c6cf12ae98472c24dcaf49dd4b7040d2df67
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-18 12:37:37 -0500
Commit message:

 plotPairs updates to match logic of plotPairsArches
 
Package: plotgardener
Commit: 868f38886ad138f9aa4ed6a1eee48b0258130430
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-18 12:26:36 -0500
Commit message:

 line indentations
 
Package: plotgardener
Commit: ffeef75e73c2ec9b656812c7b6bce0d79803d01d
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-18 12:20:47 -0500
Commit message:

 archHeight column option and color subsetting.
 
Package: crisprScoreData
Commit: 877a65be1befc142e82d54805de2d3a86d8a53b0
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-01-18 08:11:40 -0800
Commit message:

 Added CRISPRai models
 
Package: ChromSCape
Commit: e42d6b0bc8765e39300f255853ab1e6c9e3beb9b
Author: Pacome <pacome.prompsy@curie.fr>
Date: 2022-01-18 16:25:19 +0100
Commit message:

 Corrected title of volcano plots for custom DA
 
Package: BiocPkgTools
Commit: 719a7f3e0fba982c7973553991cc77b9c93bc535
Author: Sean Davis <seandavi@gmail.com>
Date: 2022-01-18 06:43:30 -0700
Commit message:

 Merge pull request #60 from jwokaty/fix-generateBiocPkgDOI-return

Return DOI or message, bump version 
Package: BiocPkgTools
Commit: 6987703a51b0829a67521029ff9282f94ba8d92f
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-01-14 10:38:16 -0500
Commit message:

 Return DOI or message, bump version
 
Package: geneplast.data
Commit: 1a5ebb54565e72108796b0fa6f5fb4b88b0eb6e7
Author: Leonardo René Campos <leofields@gmail.com>
Date: 2022-01-18 10:30:05 -0300
Commit message:

 Improving vignette.
 
Package: OmnipathR
Commit: 0aaa0e55b9cb678f0feebbf77df8a68b469319cb
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-18 13:02:08 +0100
Commit message:

 `pivot_annotations` calls `readr::type_convert` making resource specific variables the correct type
 
Package: metapone
Commit: d3da28503f1087faea5962ea2986862bfa7a0b43
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-18 16:49:36 +0800
Commit message:

 added gsea type testing
 
Package: metapone
Commit: 36ad6262af0461e8b8a2cc37556f01b0cae5c93e
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-18 16:46:51 +0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: metapone
Commit: fa22909fd246260c85ea0e99530bd33b4f101a38
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-17 16:20:28 +0800
Commit message:

 updated package with gsea type testing
 
Package: imcRtools
Commit: 5f4d99a6236de852dd2aaede5b9340a014823106
Author: Nils Eling <nilseling@users.noreply.github.com>
Date: 2022-01-17 20:49:26 +0100
Commit message:

 Merge pull request #59 from BodenmillerGroup/read_steinbock_fix

Select files more specifically 
Package: imcRtools
Commit: 7ddcd66c47433a70ae331563657449d0f8132ae7
Author: nilseling <nils.eling@gmx.de>
Date: 2022-01-17 15:41:28 +0100
Commit message:

 Select files more specifically
 
Package: imcRtools
Commit: 265b1085f57f539fc0463d1735a92bfc94f63c48
Author: Nils Eling <nilseling@users.noreply.github.com>
Date: 2022-01-12 22:13:49 +0100
Commit message:

 Merge pull request #58 from BodenmillerGroup/read_steinbock_fix

Fixed indexing issue with steinbock graphs 
Package: imcRtools
Commit: e515c6a01a7df7b7e9aa52cd381699f30ad91270
Author: nilseling <nils.eling@gmx.de>
Date: 2022-01-12 19:47:03 +0100
Commit message:

 Fixed indexing issue with steinbock graphs
 
Package: Gviz
Commit: 2f6ae8b15f004802c54d86394517a10f142cfbcc
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2022-01-10 10:19:16 +0100
Commit message:

 Version bump.
 
Package: Gviz
Commit: ec0a9172ec7bef6334d7a825bdabc14ba78668a2
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2022-01-10 10:18:58 +0100
Commit message:

 Code cleanup.
 
Package: Gviz
Commit: 61cdd882588e4d4436e4305ecde5e2638c9027fc
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2022-01-07 18:43:20 +0100
Commit message:

 Added possibility to use different aggregation functions for running windows (DataTrack)
 
Package: Gviz
Commit: cc75d479ac191ee189dcd6653dc7fdcd1e6f0462
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2022-01-06 20:52:50 +0100
Commit message:

 Code cleanup.
 
Package: Gviz
Commit: 78bbfbcdbb4310d8b118d95cf00ae4581bcca27d
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2022-01-06 16:39:34 +0100
Commit message:

 Remove AlignedReadTrack functions.
 
Package: Gviz
Commit: a6b04ea55571b3d47b0ec275ac8608438ad28bc6
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2022-01-06 16:09:36 +0100
Commit message:

 Switched to useEnsembl istead of useMart
 
Package: Gviz
Commit: 43f3ff183535c1d52bb2c3bea6e43b72f76449fd
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2022-01-05 22:27:37 +0100
Commit message:

 Reverted back the scale bar annotation (no bp for small numbers)
 
Package: scCB2
Commit: 67c50a3b526a711a8e9f0c0df264be526290a12f
Author: Zijian Ni <412182180@qq.com>
Date: 2022-01-17 19:57:05 -0600
Commit message:

 Update DESCRIPTION
 
Package: scCB2
Commit: 853128bea2c338b92b83afa431ff26f4ad88cd29
Author: Zijian Ni <412182180@qq.com>
Date: 2022-01-17 19:55:31 -0600
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/scCB2
 
Package: scCB2
Commit: a42167c531e3f4a6dffec441467c7df3a18b2668
Author: Zijian Ni <412182180@qq.com>
Date: 2022-01-17 19:48:22 -0600
Commit message:

 v1.6.0 update

1. Adjust the default mitochondrial filtering cutoff in GetCellMat()

2. Add a new feature to evaluate appropriate background cutoffs
 
Package: igvR
Commit: 38cd848fdb434b8deef483cc7c4cd69e865cf8ad
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2022-01-17 17:50:55 -0800
Commit message:

 merged, with bioc version bump
 
Package: igvR
Commit: 60c04280e5fcf5f2479fa908f659ced08d9325ca
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2022-01-17 17:48:34 -0800
Commit message:

 new build of igv.min.js (2.10.5) supporting zoomOut.  added width to getGenomicRegion
 
Package: igvR
Commit: bdf28d17892ab6d83164aa9f7f8c7c429ae848ad
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2021-10-29 15:42:00 -0700
Commit message:

 synchronous behavior restored
 
Package: igvR
Commit: ec8915f7c625e238e676a01c05d099117194f4db
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2021-10-29 15:00:54 -0700
Commit message:

 uses, and adapts to, igv.js version 2.10.2
 
Package: igvR
Commit: 08451a8dec0f50c977fb05b3a6b3545f9be82181
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2021-10-29 14:59:14 -0700
Commit message:

 default name restored
 
Package: plotgardener
Commit: 8be567a3b52353076c04f9b081a2140d3c1d6b9b
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-17 18:52:52 -0500
Commit message:

 Merge bug fixes from release
 
Package: plotgardener
Commit: a684dfe469f3d3abf12628ce05a0ab2d5b12bcb8
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-17 18:51:52 -0500
Commit message:

 Version bump
 
Package: plotgardener
Commit: e5e04a3eeb2340232c9a489ecf392f922a939e60
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-17 18:50:36 -0500
Commit message:

 plotPairsArches clip.noArches parameter
 
Package: msigdb
Commit: 0759c3422dfe1c0a54b88dd0b3533839d94720fb
Author: bhuva.d <bhuva.d@wehi.edu.au>
Date: 2022-01-18 10:40:44 +1100
Commit message:

 Added link to the mouse MSigDB hosted at WEHI to the help pages.
 
Package: HIBAG
Commit: 04c2e04edb2e8f59d3edf68cdcd2e9b37d0d2b72
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2022-01-17 16:22:55 -0600
Commit message:

 fix hlaGDS2Geno()
 
Package: OmnipathR
Commit: e2f35d59aadfa0fa6fcc91b94e4f9b3c919f4299
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-17 23:08:32 +0100
Commit message:

 `omnipath_intro` vignette: moved figure 1 to `vignettes/man/figure` (another pkgdown issue)
 
Package: idr2d
Commit: e31411388d0d37ef6dc3b949fba7d23206ed4032
Author: Konstantin Krismer <krismer@mit.edu>
Date: 2022-01-17 16:06:16 -0500
Commit message:

 Fix BioC HiC test
 
Package: FlowSorted.CordBloodCombined.450k
Commit: 34347f94703550b294c94d3ab5619b830ff169be
Author: Lucas Salas <lucas.a.salas.diaz@dartmouth.edu>
Date: 2022-01-17 15:56:30 -0500
Commit message:

 Problems with dependencies
 
Package: OmnipathR
Commit: 8b1beecaff7d4f4e68e3dec62e43df776260890b
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-17 21:03:43 +0100
Commit message:

 removing cache lock at import time if running on bioc build servers (workaround for weird bioc build failures)
 
Package: OmnipathR
Commit: 163b3add0d6c168aa85a019701af8fbb262458bf
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-17 20:49:03 +0100
Commit message:

 docs update
 
Package: DiffBind
Commit: 9c31c432488f0a25616cd51bd8b0a6822e80c57e
Author: Randall Stark <rory.stark@cruk.cam.ac.uk>
Date: 2022-01-17 19:24:18 +0000
Commit message:

 roll-up fixes: blacklist, parallel, spikein normalization, Called
 
Package: MuData
Commit: 9b25b4bd9f07c88c4fb71f835986293471b96824
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2022-01-17 18:44:27 +0100
Commit message:

 Depend on rhdf5. Version 0.99.6.
 
Package: CompoundDb
Commit: 5087751c25a653d64051cfedd792d516a423472c
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-17 17:02:38 +0100
Commit message:

 fix: fix BiocCheck warnings
 
Package: sesame
Commit: d0c345fdcdf270cca855be123cf8c2fb8a383a70
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-17 10:38:40 -0500
Commit message:

 bump to 1.13.14
 
Package: sesame
Commit: abc415b6cc655a6971bfa3dbefb22c77ade71a44
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-17 10:33:16 -0500
Commit message:

 somehow KYCG.Rmd got deleted, add back
 
Package: CompoundDb
Commit: e425e185d1c3e7522c187256ec727f2473edde74
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-17 16:14:08 +0100
Commit message:

 fix: fix BiocCheck issues
 
Package: CompoundDb
Commit: 5612d7ad055a82c289924837abfb48f582f31839
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2022-01-17 15:41:08 +0100
Commit message:

 Merge pull request #94 from rformassspectrometry/bioc_submission

refactor: address comments from @jianhong 
Package: CompoundDb
Commit: 2982283110e853e223460a1f65ace553b3ac3972
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-17 15:20:18 +0100
Commit message:

 refactor: address comments from @jianhong
 
Package: uncoverappLib
Commit: 9c5f04637872470b42493ac98bb230ab12cd19b4
Author: eiovino <emanuelaiovino.87@gmail.com>
Date: 2022-01-17 15:09:01 +0100
Commit message:

 sob panel/viewr
 
Package: MuData
Commit: ae0a8aca7ce44b44f8c1f94810e69308034f767a
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2022-01-17 15:11:31 +0100
Commit message:

 Import rhdf5 to check Windows builds
 
Package: RnBeads
Commit: 8d4f49c63fa8eb2faeb8b3c67d9f1f3cde3827c6
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2022-01-17 15:03:51 +0100
Commit message:

 ...
 
Package: RnBeads
Commit: c75db23132a169980c09d1c062e2591701516310
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2022-01-17 15:03:15 +0100
Commit message:

 Merge branch 'master' of https://github.com/epigen/RnBeads

# Conflicts:
#	DESCRIPTION
 
Package: RnBeads
Commit: 472e99f8d43c8f8b8379017b68464f8bc2c6430e
Author: Michael Scherer <mscherer@mpi-inf.mpg.de>
Date: 2022-01-13 11:02:42 +0100
Commit message:

 Added grid package to dependencies to fix BioC build
 
Package: RnBeads
Commit: 36eec5c40aef3e79367759dcfa6450916e4e62b7
Author: Michael Scherer <mscherer@mpi-inf.mpg.de>
Date: 2021-11-22 09:01:44 +0100
Commit message:

 Merge branch 'RELEASE_3_14' of git.bioconductor.org:packages/RnBeads
 
Package: RnBeads
Commit: 17eba00c27b2d2ff83caf65b7129741775b23230
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2021-11-05 12:35:32 +0100
Commit message:

 version
 
Package: RnBeads
Commit: 2624a608c49546bca887208509e7577e1f491a51
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2021-11-05 12:33:48 +0100
Commit message:

 Merge branch 'master' into RELEASE_3_14

# Conflicts:
#	DESCRIPTION
 
Package: RnBeads
Commit: 5754ab9e16efc9b7d27d92365a2e0a82d144693b
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2021-11-05 08:00:06 +0100
Commit message:

 version for release branch
 
Package: RnBeads
Commit: 8b54902b8cd605c682ad91d68970860b3291464d
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2022-01-17 15:00:41 +0100
Commit message:

 grid dependency added
 
Package: MuData
Commit: 5d324fafbf004e66cabc35b34ca3a6019c8ca53d
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2022-01-17 14:29:09 +0100
Commit message:

 Minor code style changes
 
Package: InterCellar
Commit: de40f50f866a29777e06549c95158389a99fc4c4
Author: MartaBrio <marta.interlandi01@gmail.com>
Date: 2022-01-17 12:03:07 +0100
Commit message:

 version bump 2.1.1
 
Package: InterCellar
Commit: 53c8d6d50abcd69e5f670910bc51044a9b2953f1
Author: MartaBrio <marta.interlandi01@gmail.com>
Date: 2022-01-17 11:59:51 +0100
Commit message:

 Updated citation in README
 
Package: MuData
Commit: 68c3444ff2b8178a7dddda15f8368ddb2c6c9440
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2022-01-17 11:50:02 +0100
Commit message:

 Bump the version to 0.99.3
 
Package: MuData
Commit: 10aebf2e79c1f2117fd30de3dcf5a9d0697cf2d3
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2022-01-10 17:40:04 +0100
Commit message:

 Improve test coverage
 
Package: MuData
Commit: f55af63f75e3f12930b63b13399904d2bc2ceb85
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2022-01-10 15:49:27 +0100
Commit message:

 Error out when no HDF5Array and backed=TRUE
 
Package: MuData
Commit: 9df90de2ae9463106203880b2243e12c80a15eb3
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2022-01-10 15:38:54 +0100
Commit message:

 Depend on rhdf5
 
Package: MuData
Commit: bdf3b45723b6f3061b970c38bbe80a1ccddab097
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2022-01-10 15:31:59 +0100
Commit message:

 Use h5ls in vignettes instead of non-standard notation
 
Package: MuData
Commit: fe9356a4c9587dd01f46e6f4b438e1539372e6ee
Author: Ilia Kats <ilia-kats@gmx.net>
Date: 2021-12-21 13:28:26 +0100
Commit message:

 first implementation of metadata read/write
 
Package: MuData
Commit: 9e8b2a91a1858a5b800c028077da4daf8ca4a785
Author: Ilia Kats <ilia-kats@gmx.net>
Date: 2021-12-21 09:31:53 +0100
Commit message:

 lowercase function names
 
Package: MuData
Commit: 0a102e66a0c3b12538dc2553201064271448f52e
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2021-12-21 00:43:11 +0100
Commit message:

 Fix check_mod_order
 
Package: MuData
Commit: 289e65be4032cc15d9e1f108e59fa26c3d5be1e1
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2021-12-21 00:32:57 +0100
Commit message:

 Fix imports
 
Package: MuData
Commit: 1eed2fc7ef2cfdb7270451a8adb8796324cb83df
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2021-12-21 00:03:23 +0100
Commit message:

 Preserve modality order
 
Package: MuData
Commit: a18d5b7e4125b53501091e19b72e925679585767
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2021-12-20 23:13:44 +0100
Commit message:

 Improve vignettes
 
Package: OGRE
Commit: df30d457a4ee0a7d5a6e8723e00823b68aeac8cb
Author: svenbioinf <svenbioinf@gmail.com>
Date: 2022-01-17 10:06:30 +0100
Commit message:

 version bump
 
Package: rrvgo
Commit: a523d6800ae227da73376db43c252eadf2a3f6f9
Author: Sergi Sayols Puig <sergisayolspuig@gmail.com>
Date: 2022-01-17 09:32:45 +0100
Commit message:

 deprecate org.Pf.plasmo.db
 
Package: rrvgo
Commit: 4cce0b995acb92be8ab6ea1fcc99278dbafde50a
Author: Sergi Sayols Puig <sergisayolspuig@gmail.com>
Date: 2022-01-17 09:28:51 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: rrvgo
Commit: 503aecd7f3102f651841d5cc3b7f944ca0f32d7f
Author: ssayols <ssayols@users.noreply.github.com>
Date: 2021-12-07 09:50:04 +0100
Commit message:

 altmetric html badge 
Package: statTarget
Commit: f7572a2452a8e24edb5e00602862b45f2a978aae
Author: 13479776 <hemi.luan@gmail.com>
Date: 2022-01-17 15:48:18 +0800
Commit message:

 Remove the RGtk2
 
Package: FlowSorted.CordBloodCombined.450k
Commit: eda84bb560490d691f61907076cb4e205806fc82
Author: Lucas Salas <lucas.a.salas.diaz@dartmouth.edu>
Date: 2022-01-16 21:17:02 -0500
Commit message:

 Correcting dependencies
 
Package: GSEABenchmarkeR
Commit: 55c4db7e451fa6578904e3a99738b6e85bf4babe
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2022-01-16 19:47:53 -0500
Commit message:

 loadEData TCGA: fix cTD version
 
Package: GSEABenchmarkeR
Commit: 6ee760a1449c5807174014d0e28dfab4eb076756
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2022-01-16 19:47:29 -0500
Commit message:

 loadEData TCGA: fix cTD version
 
Package: EnrichmentBrowser
Commit: cca26b294c05996927992c78d0cf16974645f63a
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2022-01-16 19:01:32 -0500
Commit message:

 getGenesets: new msigdb collections
 
Package: SeqArray
Commit: 173f45eb4e287cb8f937c88828f334d069c468b6
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2022-01-16 17:07:54 -0600
Commit message:

 bug fixes
 
Package: sesame
Commit: 9b7f88e31b92ff389cb53cdb2e03e64c5ab6afda
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-16 10:49:08 -0500
Commit message:

 bump to 1.13.13, fix smaller continuous data bug. add f_min and n_min in dbStats
 
Package: DEqMS
Commit: 4edaba711dee863b42784600ba1046b619af6689
Author: Yafeng Zhu <yafengzhu@MacBook-Pro.local>
Date: 2022-01-16 17:26:31 +0800
Commit message:

 fix url download error
 
Package: statTarget
Commit: d1390b39239ec8bdcc9f0e837ca5048ecd4197c3
Author: 13479776 <hemi.luan@gmail.com>
Date: 2022-01-16 12:15:48 +0800
Commit message:

 vignettes update
 
Package: BiocCheck
Commit: 8e3f611b66c85a255ac48e5225cd11da1058b391
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-15 18:43:13 -0500
Commit message:

 version bump 1.31.28
 
Package: BiocCheck
Commit: 05d8b2b053f069b0541bd73921ddf03d72d7b9f0
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-15 18:43:02 -0500
Commit message:

 unload loaded namespaces
 
Package: BiocCheck
Commit: e24089f2c6a16571274773c50a72f50154406303
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-15 18:42:26 -0500
Commit message:

 pass lib.loc down to functions that use it
 
Package: BiocCheck
Commit: a6c2172dfaa7bfa2d7e8c2387e21e052a99b201b
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-15 18:13:03 -0500
Commit message:

 version bump 1.31.27
 
Package: BiocCheck
Commit: 4ad1d34cebc86a0806cf42216846dfe74a20a08f
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-15 18:11:54 -0500
Commit message:

 update test_checkDescriptionNamespaceConsistency
 
Package: BiocCheck
Commit: 2ed082473e7f5b0bd017531ea9f95ea05c9c30e2
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-15 17:55:07 -0500
Commit message:

 update test_checkForVersionNumberMismatch
 
Package: BiocCheck
Commit: be3df4ec1fd7befc4c35dd1ecf1243f0342fed83
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-14 21:26:36 -0500
Commit message:

 shorten examples and use tempdir from check_test_package
 
Package: BiocCheck
Commit: 78cd8c53f7d51f3291976330e3cce29c07d15c47
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-14 21:14:53 -0500
Commit message:

 use tempfiles as package names
 
Package: BiocCheck
Commit: 9e0bc771929abbc0675db784b5fd771a8472c04d
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-14 18:19:21 -0500
Commit message:

 only look at package names from parseNamespaceFile
 
Package: BiocCheck
Commit: 26abb931c736f89ef04b1bbd47a4dd332772da28
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-14 17:42:18 -0500
Commit message:

 remove double colons
 
Package: BiocCheck
Commit: 9b8701040354972fb1412c500c1e069697c36776
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-14 17:29:12 -0500
Commit message:

 add lib.loc argument to find installed dummy package
 
Package: OmnipathR
Commit: e42ef1a687df833af7ef5489717bb37fbdd5ea33
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 23:04:09 +0100
Commit message:

 added bookdown to suggested packages
 
Package: OmnipathR
Commit: a94d60935608f68d91262ed93c8ec15fcd08efe4
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 22:55:11 +0100
Commit message:

 v3.3.9 - version bump
 
Package: OmnipathR
Commit: c4e93d766beddb79f8a1e5999e3810cf26363016
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 22:53:04 +0100
Commit message:

 rebuilt pkgdown site
 
Package: OmnipathR
Commit: e832968b3ba63db95690571ed1f87b67b7016006
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 22:52:26 +0100
Commit message:

 new exported function: `import_small_molecule_protein_interactions`
 
Package: OmnipathR
Commit: 17f1bfddbe076fde01e7dd5f7509b3ce72b6f00a
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 22:52:09 +0100
Commit message:

 new HTML docs page: `import_small_molecule_protein_interactions`
 
Package: OmnipathR
Commit: 8521b9e4341241a1b838260526ce58897f7a3fea
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 22:51:10 +0100
Commit message:

 OmniPath Intro vignette: added point about small molecule interactions + cleaned up some pkgdown crap
 
Package: OmnipathR
Commit: e4827323734d0b1561184b8ff24e05d58fc3eafb
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 22:50:22 +0100
Commit message:

 Bioc Workshop vignette: added point about small molecule interactions
 
Package: OmnipathR
Commit: 925f93aef65dacf87f5eeb99eae2f53a7d2067af
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 22:49:40 +0100
Commit message:

 new function: `import_small_molecule_protein_interactions`
 
Package: OmnipathR
Commit: 2a56ef9b3ad4669a58cafcab6ab55fd7016cab17
Author: deeenes <turei.denes@gmail.com>
Date: 2022-01-15 22:49:06 +0100
Commit message:

 added `dontrun` to examples using `consensuspathdb_download` to avoid timeouts on bioc build servers
 
Package: pathwayPCA
Commit: a11c55e0bdf709423941ef0860ef5fedf0858f54
Author: gabrielodom <gabriel.odom@fiu.edu>
Date: 2022-01-14 19:07:14 -0500
Commit message:

 version patch bump

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

# Conflicts:
#	DESCRIPTION
 
Package: pathwayPCA
Commit: 88b5892d1a533a5fbd2b065b59cfc61a04fc0145
Author: gabrielodom <gabriel.odom@fiu.edu>
Date: 2022-01-14 19:02:10 -0500
Commit message:

 The build was failing due to changes to StandardizedExperiment objects.
 
Package: plotgardener
Commit: c690da2c0c0f490f2aece10c4c8cd15dbda4e00f
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-14 17:51:08 -0500
Commit message:

 Merge bug fixes from release
 
Package: plotgardener
Commit: a959e0addff3e12927cb5479e3a58ec4d9a0988e
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-14 17:48:09 -0500
Commit message:

 Version bump
 
Package: plotgardener
Commit: d9f4eadd49af0d0f48a4733a663ec231c7e1e520
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-14 17:37:41 -0500
Commit message:

 IRanges dependency for arches clipping logic
 
Package: plotgardener
Commit: abcd1e88e1f24eb4eafee73e4860d8c9f289edff
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-14 17:36:58 -0500
Commit message:

 Fixed logic for clipped arches
 
Package: plotgardener
Commit: abbafbada6d2ecd27c7f6b83bbcef7b4138d06c7
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-14 17:36:22 -0500
Commit message:

 Remove debugging code from annoDomains
 
Package: plotgardener
Commit: a68ad6214b7ddc3f52a89a4a2a5d60f7868373ca
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-14 14:14:25 -0500
Commit message:

 annoDomains rectHic bug fix
 
Package: plotgardener
Commit: 8d01f4ee201debaa63f35405dbe1140ee2aa9bba
Author: Nicole Kramer <nekramer@live.unc.edu>
Date: 2022-01-13 15:29:16 -0500
Commit message:

 Added range parameter for plotPairsArches heights
 
Package: GENESIS
Commit: 803e7e2b4ba580cbfd07af7fb9f28c86fd0b9ebf
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2022-01-14 14:20:51 -0800
Commit message:

 Merge pull request #83 from UW-GAC/sparsematrix_bug

bug fix: makeSparseMatrix handles numeric sample IDs 
Package: GENESIS
Commit: dd21bc8d2cf4c6199b24f38838b06377fa6c9ef7
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2022-01-14 14:01:28 -0800
Commit message:

 bug fix: makeSparseMatrix handles numeric sample IDs
 
Package: GENESIS
Commit: 0bd390ad00b4658234fac82ea84d2eb2ee51c935
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2022-01-07 09:35:10 -0800
Commit message:

 Merge pull request #81 from UW-GAC/github_actions

replace travis build with github actions 
Package: GENESIS
Commit: 7082f332823a04cd35eaacc458e0b6160ef45ad9
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2022-01-07 09:33:28 -0800
Commit message:

 future-proof by adding 'main' to list of checked branches
 
Package: GENESIS
Commit: d4e5ba82941eb902cf0941d8cca2a1757c8f59c5
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2022-01-06 16:11:27 -0800
Commit message:

 only run checks on linux
 
Package: GENESIS
Commit: 6b42112f5516adafe708a12a21ef5bf347a0089e
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2022-01-06 15:49:50 -0800
Commit message:

 replace tabs with spaces in yaml
 
Package: GENESIS
Commit: acdcde5ebaafe4fc458d65c010f42e4551597341
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2022-01-06 14:12:42 -0800
Commit message:

 replace travis build with github actions
 
Package: FlowSorted.Blood.EPIC
Commit: d1e101be7940925e8e9c7fadb87a7defd0bb7bf6
Author: Lucas Salas <lucas.a.salas.diaz@dartmouth.edu>
Date: 2022-01-14 16:30:20 -0500
Commit message:

 issue calling a namespace and global variable
 
Package: sesame
Commit: d7dfcd079c25ade45a2b10494fa42b3709b49219
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-14 16:08:27 -0500
Commit message:

 bump to 1.13.12, update to KYCG vignette
 
Package: sesame
Commit: e99014ab8ec4c429ee084eb1d13621b6606623fa
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-14 14:08:24 -0500
Commit message:

 2nd pass, kycg vignette
 
Package: sesame
Commit: 27f65434841eee7f1a3c86e49330c9578d62be0e
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-14 08:32:30 -0500
Commit message:

 before deleting getDatabaseSetOverlap
 
Package: sesame
Commit: a33db791da21e7648951e2a194e2b2791ab2e215
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-13 15:47:37 -0500
Commit message:

 added frac_dtna in QC
 
Package: sesame
Commit: c0aaeda484f7b86e48dcef35a27b4c92428e6403
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-13 15:38:59 -0500
Commit message:

 fix to num_dtna
 

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