Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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

GIT Logs

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

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

Package: tidybulk
Commit: 9d162fefa39fdf9d1b3e780fb2cbe4110f4a4f8f
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-07-01 13:46:14 +1000
Commit message:

 version UP from Bioconductor dev

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

Conflicts:
	DESCRIPTION
 
Package: tidybulk
Commit: 0015b972d1fb8208601050e04b7bcd70fe4b2b62
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 14:00:08 +1000
Commit message:

 update dependencies
 
Package: tidybulk
Commit: 9d98380d3a5731caadda9bbfec296d3f6c11465c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 12:46:08 +1000
Commit message:

 Merge pull request #242 from stemangiola/dev

Dev 
Package: tidybulk
Commit: 74c026f6a2913fa77ff46f28cf35c43705545854
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 12:16:48 +1000
Commit message:

 Merge pull request #241 from stemangiola/deprecate_log_transform_for_function

deprecation untested 
Package: tidybulk
Commit: 9c8ef7a30a3460f7795d197d96281e57765971bf
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 11:49:27 +1000
Commit message:

 Merge branch 'deprecate_log_transform_for_function' of github.com:stemangiola/tidybulk into deprecate_log_transform_for_function
 
Package: tidybulk
Commit: f47d148a0468022255c99474d63eb2e558478112
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:52:58 +1000
Commit message:

 fix CHECKs
 
Package: tidybulk
Commit: c00ae278af8b01b24b14fbe975cdacd80f94ff6d
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:21:39 +1000
Commit message:

 deprecation untested
 
Package: tidybulk
Commit: 38d06885cd65fca63e9c6738a8ceb9f6d446d3fa
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 11:48:27 +1000
Commit message:

 drop tsne test
 
Package: tidybulk
Commit: 0c2532467377a30de4f3f19a189c67ceac53da49
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 11:29:38 +1000
Commit message:

 Merge branch 'deprecate_log_transform_for_function' of github.com:stemangiola/tidybulk into deprecate_log_transform_for_function
 
Package: tidybulk
Commit: 0690a9f14df08a8d756e52055b222d09f21e0702
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:52:58 +1000
Commit message:

 fix CHECKs
 
Package: tidybulk
Commit: b399314080ee8cb7c423af3618560fef601ae2ff
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:21:39 +1000
Commit message:

 deprecation untested
 
Package: tidybulk
Commit: 527ca24dcfc5a90717fb8dae42d2b7f4978d389c
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 11:22:57 +1000
Commit message:

 make tests more detailed
 
Package: tidybulk
Commit: c3e317cbbaf8c89838c670814077eb9b0cc86631
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 10:58:37 +1000
Commit message:

 use |> for tests
 
Package: tidybulk
Commit: ffc068075fa24d1073fbb09e79e80b889c30b06d
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-28 10:58:22 +1000
Commit message:

 add news and version UP
 
Package: tidybulk
Commit: 1b48d42b7bf990b73ca2ad2d8d5c631ea67e4439
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-27 08:44:59 +1000
Commit message:

 Merge pull request #244 from stemangiola/parallel-cibersort

implementation parallel cibersort 
Package: tidybulk
Commit: 7830bc25116d3c8f85885b71759a502e624ff9bf
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 19:55:35 +1000
Commit message:

 Update check-bioc.yml 
Package: tidybulk
Commit: 59765dd6462c78f9b3a4d48e9fabca5595cf0f21
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 19:07:42 +1000
Commit message:

 Update check-bioc.yml 
Package: tidybulk
Commit: 6898f8d670b9c94552641082e6b1d3562f1219a3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 13:21:13 +1000
Commit message:

 Merge pull request #235 from stemangiola/polish_aggregation_tibble

Polish aggregation tibble 
Package: tidybulk
Commit: a1719eed0c17b243c99f701b1b24a81f4f97abd8
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:52:58 +1000
Commit message:

 fix CHECKs
 
Package: tidybulk
Commit: a439f770ae982636f4269d880fcaefc361614543
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:39:36 +1000
Commit message:

 add docs
 
Package: tidybulk
Commit: 4e3b77c2759e94216225b21b0ec45a526fa9bb1d
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:30:36 +1000
Commit message:

 fix CHECK
 
Package: tidybulk
Commit: 38fcfc03fb5b97cb0129c4c65e45dfc067aa637d
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:24:59 +1000
Commit message:

 Merge branch 'deprecate_log_transform_for_function' of github.com:stemangiola/tidybulk into deprecate_log_transform_for_function
 
Package: tidybulk
Commit: 219709674727c4a5803efd5a9f71e3cfd4d2fe72
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:21:39 +1000
Commit message:

 deprecation untested
 
Package: tidybulk
Commit: b97eec08ee3e28af6130b84c5fa1499d5b2aacec
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 12:21:39 +1000
Commit message:

 deprecation untested
 
Package: tidybulk
Commit: 73175cd2c5eb5d5756c6892a9170b11d319eaeed
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 11:36:10 +1000
Commit message:

 Merge pull request #236 from stemangiola/robustify_deconvolution_SE

allow other feature column for SE 
Package: tidybulk
Commit: 86d3107a02df148d86f115b01adcb6e03e1f32ec
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 11:35:06 +1000
Commit message:

 Merge pull request #238 from stemangiola/allow-mapping-to-other-genomes

avoid human annotation 
Package: tidybulk
Commit: 18f4cf0b7412ad1481e5b1af91d4ca305f961a62
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 11:34:09 +1000
Commit message:

 Merge pull request #239 from stemangiola/deprecate_dot_contrasts

deprecate .contrasts and update tests 
Package: tidybulk
Commit: 2b729ef0f3b2931f9094253d4f72e42ab4a10dbd
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 11:33:58 +1000
Commit message:

 Merge branch 'dev' into deprecate_dot_contrasts 
Package: tidybulk
Commit: 0bc0619814d1c657c18a1b16ec891d372b88eccf
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 11:27:32 +1000
Commit message:

 fix aggregation
 
Package: tidybulk
Commit: c0f2962c1064cfc92377bdd64be68342ebe86660
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 10:22:36 +1000
Commit message:

 merge dev

Merge branch 'dev' into polish_aggregation_tibble

Conflicts:
	R/methods_SE.R
	R/utilities.R
	tests/testthat/test-bulk_methods_SummarizedExperiment.R
 
Package: tidybulk
Commit: b31ffe0aac1cd03bc162fe8d86b45c624e09f0f6
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 01:27:40 +1000
Commit message:

 Merge pull request #237 from stemangiola/SE_to_tidybulk_new_vocabulary

implement new vocabulary 
Package: tidybulk
Commit: 6def641847a7e858258da36828c559b3e58d855e
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-26 00:01:55 +1000
Commit message:

 fix back deconvolution
 
Package: tidybulk
Commit: 9f08092934b1e2c7a0a05b153ee6c203b0fcfb8f
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-25 23:50:18 +1000
Commit message:

 fix tests
 
Package: tidybulk
Commit: d4707955cb66ee6edc3a8def8343b59255be9540
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-25 17:19:54 +1000
Commit message:

 fix tests
 
Package: tidybulk
Commit: a76efa9199cc0213721e0f90c91942da173b96e6
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-25 16:42:49 +1000
Commit message:

 fix examples
 
Package: tidybulk
Commit: 4a867ff378ad1e735616d165f57c2cb7247f18ac
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-25 13:22:33 +1000
Commit message:

 fix dependencies
 
Package: tidybulk
Commit: 7b4b3102bdb6c7e7a62d663cdc220a71e03e1322
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-25 12:58:41 +1000
Commit message:

 fix tests
 
Package: tidybulk
Commit: 0f31e395f515b10f0b4a34eb6fb74e4d48d0dce3
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-25 12:44:06 +1000
Commit message:

 get as_tibble from tidySE for tidybulk()
 
Package: tidybulk
Commit: 78c6838a3d0956e88adf16c95d9944c6c1a4399f
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-25 11:04:23 +1000
Commit message:

 temporary save to work on other branch
 
Package: tidybulk
Commit: a284fc65c15f4572b50be9fb34a4d9f8017e6898
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-25 10:25:05 +1000
Commit message:

 deprecate .contrasts and update tests
 
Package: tidybulk
Commit: 1a1a7580f61118e07783dbf015bfee8de796e700
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 19:45:58 +1000
Commit message:

 fixed pivot_
 
Package: tidybulk
Commit: 5ddf54a6ded25717193150343405f7daea05c809
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 19:20:56 +1000
Commit message:

 update docs
 
Package: tidybulk
Commit: 601aa4a0dedbe655aed297a1ec112dc47cb2294c
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 19:12:13 +1000
Commit message:

 avoid human annotation
 
Package: tidybulk
Commit: f93a90af07f0bcdf4d13291936f12b5adbc0b7e8
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 19:03:01 +1000
Commit message:

 fix tidybulk()
 
Package: tidybulk
Commit: fedd878f7f1efa5b64c440bf893870cdf543e164
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 17:55:00 +1000
Commit message:

 fix typo
 
Package: tidybulk
Commit: 60f426082d1607a8b0e6aed541eb0db721fe0ef2
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 17:28:05 +1000
Commit message:

 allow other feature column for SE
 
Package: tidybulk
Commit: f8d38ba4ec69182db76e8ce5598374e28a9fa1af
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 15:44:57 +1000
Commit message:

 Merge branch 'dev' of github.com:stemangiola/tidybulk into dev
 
Package: tidybulk
Commit: f4f58229f0daa1364cfc9ae8b70486cc94ec10fc
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-13 09:49:47 +1000
Commit message:

 replace if_else once
 
Package: tidybulk
Commit: cf637b51fee04b9b3bc79a5c07d68ea9eb023f86
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 15:36:13 +1000
Commit message:

 Merge branch 'master' of github.com:stemangiola/tidybulk
 
Package: tidybulk
Commit: 32f915febbc3c353b714eca7902ff611e76089a7
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-24 15:35:36 +1000
Commit message:

 implement new vocabulary
 
Package: tidybulk
Commit: 558cf13478ec777dd3e56b95f2f9c6884da0145b
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-14 01:55:26 +1000
Commit message:

 simplified aggregate for se and add test
 
Package: tidybulk
Commit: 948256a1705a2454e2f9778b36df96388746bf54
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-13 23:10:20 +1000
Commit message:

 fix bug
 
Package: tidybulk
Commit: 442249f6a49830ab252d92722a2bee8d50446170
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-13 14:41:51 +1000
Commit message:

 fix bug
 
Package: tidybulk
Commit: 758e08b71be8bc495dea58665d030580ca823069
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-13 14:21:26 +1000
Commit message:

 polish and make more robust also for SE
 
Package: tidybulk
Commit: 29efe9c341f14e3a1ae7cef02ce992a56b07b7bc
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-13 11:59:19 +1000
Commit message:

 make non standard columns not a problem
 
Package: tidybulk
Commit: 11e05b391d0bc99a16d46bf544e1d16666a6463c
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-13 09:49:47 +1000
Commit message:

 replace if_else once
 
Package: tidybulk
Commit: 1c68731f4f9ead006b40bf0d731eade7953eeb27
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-06-07 13:39:46 +1000
Commit message:

 implementation parallel cibersort
 
Package: tidybulk
Commit: e92693fb29321ad42f58bf2e3ce0de545a9fef9a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2022-05-29 09:24:39 +1000
Commit message:

 Merge pull request #234 from stemangiola/update-action-3.15

Update github action to Bioc 3.15 
Package: tidybulk
Commit: 4a110fa5bb44c1c9fd2cb25f4554708ab66843ec
Author: Maria Doyle <maria.doyle@petermac.org>
Date: 2022-05-28 19:51:58 +0100
Commit message:

 Edit to action
 
Package: tidybulk
Commit: d35f7a1fbf80be851ee4357ff000b7df7d9ebe43
Author: Maria Doyle <maria.doyle@petermac.org>
Date: 2022-05-27 18:11:35 +0100
Commit message:

 Update github action to Bioc 3.15
 
Package: tidybulk
Commit: c9fef75c13b3a4ddc169a9a9e470ea17ca49d8d7
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2022-04-28 19:25:17 +1000
Commit message:

 fix bug imputation
 
Package: flowViz
Commit: bb81ab4fb54feae00d6cc6327c45da970fd78b05
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 18:27:08 -0700
Commit message:

 merge
 
Package: flowViz
Commit: 55e061bcedf76173ff66cc31201a6f76081a0ba6
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 18:26:24 -0700
Commit message:

 update
 
Package: flowViz
Commit: 2eaf8d90b543fbd33336d9c3e71410d6b67788a5
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:14:20 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 
Package: flowViz
Commit: 7dbf6eaed3a227c70e4b684e7afbcc3959ea704f
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:14:20 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 
Package: openCyto
Commit: 648c5ca9a27d531dedfe4798a47a685c035ae867
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 16:54:06 -0700
Commit message:

 merge
 
Package: openCyto
Commit: 4bd64c02608fe1a82dab9e1bea115dad121e4a6d
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 16:52:01 -0700
Commit message:

 update email
 
Package: openCyto
Commit: 16e66b8c44490289c7823bfa0a80110ff7f883ee
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 16:50:34 -0700
Commit message:

 Merge branch 'devel'
 
Package: openCyto
Commit: 7a7834ab49366cc1b764e85b8be16fbb03df2f11
Author: Mike Jiang <mike@ozette.ai>
Date: 2022-02-01 17:07:33 -0800
Commit message:

 Support empty dims (#235)

* add rmarkdown to Suggests

* fix bioc error

* Support empty dims

* fix_bug 
Package: openCyto
Commit: 783e9ccbd7fa8e9a095c2f3dd713959eba005f12
Author: mikejiang <mike@ozette.ai>
Date: 2022-01-26 18:11:17 -0800
Commit message:

 Merge branch 'master' of github.com:RGLab/openCyto
 
Package: openCyto
Commit: 8c438714e9ded55058786e3f0f6a1b0015304941
Author: Dillon Hammill <dillonh21@live.com.au>
Date: 2021-12-01 15:32:41 +1100
Commit message:

 Minor improvements to openCyto (#229)

* Add data.table method to gatingTemplate().

* Add informative error message when dims are empty. 
Package: ncdfFlow
Commit: 02081a12539276075d504490375446356624d0ad
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 16:48:53 -0700
Commit message:

 update email
 
Package: ggcyto
Commit: fbd1e655e8156f77ce790ad612bd3ffe7be39fae
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 16:45:06 -0700
Commit message:

 update email
 
Package: ggcyto
Commit: 6dbcf57f580b8c5a3106301e7528cce4d8f3a044
Author: mikejiang <mike@ozette.ai>
Date: 2022-05-09 21:39:20 -0700
Commit message:

 R/faust_gating_plot.R
 
Package: ggcyto
Commit: bf4c08ee578278aba1b6496086264c3d6f34bff3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2021-01-27 14:37:25 -0800
Commit message:

 bump
 
Package: ggcyto
Commit: 6612cf4023d80d0b6bf465e4100ff249afd438e9
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2021-01-21 16:53:48 -0800
Commit message:

 Update DESCRIPTION 
Package: ggcyto
Commit: a0ddd2a5d7f46e73d61ea3cfa22895d44b40d67f
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2021-01-21 16:53:15 -0800
Commit message:

 Merge pull request #74 from RGLab/add-license-1

Create LICENSE file 
Package: ggcyto
Commit: c9fb61ccc30382a4b63b39f9f0b19a959f375aa2
Author: Greg Finak <greg.finak@gmail.com>
Date: 2021-01-21 16:52:46 -0800
Commit message:

 Create LICENSE 
Package: ggcyto
Commit: a61a0eed7c9aa4402c8958defdb0cb70a4ece91d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2021-01-08 09:36:29 -0800
Commit message:

 dispatch cytoframe method to flowFrame
 
Package: ggcyto
Commit: 422b961e8f75997f121857071c02c52eb9e074ce
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2021-01-04 15:39:23 -0800
Commit message:

 fix test
 
Package: ggcyto
Commit: 784e61d78a42faf9dfaab007dc11efd2c033393e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2021-01-04 15:26:25 -0800
Commit message:

 manually dispatch cs method to fs
 
Package: ggcyto
Commit: a144925388beba3d2610784f00cc9de0045c4912
Author: Mike Jiang <wjiang2@fredhutch.org>
Date: 2020-11-14 20:23:35 -0800
Commit message:

 Create build.yml 
Package: crisprScore
Commit: ccedbb052b5f80fc223d1a15dd84d170407141e7
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-30 16:43:19 -0700
Commit message:

 Added RuleSet3 sequence
 
Package: crisprScore
Commit: e227c4b2d6df991f0815321f870a991b946626a5
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-30 14:57:16 -0700
Commit message:

 Updating basilisk
 
Package: flowStats
Commit: beb2700bdd365effd87dd2a500bbc9b51b4f2ee3
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 16:33:48 -0700
Commit message:

 bump
 
Package: flowStats
Commit: ec91154454a95d778ab30f7fd60b86a39d4538a8
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-30 16:32:17 -0700
Commit message:

 update email
 
Package: flowStats
Commit: 61a3a803ec3cad0acc23a4d25a3c25a2ab0b06a6
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2022-04-26 15:02:55 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_15 branch
 
Package: flowStats
Commit: 695a6e3f2a8b0dddf0818f97a1ad57f07c37d89e
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2022-04-26 15:02:55 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
 
Package: crisprScoreData
Commit: d81baec36d95bd6cc62361e594c4e175d2500948
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-30 15:56:41 -0700
Commit message:

 Adding rs3 data
 
Package: GenomicDistributions
Commit: 875ee120c34e7ce6687680e6315b31cd01f69431
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-06-30 17:32:23 -0400
Commit message:

 Merge pull request #197 from databio/dev

v1.5.2 
Package: GenomicDistributions
Commit: 51f55a83322bb18a07b75da8fa90fde607cfb71c
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-06-30 17:16:30 -0400
Commit message:

 set up different colors for plotFeatureDist with GRList input
 
Package: GenomicDistributions
Commit: 88203e5b7248363bb0946af6b9732b8f203803f6
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-06-30 16:40:35 -0400
Commit message:

 remove redundant argument
 
Package: GenomicDistributions
Commit: e028837ce52827d00d498ac4e761abd5730c6379
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-06-30 16:24:53 -0400
Commit message:

 update calc chrom plot function for GRlist input
 
Package: GenomicDistributions
Commit: 36056387a487ba2ca24837711616697ba4cf5798
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-06-30 16:15:41 -0400
Commit message:

 Update DESCRIPTION
 
Package: GenomicDistributions
Commit: a16569d09eb7e751261bdbcbd1b3013163443db1
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-06-30 16:08:22 -0400
Commit message:

 big fix with new update

loading reference data from GDData changed
 
Package: GenomicDistributions
Commit: c74fef4f2bff3bef42862a4d811f04549e3f760b
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-06-20 20:51:48 -0400
Commit message:

 partitionList - fix issue if 5' or 3' UTR are NULL
 
Package: GenomicDistributions
Commit: 4ffd6162e9f228ddb9000c5257ee217fd536c8e9
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-06-20 19:56:25 -0400
Commit message:

 remove "reduce" - works without and was triggering error
 
Package: singleCellTK
Commit: 99e76b9c3899ca13df27dea871b9e1b183bb1636
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-30 14:32:34 -0400
Commit message:

 Add master branch to GitHub Action workflows
 
Package: singleCellTK
Commit: c22dbbf9cd60cb853ed12b22f7b532663eb83368
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-30 11:24:27 -0400
Commit message:

 Fix CHECK warning
 
Package: singleCellTK
Commit: 2f1fa6bffbf65d5cf5d83180014f29f4f19c9608
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-30 10:50:21 -0400
Commit message:

 Fix CHECK warning
 
Package: singleCellTK
Commit: 58223dcad79003ca29373ec7ce6c8ed8734adf86
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-29 20:29:14 -0400
Commit message:

 Fix CHECK warning
 
Package: singleCellTK
Commit: 7d46c6eb7386bdd33153f0d3e9417dca2e25b6c3
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-29 19:30:51 -0400
Commit message:

 new version 2.7.1
 
Package: singleCellTK
Commit: f0b0d74b60ddab07b667b8c4bc35f77a5b4b2679
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-28 18:07:14 -0400
Commit message:

 Fix check errors
 
Package: singleCellTK
Commit: fc7a1024b865329dbdd30ea4fddb6f8ffeda742b
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-28 16:52:12 -0400
Commit message:

 Fix README
 
Package: singleCellTK
Commit: 976db8699070c1ca6e6cbe90ebea50dbb5d45406
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-28 16:51:30 -0400
Commit message:

 Added more unit tests
 
Package: singleCellTK
Commit: cb664b173af757766b15407a8210991292df4cfc
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-28 11:58:58 -0400
Commit message:

 Merge remote-tracking branch 'bioc/master' into devel
 
Package: singleCellTK
Commit: 2b06c0eeb5e1e04abec71833c6a509b08b9d4aaa
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-25 18:18:49 -0400
Commit message:

 roxygen
 
Package: singleCellTK
Commit: 2f8d6a0effd5c53884e1e094d4e6f09ae1b268f6
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-25 17:35:08 -0400
Commit message:

 Update documentation, together with minor bug fixes
 
Package: singleCellTK
Commit: b8cd449981aa2ae314c031e0043e8837a70ce396
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-23 17:59:06 -0400
Commit message:

 Update documentation of workflow related to new HVG and scaling scheme
 
Package: singleCellTK
Commit: 18a0f0e66741532afb628da4fd25cfd63243faba
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-23 10:38:52 -0400
Commit message:

 Fix CHECK and BiocCheck
 
Package: singleCellTK
Commit: 408838a087e0c65e5c62ca0641bcc117beac969c
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-22 21:49:13 -0400
Commit message:

 upgrade R 4.2.0
 
Package: singleCellTK
Commit: bf4524f089fcfcb7626bba790b9705a83713fec7
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-22 16:55:48 -0400
Commit message:

 Refine changes previously made, and minor bug fixes
 
Package: singleCellTK
Commit: d3b410fcee1faf0549c74eb9167226010b7b5b4e
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-18 08:35:21 -0400
Commit message:

 Update UI according to the last commit
 
Package: singleCellTK
Commit: 007a2c8d79cb7bb24d71bd741a3e2252014374d5
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-16 14:54:41 -0400
Commit message:

 Efficiency and user experience improvement & BUG fixes for TSCAN workflow
 
Package: singleCellTK
Commit: 497cbfb4a1c1fe69aacee9272526ca70938d9b90
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-14 13:30:54 -0400
Commit message:

 Reformat the use of withConsoleMastRedirect; A few UI bug fixes
 
Package: singleCellTK
Commit: d401387bc9e458280ed5a7090ef98aaf5aa8ca04
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-12 11:04:58 -0400
Commit message:

 Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel
 
Package: singleCellTK
Commit: fadfb773d0367706c0ad63c74b5e1a1992666478
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-12 11:03:33 -0400
Commit message:

 Minor UI fixes
 
Package: singleCellTK
Commit: b0f8638d1d0af728df1de589f8e8be3e2a6c4e30
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-06-11 17:40:49 -0400
Commit message:

 Merge pull request #600 from npervaiz/devel

Import data UI modified 
Package: singleCellTK
Commit: 388b4b98b177184e0fa71fe6301345dddc823544
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-06-10 11:28:31 +0200
Commit message:

 minor tweak fixed
 
Package: singleCellTK
Commit: cc19b5c6dff3a5ac91408b40deddaa799495e16a
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-06-10 10:55:45 +0200
Commit message:

 Merge branch 'devel' of https://github.com/npervaiz/singleCellTK into devel
 
Package: singleCellTK
Commit: 9f17a6fbf92f54dcdc795bf9fa56cfa70a9bbf67
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-06-10 10:55:33 +0200
Commit message:

 Import data UI modified
 
Package: singleCellTK
Commit: 3bf995b93c9298401e5f2fd69309fa1fc1d96e01
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-06-09 09:21:22 -0400
Commit message:

 Merge pull request #599 from mvfki/devel

IMPORTANT BUG FIXES & Finished A La Carte Workflow Tutorial 
Package: singleCellTK
Commit: 4ec62125dfd749b4d376e25962d6e3f47638b81e
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-07 22:26:15 -0400
Commit message:

 Finished a la carte workflow UI+console tutorial
 
Package: singleCellTK
Commit: 645f92e931d572241203ca85fd6dadc488004c39
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-06 09:50:41 -0400
Commit message:

 IMPORTANT BUG FIXES
 
Package: singleCellTK
Commit: c60f1a842d241e40b62a6b633629b75805476b17
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-01 15:35:21 -0400
Commit message:

 Merge upstream and fix conflict
 
Package: singleCellTK
Commit: ecc0e9c22455965afc19f0afd38f6a954cd75511
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-06-01 15:17:48 -0400
Commit message:

 Update A La Carte Workflow tutorial UI part
 
Package: singleCellTK
Commit: 278fde5ad6f9fc145c6bf09912ecb5e3ba57a968
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-06-01 10:09:50 -0400
Commit message:

 Merge pull request #598 from irzamsarfraz/devel

Refactor due to seurat scaling 
Package: singleCellTK
Commit: e44c3271e1fc95631edda75f67d89e9e5a959bf5
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-06-01 17:17:15 +0500
Commit message:

 doc fixes
 
Package: singleCellTK
Commit: 7b825068b6c624e493fe716678ea2cc2e4aa6329
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-06-01 12:29:08 +0500
Commit message:

 Re-indent and re-format code
 
Package: singleCellTK
Commit: 33be31605ba19770a51496abc9fcdfde25e293e6
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-06-01 12:24:51 +0500
Commit message:

 Minor fixes
 
Package: singleCellTK
Commit: 66ec074255f2b1543bd7fa1771c0a9bca87cc74b
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-06-01 02:42:50 +0500
Commit message:

 Updates to seurat scaling
 
Package: singleCellTK
Commit: 71ca398086f01a5dd56ad7a3fb49e77f8a47175e
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-06-01 00:19:38 +0500
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
 
Package: singleCellTK
Commit: 2939876e951b0a26347ca8578b001a83deb1163a
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-06-01 00:18:33 +0500
Commit message:

 Some fixes due to new seurat scaling mechanism
 
Package: singleCellTK
Commit: cd24c4e7589b1c9210b17b8aad6def463a81e757
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-30 18:53:42 -0400
Commit message:

 Update feature selection related functions
 
Package: singleCellTK
Commit: ce2f68ec466da4e9b003bcc6d2068701628df04b
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-30 01:23:23 +0500
Commit message:

 Fixed seurat scale data
 
Package: singleCellTK
Commit: e6aed25ce12a04634dd0574c067fe44b70a1aeee
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-29 16:18:13 -0400
Commit message:

 Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel
 
Package: singleCellTK
Commit: 3ca054ed9294cf7e184fad8ecf21ab05327fe10e
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-29 16:18:04 -0400
Commit message:

 Updating A La Carte Workflow Tutorial
 
Package: singleCellTK
Commit: 14e9c5c5ea31ef8e84622156a8edb46b09576840
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-05-26 18:00:32 -0400
Commit message:

 Merge pull request #597 from npervaiz/devel

TSCAN example case bug fixed 
Package: singleCellTK
Commit: 09a8d3ee091bca3a71bfa3f5a183deb85e15b83a
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-05-26 19:22:30 +0500
Commit message:

 TSCAN example case bug fixed
 
Package: singleCellTK
Commit: 99cbb22d9206b3d9e47bd2a0e42e92918f62b901
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-24 21:21:23 +0500
Commit message:

 Fixed conflicts

Merge remote-tracking branch 'upstream/devel' into devel

# Conflicts:
#	inst/shiny/server.R
#	inst/shiny/ui_05_1_diffex.R
#	inst/shiny/ui_05_2_findMarker.R
 
Package: singleCellTK
Commit: 196fd25ba8aecac2f5d65b8998a3574102546d37
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-24 20:25:29 +0500
Commit message:

 Some updates
 
Package: singleCellTK
Commit: d11fa26f1b8df50e659c309867372d3b31aaa8fe
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-05-24 10:17:23 -0400
Commit message:

 Merge pull request #596 from mvfki/devel

A BUNCH of UPDATES 
Package: singleCellTK
Commit: 989bff0c2a006ecb7868ee563086b13c1e3368fc
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-23 17:44:30 -0400
Commit message:

 Fix check error
 
Package: singleCellTK
Commit: 4611a40dade667aa2fd3d2b1a37cc7c290bd5e81
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-23 17:23:14 -0400
Commit message:

 Add params of dimreduce to metadata & minor updates for clustering funcs
 
Package: singleCellTK
Commit: 87eb03afab33174358f544ca7c478cd0bb0d2bef
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-23 14:48:24 -0400
Commit message:

 Update HVG PCA UMAP cluster UI
 
Package: singleCellTK
Commit: 57aa02ae83105e176caa239f76f5a2657d863fdb
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-21 14:52:20 +0500
Commit message:

 re-enabled seurat tab lock
 
Package: singleCellTK
Commit: 6d75dab333a6629ba0d28687833fbf317607afa7
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-21 03:22:54 +0500
Commit message:

 Run scaling on the go for seurat tab
 
Package: singleCellTK
Commit: 3269f038a090c02f43b4d7fd9267ef9a7fae0e8b
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-20 10:24:52 -0400
Commit message:

 Merge upstream and fix conflicts
 
Package: singleCellTK
Commit: 3c69e4889b207dd227437edfc6a7f9799c953395
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-20 10:21:21 -0400
Commit message:

 Add UI tutorial screenshots
 
Package: singleCellTK
Commit: 4455e626416eb016593846a118614325fe7afd60
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-20 10:19:31 -0400
Commit message:

 Draft UI tutorial
 
Package: singleCellTK
Commit: ef10cb29eae3e95053b5f7793863dbca054147ea
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-20 10:07:18 -0400
Commit message:

 Function updates for HVG, PCA, UMAP and TSNE
 
Package: singleCellTK
Commit: 4fa83ae41bd9cc104abc2944f0c302058fd15a06
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-20 00:26:43 +0500
Commit message:

 Updates
 
Package: singleCellTK
Commit: 3ea40042f861e32c569baea3f98d443dca4d57a8
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-05-19 10:38:58 -0400
Commit message:

 Merge pull request #594 from npervaiz/devel

notification spinner added to UI 
Package: singleCellTK
Commit: 92aa5f9558e1b9f3f102c9463aca47e0aecc1e3f
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-05-19 17:08:55 +0500
Commit message:

 edits in notification spinner
 
Package: singleCellTK
Commit: 158a64f6bf392aa29723218b981aa1f9d3cf3ba7
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-05-19 17:00:46 +0500
Commit message:

 notification spinner in UI with minor changes
 
Package: singleCellTK
Commit: 15bce2589fa54a4996314ff082b190592cc483c3
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-05-18 21:31:57 +0500
Commit message:

 notification spinner added to UI
 
Package: singleCellTK
Commit: c473656034ccdba29792070c355e15dc2b3f1a91
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-13 19:29:45 -0400
Commit message:

 Fix R CMD check error
 
Package: singleCellTK
Commit: 51b7baf6d7c4fc8a4db04ab67fc137b5195978d7
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-13 18:20:07 -0400
Commit message:

 Update doc accordingly
 
Package: singleCellTK
Commit: 725ad206d7adace5e4040d41d075bf69d2d56c6f
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-13 17:50:39 -0400
Commit message:

 Update volcano plot func to support featureDisplay setting; update this feature for all other DEG UI
 
Package: singleCellTK
Commit: 5dc5938b976f4157503723e174de9004c69d37f4
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-13 16:07:00 -0400
Commit message:

 apply global displayFeature setting to DEG heatmap
 
Package: singleCellTK
Commit: 4bbed9d93c723f6c6cbaa3baa84356bbba561b24
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-12 17:35:00 -0400
Commit message:

 Update clustering documentation accordingly
 
Package: singleCellTK
Commit: 6a491cbdfadee4765502c9ae63f78797a2c32370
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-12 12:40:10 -0400
Commit message:

 Update clustering UI accordingly
 
Package: singleCellTK
Commit: 6260d088b877130c6f71927eb4afca6b21dad115
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-11 17:30:49 -0400
Commit message:

 Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel
 
Package: singleCellTK
Commit: 3d74f74e0a5902da2b490a9f9de17d7c2567c71f
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-05-11 17:30:32 -0400
Commit message:

 Add Leiden option for runScranSNN; related bug fixes
 
Package: singleCellTK
Commit: 9bc8dee72d3675473e75eb4f7e172c4a30376c35
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-05-11 16:15:09 -0400
Commit message:

 Merge pull request #593 from npervaiz/devel

new example dataset added 
Package: singleCellTK
Commit: 17197cc98bc30f62f1f3211c23e2d6406984e6cd
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-05-11 13:45:43 +0500
Commit message:

 New example dataset added
 
Package: singleCellTK
Commit: c31c1d25f343f691124844b999e820e8cdc78be4
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-05 21:00:44 +0500
Commit message:

 Merge upstream

Merge remote-tracking branch 'upstream/devel' into devel

# Conflicts:
#	inst/rmarkdown/seurat/reportSeuratResults.Rmd
 
Package: singleCellTK
Commit: b5237f8df55a7ba3df3b3fea424b29b5b360a4d9
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-05-05 18:34:40 +0500
Commit message:

 import new example data
 
Package: singleCellTK
Commit: 17dd5b6c857793ac65772fa655f1c4c079f521ed
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-03 16:01:13 +0500
Commit message:

 Minor update
 
Package: singleCellTK
Commit: 4f48619253c5542b82eff6071bf5e1c3e0954c2c
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-03 14:53:06 +0500
Commit message:

 Updates to module filter
 
Package: singleCellTK
Commit: dd7d0e0abaa937705d95739796d781b988154b87
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-02 03:01:59 +0500
Commit message:

 Added module filter to diffex
 
Package: singleCellTK
Commit: 19d2be3d313203442a9bb591ef1eb3c264ff18c4
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-05-01 21:39:46 +0500
Commit message:

 Updates to module filter and added it to find markers tab
 
Package: singleCellTK
Commit: 07829f44237521beddac3c697bf8b1697ad6e758
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-04-29 19:08:42 -0400
Commit message:

 Merge pull request #591 from npervaiz/devel

documentation edits 
Package: singleCellTK
Commit: f34b2ba63ddbd184a38678eecf351f22ffa5c143
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-04-29 21:27:18 +0500
Commit message:

 edits in TSCAN function name
 
Package: singleCellTK
Commit: 75217830529187d98b7fb3d63b485893792ed24c
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-04-29 15:21:57 +0500
Commit message:

 documentation edits
 
Package: singleCellTK
Commit: 2aa4daf296fa5b5ccd5499ab105e2d4bd43d4034
Author: npervaiz <36128281+npervaiz@users.noreply.github.com>
Date: 2022-04-29 14:24:35 +0500
Commit message:

 Merge branch 'devel' into devel 
Package: singleCellTK
Commit: 884944b6680b391e1f2660d0bd76145e04cef424
Author: nida pervaiz <nidapervaiz27@gmail.com>
Date: 2022-04-29 11:58:27 +0500
Commit message:

 documentation of TSCAN added
 
Package: singleCellTK
Commit: ffd57372470452de7fe0dddbeb21c40b8d7ad6c1
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-04-28 12:22:52 -0400
Commit message:

 Merge branch 'master' into devel
 
Package: singleCellTK
Commit: 1bd1eb06468a5d46100e998c0bb3c86c86033246
Author: Yichen Wang <wangych@bu.edu>
Date: 2022-04-28 12:21:44 -0400
Commit message:

 new version 2.6.0
 
Package: singleCellTK
Commit: b95f0e4c81416476317060786f01d579e5dfdce1
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-04-27 14:49:21 -0400
Commit message:

 Merge pull request #589 from salzcamino/master

Fix Seurat Report knit 
Package: singleCellTK
Commit: 1b5bcd6bfe0fe7b0531e8c813c9b4922310f22d8
Author: Salam AlAbdullatif <salamha@bu.edu>
Date: 2022-04-27 11:50:21 -0400
Commit message:

 Merge pull request #35 from compbiomed/devel

Devel 
Package: singleCellTK
Commit: a360ad8974228ea896bae937bae3854498e86660
Author: salzcamino <salamha@bu.edu>
Date: 2022-04-27 11:46:39 -0400
Commit message:

 fix seurat report knit error
 
Package: singleCellTK
Commit: 68603b62e4a9bd0cc1c30b6aca2b730ffa9e20ae
Author: Salam AlAbdullatif <salamha@bu.edu>
Date: 2022-04-27 11:15:00 -0400
Commit message:

 Merge pull request #34 from compbiomed/master

upstream 
Package: singleCellTK
Commit: 023e69999b4dcd9f24a6e602fa673466599b00c3
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-04-26 16:26:15 +0500
Commit message:

 Updates to seurat report
 
Package: singleCellTK
Commit: 4ff948d8b8180afe236ead6bc4ba788db16c3fc7
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2022-04-23 09:52:29 -0400
Commit message:

 Merge pull request #588 from irzamsarfraz/devel

Fixed showSession issue with seurat reports 
Package: singleCellTK
Commit: ec708e7db574df4f755b05b42cca47e1a4be0d64
Author: Irzam Sarfraz <irzam9095@gmail.com>
Date: 2022-04-23 16:37:33 +0500
Commit message:

 Minor updates to seurat reports
 
Package: fishpond
Commit: a42e45d32dde0d793bcf954e13341bced5afd33a
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-30 12:32:29 -0700
Commit message:

 small vignette tweaks
 
Package: fishpond
Commit: 00d64ef1fa633839eb061f0b2a92cd23f28086c2
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-30 09:05:01 -0700
Commit message:

 remove library call for scran
 
Package: CDI
Commit: 4b96df44faffda179348f4cf2530c8416e19a518
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 13:48:44 -0400
Commit message:

 rm DS_Store:
 
Package: CDI
Commit: c67824786aa4ecdf53f5183314762f2e015a77fd
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 13:47:43 -0400
Commit message:

 DES
 
Package: CDI
Commit: 7e7a942fb822155cf995c4ffb61a5ee3343508a8
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 13:46:31 -0400
Commit message:

 DES
 
Package: CDI
Commit: 3db041339de396c00146eedd056c6a6e4e5520c8
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 13:45:57 -0400
Commit message:

 equal last
 
Package: DESeq2
Commit: 37fad26636ba0d3582017f1bae318eca91461d95
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-30 10:44:36 -0700
Commit message:

 fix docs, thanks igordot
 
Package: CDI
Commit: f72eaab7174bddba49787d79f07fc8cb30d6141f
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 13:08:37 -0400
Commit message:

 equal
 
Package: CDI
Commit: ca5d89b718356d8a1eff58602d9cbdc0a0a27647
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 12:33:31 -0400
Commit message:

 minor
 
Package: CDI
Commit: 2dd35bbb6fccb2d3170168bd00ed2332fee78214
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 12:15:26 -0400
Commit message:

 equal sign again
 
Package: trackViewer
Commit: 6be3df9605f8ab730d778a22faad716f88a12600
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-30 12:11:53 -0400
Commit message:

 fix a typo.
 
Package: trackViewer
Commit: 835f138ab7a3de0b2ba096fa15a4065fad4d5ceb
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-30 11:59:49 -0400
Commit message:

 add support for motif logo for lollipop plot.
 
Package: CDI
Commit: 2a45189d954e01823249943dfc9ac81d866e30c1
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 11:56:14 -0400
Commit message:

 bumper
 
Package: CDI
Commit: 433d292371cf5ff33be3c8126699b51a22e48506
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 11:55:37 -0400
Commit message:

 rm equal signs
 
Package: cbaf
Commit: c34262fbd9859cbd216a85c9d4b3971f88d03777
Author: Arman <shahrisa.arman@hotmail.com>
Date: 2022-06-30 20:19:22 +0430
Commit message:

 - Fixing an incompatibility issue with cBioportalData package
 
Package: CDI
Commit: 227c0ea9ee56336708c05f3f53c899c22117906f
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 11:38:52 -0400
Commit message:

 rm equal signs
 
Package: CDI
Commit: 2c322afc6ca4df1a903c9bd490f84fd98847d427
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 11:13:01 -0400
Commit message:

 rm equal sign
 
Package: CDI
Commit: 890287a7b04c5a489912019458ac0ff44f16d6e4
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 11:11:52 -0400
Commit message:

 description rev
 
Package: CDI
Commit: 1c8c9abe8ff7d4fdf194417c63446a689cae7763
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 11:03:18 -0400
Commit message:

 rm ds
 
Package: CDI
Commit: 87024e008bbc41e2747590e208a446c7b6369b9d
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 10:59:53 -0400
Commit message:

 Merge branch 'master' of https://github.com/jichunxie/CDI
 
Package: CDI
Commit: 82c1aac6aaba8d9a8fe1a2d672fcf4fb74208bd7
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-30 10:47:03 -0400
Commit message:

 Merge pull request #5 from jichunxie/main

merge 
Package: CDI
Commit: dface86f795a958378d94ff9264c2080ba5f3f68
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 10:46:09 -0400
Commit message:

 add DES
 
Package: CDI
Commit: 2772628a191ddb25d1bba101e3d955561648f4ce
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 10:33:59 -0400
Commit message:

 Merge branch 'main' of https://github.com/jichunxie/CDI
 
Package: CDI
Commit: e0771d5e0ce7ce9d46f9c0b86228da3a23dd3ffa
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 10:33:43 -0400
Commit message:

 resolve
 
Package: CDI
Commit: 455abe555f550206570352120fc96654f560afb1
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-30 10:27:18 -0400
Commit message:

 Merge pull request #4 from jichunxie/master

Merge pull request #3 from jichunxie/main 
Package: CDI
Commit: 3371fa3964325e784d362e4bf6e395d10acddd6f
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-30 10:25:21 -0400
Commit message:

 Merge pull request #3 from jichunxie/main

Merge pull request #2 from jichunxie/master 
Package: CDI
Commit: aa541c5bd860fc6b727a71e115415aa0d4508117
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-30 10:10:50 -0400
Commit message:

 Merge pull request #2 from jichunxie/master

Master 
Package: CDI
Commit: 3d501b42dbd9878bdfe1fe103e4858a04277d15a
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-30 10:10:32 -0400
Commit message:

 Merge branch 'main' into master 
Package: CDI
Commit: 688b4f407c4c74e3c8bb670a34c3d57dbcdc9e6a
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 10:03:24 -0400
Commit message:

 09903
 
Package: CDI
Commit: 628ef8887a6183d092d9e5e02ffc56a25da947ca
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-28 18:00:07 -0400
Commit message:

 Delete .DS_Store 
Package: CDI
Commit: 5936c3f32d40cf94a6fdfb274deb67748833daae
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-28 17:59:51 -0400
Commit message:

 Delete .DS_Store 
Package: CDI
Commit: 6912711c41c2009c3f83df4a3a952a06da497dbc
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-28 17:59:34 -0400
Commit message:

 Delete .DS_Store 
Package: CDI
Commit: d9d1aa029e99c08dd729d560654b5824291fe2d8
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2022-06-28 17:59:23 -0400
Commit message:

 Delete .DS_Store 
Package: CDI
Commit: 3dc9e9c0fc6132bb6dfee239fb5f2473d572e5c5
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2021-12-09 09:44:45 -0500
Commit message:

 Update README.md 
Package: CDI
Commit: 3fc35c9a69282ba0ba4618a2b34d5b8de674b4c8
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2021-12-09 09:36:58 -0500
Commit message:

 Merge branch 'main' into main 
Package: CDI
Commit: a2c7c01a46c4993acf926608184c24eddb398bd0
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2021-12-06 20:22:15 -0500
Commit message:

 version number
 
Package: CDI
Commit: 37013275657d4c2feb2048b3b77449d08fb91328
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2021-12-06 18:31:17 -0500
Commit message:

 Merge pull request #1 from jichunxie/master

Master 
Package: CDI
Commit: 4c93e949622d7f33d964bd744bfc7e2bfb076fd9
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2021-09-17 17:04:13 -0400
Commit message:

 Create README.md 
Package: CDI
Commit: 41927c6a4856806b911e4168552e2aa9376ff31c
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2021-09-17 17:01:50 -0400
Commit message:

 Delete README.md 
Package: CDI
Commit: 73235a509e25c89c9789c1da12fc05f68cf7a805
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2021-09-17 17:00:50 -0400
Commit message:

 Update README.md 
Package: fishpond
Commit: 2755518e7c18a122e9e9439dc555605a55d327db
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-30 07:59:56 -0700
Commit message:

 update vignette re scaling
 
Package: CDI
Commit: 7a2929e02c1a04b75df4836b1268d134d59ebdd8
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 10:49:53 -0400
Commit message:

 bump
 
Package: CDI
Commit: b186e9728dcca69d0f3a91282fe7f4045c46fcb2
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 10:49:10 -0400
Commit message:

 tmp
 
Package: CDI
Commit: a03165a9dafd03d91437f617aeb4aaa774f8a579
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-30 10:48:05 -0400
Commit message:

 tmp
 
Package: OncoSimulR
Commit: 5505160f5e9b3beb7bfce0566c306fde2d39af5b
Author: ramon diaz-uriarte (at Phelsuma) <rdiaz02@gmail.com>
Date: 2022-06-30 14:59:27 +0200
Commit message:

 3.99.3: failing a test in Mac OS
 
Package: MSA2dist
Commit: 4d5aedddcfacf84ca7e71f13714d6fbed0de0e3d
Author: Kristian Ullrich <ullrich@evolbio.mpg.de>
Date: 2022-06-30 14:17:50 +0200
Commit message:

 #added cds2codonaln
 
Package: CTSV
Commit: 08e792ed81d199e36b0576308e81acd4543afd0a
Author: jinge.yu
Date: 2022-06-30 16:53:41 +0800
Commit message:

 "delete files"
 
</div>
Package: CTSV
Commit: 232ca2c564ef126a3ab6bc17e9f68f0fa06b5187
Author: jinge.yu
Date: 2022-06-30 16:41:42 +0800
Commit message:

 0.99.9
 
</div>
Package: CTSV
Commit: 5df6f34eb90538b98856b7ff734a5a847a3411ee
Author: jinge.yu
Date: 2022-06-30 16:37:08 +0800
Commit message:

 "Bump version to 0.99.9"
 
</div>
Package: mnem
Commit: d307a121fa06eb1a6ef3b41bdac601b594104b3a
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-06-30 10:28:40 +0200
Commit message:

 forgot to add moreboxplot help file
 
Package: imcdatasets
Commit: c342a47234f4c5c19b7532d6237761fb7eeea73b
Author: Nicolas Damond <nicolas.damond@gmail.com>
Date: 2022-06-30 08:26:41 +0000
Commit message:

 add deprecation notes from 1.4.1
 
Package: imcdatasets
Commit: 9b0d63d9697ed3ed808f2fc89b65d0da74a87e84
Author: Nicolas Damond <nicolas.damond@gmail.com>
Date: 2022-06-29 16:29:51 +0000
Commit message:

 fix deprecation notes
 
Package: nempi
Commit: f5a9ae34c7c74f0fe5647d3dcbafa7e3f400fb23
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-06-30 10:26:37 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: epiNEM
Commit: cd268603f7d826bf6954f3cf2a1e244ae6c4ead2
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-06-30 10:25:27 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: bnem
Commit: e472cb1ae963ef1fc39e0ee1e4011a1becb78829
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-06-30 10:24:10 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: mnem
Commit: 23c40dd72349876fd4804d29082605ebb7f06356
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-06-30 10:20:17 +0200
Commit message:

 improved special boxplot and added it to export
 
Package: mnem
Commit: 5f05242c8fc75c0a49f28532ff57ae6433c4fe0a
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-06-30 10:09:41 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: mnem
Commit: 08036a318fe738c7eac57119ba5f5f7964c4cd2b
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-03-16 15:32:06 +0100
Commit message:

 make boxplots transparent if violin plots are added; better description of plotDnf
 
Package: mnem
Commit: fba6f7bc1f8049aeed75e7479bffd118c101b6e8
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-03-11 17:31:53 +0100
Commit message:

 some boxplot bugfxining
 
Package: OmnipathR
Commit: 679bb79e319af246a16968d27d64d8d6937a331a
Author: deeenes <turei.denes@gmail.com>
Date: 2022-06-30 00:45:17 +0200
Commit message:

 v3.5.5 - version bump
 
Package: OmnipathR
Commit: 45e62981ecc35b654f51de62a57c7a56e78a3afa
Author: deeenes <turei.denes@gmail.com>
Date: 2022-06-30 00:44:34 +0200
Commit message:

 wrong first argument in `count_references`; fixes #43
 
Package: crisprScore
Commit: 0e4d3fc31eefd920c23cfedb8174084c314f4049
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-29 14:25:14 -0700
Commit message:

 Updated vignette
 
Package: crisprScore
Commit: 3c51985370d69dab9bdb92d945934fa7fb05513e
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-29 14:10:18 -0700
Commit message:

 Bumping version up
 
Package: crisprScore
Commit: bcfa4011545461265d403f3f4024b2f9965485c1
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-29 14:08:58 -0700
Commit message:

 Readu to merge
 
Package: crisprScore
Commit: c325cb35cb229eeef3b6287e0a0865609dc4097b
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-29 12:54:33 -0700
Commit message:

 Adding DeepSpCas9
 
Package: iSEEu
Commit: 1c06b9f0681c1c622563d0c0c6ef75768055a252
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2022-06-29 18:19:58 +0100
Commit message:

 fix git issue of safe directory (#107)

 
Package: iSEEu
Commit: 49ef55cf9a8099f29ae1786102697c2be36f9d8d
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2022-06-29 17:26:12 +0100
Commit message:

 udpdate badges based on biocthis (#106)

 
Package: crisprScore
Commit: 8b60ef3ffe3e14b0c9e004835d1e8b8dd1f41f2b
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-29 10:07:49 -0700
Commit message:

 Updated manual
 
Package: factR
Commit: 7d903e924873e063fb9c620c9408a5bd41192214
Author: Fursham Hamid <fursham.h@gmail.com>
Date: 2022-06-29 16:48:38 +0100
Commit message:

 Switched off AHub dl for BioCheck
 
Package: enhancerHomologSearch
Commit: 813cd5c2601c6b89bc9cacc316126beec8150b15
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-29 11:22:04 -0400
Commit message:

 improve the speed for searchTFBP
 
Package: enhancerHomologSearch
Commit: 853f65a1c8b5b921b16ceb8598c42cf101934b78
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-28 17:39:17 -0400
Commit message:

 fix the issue for sample size is bigger than shuffled sequences.
 
Package: enhancerHomologSearch
Commit: 23873f8c7092cfe6c6f2a64e3a231e854668f10c
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-28 17:08:45 -0400
Commit message:

 add ushuffle
 
Package: enhancerHomologSearch
Commit: c0d0d37bd3d3de64dce4d1a5ac9cc510505a30e5
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-28 12:54:55 -0400
Commit message:

 Add reverseComplement search for conservedMotifs.
 
Package: iSEEu
Commit: ebb623635489dbf6fb3e454e687265c6f01ab8cc
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2022-06-29 15:39:47 +0100
Commit message:

 use bioc-devel docker image for github action (#105)

* use bioc-devel docker image

* fix name of docker repo 
Package: TPP2D
Commit: f4fc4dbba8c0d2c83a7a49a0b0da45a505fbec93
Author: Nils Kurzawa <nils.kurzawa@embl.de>
Date: 2022-06-29 16:30:43 +0200
Commit message:

 added a filtering step in data import to prevent NA entries
 
Package: OncoSimulR
Commit: 4001b0c51cef3ea936607dffb7f97309f9582ccc
Author: ramon diaz-uriarte (at Phelsuma) <rdiaz02@gmail.com>
Date: 2022-06-29 15:37:33 +0200
Commit message:

 3.99.2
 
Package: OncoSimulR
Commit: 0dae6b3f52c78e4356bd656e2bf7d4046f4e4958
Author: ramon diaz-uriarte (at Phelsuma) <rdiaz02@gmail.com>
Date: 2022-06-29 14:44:37 +0200
Commit message:

 3.99.2
 
Package: GRaNIE
Commit: 6d7dcf841fdd7a010ea8742abe83be2b4568ddd9
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-06-29 14:53:15 +0200
Commit message:

 version bump in devel
 
Package: GRaNIE
Commit: 11ee342902b1ec387c006b1b06915523304d7d8d
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-06-29 14:51:06 +0200
Commit message:

 Removed the constraint to only use 50% of the cores max for parallel tasks
 
Package: GRaNIE
Commit: 6d331b218c7b4bc1d0ff14ce5ec7746c329731c9
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-06-29 14:11:52 +0200
Commit message:

 version bump in devel
 
Package: GRaNIE
Commit: c1c65b2c577c06c7b501b4d2e965c185b83fbe2e
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-06-29 14:10:37 +0200
Commit message:

 bug fix: Documentation related fixes to eliminate warnings during build
 
Package: GenomicScores
Commit: 68c0d0e8d8f1acb42c7522d93e8ec9592a4157ba
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2022-06-29 09:51:39 +0200
Commit message:

 Updated frozen AH resource list
 
Package: CDI
Commit: 779f07c263426b53fc5cc514652ea9474d8286bf
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-28 17:45:34 -0400
Commit message:

 sce, parallel
 
Package: FRASER
Commit: cee9564e491cdbfbedf0d15e657334ecec6cfb8c
Author: Christian Mertes <mertes@in.tum.de>
Date: 2022-06-28 16:53:17 +0200
Commit message:

 version bump 1.9.0 -> 1.9.1
 
Package: FRASER
Commit: 3b9ea8e66fefb8cf026b37f49ac7f1892f6a38c6
Author: Christian Mertes <mertes@in.tum.de>
Date: 2022-06-28 16:49:40 +0200
Commit message:

 Merge remote-tracking branch 'bioc/master'
 
Package: FRASER
Commit: 9830c79cdbedba8ef4d7515b5a6b2b3aee9c5547
Author: nickhsmith <smithnickh@gmail.com>
Date: 2022-06-28 16:47:53 +0200
Commit message:

 add checks for NSR to overlap a split read (#41)

* Add check for non spliced reads
* Bugfix for the merging where some non spliced reads kept within the dataset without a corresponding junction.

Co-authored-by: Smith Nicholas <smith@in.tum.de>
Co-authored-by: Christian Mertes <mertes@in.tum.de> 
Package: FRASER
Commit: 6e2ce01473bd453baabb030760d77e1c131a9a5f
Author: nickhsmith <smithnickh@gmail.com>
Date: 2022-04-07 15:38:33 +0200
Commit message:

 use inclusive cutoffs for aberrant event detection (#37)

Co-authored-by: Christian Mertes <mertes@in.tum.de> 
Package: CDI
Commit: 59197ea8f4fb3e570a7abe7729899a747939d651
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-28 17:22:27 -0400
Commit message:

 readme
 
Package: CDI
Commit: eeedfe33e34a59dd1db2d31e150f88c39644f2e8
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2022-06-28 17:19:58 -0400
Commit message:

 sce,parallel,unittest
 
Package: ATACCoGAPS
Commit: 5d651105b59b007d8836f9ce90651d533ea61fee
Author: rossinerbe <rossinerbe@gmail.com>
Date: 2022-06-28 16:42:56 -0400
Commit message:

 increment version
 
Package: ATACCoGAPS
Commit: 9a6d0bd6167d859d70f13c420251453be0db40f6
Author: rossinerbe <rossinerbe@gmail.com>
Date: 2022-06-28 16:41:42 -0400
Commit message:

 namespace and example fixes
 
Package: ChemmineOB
Commit: 60c786445e87990186f2459ef4d368a509d73f58
Author: khoran <khoran@cs.ucr.edu>
Date: 2022-06-28 12:22:13 -0700
Commit message:

 added comment in vignette about windows comptability
 
Package: cbaf
Commit: cfafb4f0397ed943f5efc2ecfcbe9dd9536b7582
Author: Arman <shahrisa.arman@hotmail.com>
Date: 2022-06-28 23:17:29 +0430
Commit message:

 Correcting a variable name
 
Package: cbaf
Commit: 70d117192b775cafa339458ec3213890732ad735
Author: Arman <shahrisa.arman@hotmail.com>
Date: 2022-06-23 09:47:41 +0430
Commit message:

 - Fixing documantation for oneOfEach
 
Package: cbaf
Commit: 36368f830d7856c8f7b4b0b43a56e235f44cc35e
Author: Arman <shahrisa.arman@hotmail.com>
Date: 2022-06-23 09:23:55 +0430
Commit message:

 - adding oneOfEach functionality.
 
Package: GRaNIE
Commit: 782bb98cb1bc155777adff501c1df2c84ef2f0a0
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-06-28 20:21:08 +0200
Commit message:

 version bump in devel
 
Package: GRaNIE
Commit: 9fc6563e2609faa376438a6e8daeeb8910354569
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-06-28 20:20:40 +0200
Commit message:

 bug fix: Various small important bugfixes
 
Package: SeqVarTools
Commit: 58494fa477bd3afc16a9ecee75a2abecba73acc3
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2022-06-28 10:36:00 -0700
Commit message:

 correct for seqAlleleCount returning NA when no samples selected

seqAlleleCount is called separately for males and females for
sex chromosomes. Previously it would return 0 when no samples
were selected, but as of SeqArray 1.37.1 it returns NA in that
case. Thus the SeqVarData allele count functions were returning
NA in cases where all samples were male or female. Correct for
that by setting count=NA to 0 when selecting samples by sex.
 
Package: signeR
Commit: 020b090c5e7955af56723b557e358adb5fe8eb7d
Author: Renan Valieris <rvalieris@users.noreply.github.com>
Date: 2022-06-28 13:44:55 -0300
Commit message:

 Merge pull request #23 from adefelicibus/fix-doc

fix modules doc 
Package: signeR
Commit: a16201fda4fcfc578a6d76b40005888ab0410d8f
Author: Alexandre Defelicibus <adefelicibus@gmail.com>
Date: 2022-06-28 13:43:46 -0300
Commit message:

 bumped
 
Package: signeR
Commit: c92ad1509c2a5f9e7f1aec3c9c3005992de2bece
Author: Alexandre Defelicibus <adefelicibus@gmail.com>
Date: 2022-06-27 17:54:42 -0300
Commit message:

 layout improvement
 
Package: signeR
Commit: 3e5b340eebeb47c3a6e58263c9197b345c38bc58
Author: Alexandre Defelicibus <adefelicibus@gmail.com>
Date: 2022-06-27 16:07:09 -0300
Commit message:

 fix modules doc
 
Package: BiocPkgTools
Commit: 4e2d22a963cfce3da6e93574cd82f22c6458be33
Author: Sean Davis <seandavi@gmail.com>
Date: 2022-06-28 16:10:26 +0100
Commit message:

 Merge pull request #61 from jwokaty/add-back-b9-doi

Add back 'B9' in DOI to match older Bioconductor packages 
Package: BiocPkgTools
Commit: eae0bd575686be30c6058bd843bba3cbfce07d9b
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-03-02 13:48:29 -0500
Commit message:

 Add back 'B9' in DOI to match older Bioconductor packages
 
Package: BiocPkgTools
Commit: 3583a542ff17bcfb4147322f4a0d089494e91ead
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-28 09:59:55 -0400
Commit message:

 version bump 1.15.1
 
Package: BiocPkgTools
Commit: d0400958135583fd9b0d529a5e2eeb520938f30d
Author: Marcel Ramos <LiNk-NY@users.noreply.github.com>
Date: 2022-06-28 09:55:31 -0400
Commit message:

 Merge pull request #62 from seandavi/repositoryStats

Add repositoryStats function from AnVIL, credit to @mtmorgan 
Package: BiocPkgTools
Commit: c3fa3dadd0c7bba66970513c68ca0aec8f6afa7a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-17 15:15:21 +0000
Commit message:

 whitespace updates
 
Package: BiocPkgTools
Commit: 2b704ade7d336c833e64cdf0dc498d283a1104e2
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-17 15:15:02 +0000
Commit message:

 update to use RMarkdown in docs
 
Package: BiocPkgTools
Commit: a4022bd4921cb7f389a2437ea700f9a0ff299949
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-17 15:13:55 +0000
Commit message:

 update documentation
 
Package: BiocPkgTools
Commit: c7142e1275b840bcb39bf99a23e093f4008c57f2
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-17 10:29:01 -0400
Commit message:

 add repositoryStats function
 
Package: rhdf5filters
Commit: 925ea843b51059d2cb08e3796bc270819300465c
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-06-28 12:10:36 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/rhdf5filters
 
Package: rhdf5filters
Commit: 697eaa248f4227f00ff30b952b6abfbac87019aa
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-02-01 11:28:37 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/rhdf5filters
 
Package: rhdf5filters
Commit: 7619144d9539e8a5ea635ae70b1a5704ef09597b
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-07-21 10:48:44 +0200
Commit message:

 Fix broken DESCRIPTION file
 
Package: rhdf5filters
Commit: 575fda282ca1e6fb5a7f5e1e12a263dda79e13f6
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-07-12 15:13:38 +0200
Commit message:

 Update package description
 
Package: rhdf5filters
Commit: d200f4eacda87aaadaf391f73477063f5fdd9094
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-07-12 14:22:27 +0200
Commit message:

 Add pkgdown logo
 
Package: rhdf5filters
Commit: e19c4044435400f878639ee2546680334a4b3eb7
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-07-12 14:21:09 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/rhdf5filters
 
Package: rhdf5filters
Commit: 31a97e1630333e0a2d6fa9d9ae089f093832230c
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-04-30 14:12:11 +0200
Commit message:

 Update NEWS.md 
Package: GRaNIE
Commit: 2e9288de1acaa58a9335f972bef9a2b2db081a2a
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-06-28 11:29:27 +0200
Commit message:

 version bump in devel
 
Package: GRaNIE
Commit: d9c91152ae7fb5df16266161d72e08898e396d70
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-06-28 11:28:55 +0200
Commit message:

 bug fix: Various small importnt bugfixes
 
Package: scATAC.Explorer
Commit: 68c5c49d21ec1b9c1adfad221060e58db5b5abe8
Author: Arrian Gibson-Khademi <agibsonk@uwo.ca>
Date: 2022-06-28 00:06:49 -0400
Commit message:

 Merge branch 'main'
 
Package: scATAC.Explorer
Commit: 082b20e490ae273acf190420e9bc2bf5bcddcf5d
Author: Arrian Gibson-Khademi <agibsonk@uwo.ca>
Date: 2022-06-28 00:04:22 -0400
Commit message:

 added 3 new datasets
 
Package: flowCore
Commit: 8f5be04aba19cfd6823f3ded5d4c3f2bbd2d368e
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-27 20:06:07 -0700
Commit message:

 merge
 
Package: flowCore
Commit: 62a5e26a6d2ba43ee36e5779ce8dec6684787cee
Author: Mike Jiang <wenxin.jiang@gmail.com>
Date: 2022-06-27 20:01:54 -0700
Commit message:

 fix Latin encoded keyword in GvHD (#232)


* update email

* rm \x encoded str from GvHD

* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

* bump x.y.z version to odd y following creation of RELEASE_3_15 branch


Co-authored-by: mikejiang <mike@ozette.ai>
 
Package: flowCore
Commit: 56bc6a814c6df5ea0495cedc5624a48d88305c69
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-27 11:56:10 -0700
Commit message:

 update yaml
 
Package: enhancerHomologSearch
Commit: f852a6a56fb98f80451d3f5ec52c5b1167bdab05
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-27 16:33:39 -0400
Commit message:

 fix the issue if more than 2 Enhancers for conservedMotifs.
 
Package: enhancerHomologSearch
Commit: a8c1ba2041f7173b9b69326fe7b188b58d15c199
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-27 16:13:25 -0400
Commit message:

 add html output for conservedMotifs
 
Package: enhancerHomologSearch
Commit: 893ea2a2f11af67828b654b0dd985e24ec793bcf
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-27 11:22:34 -0400
Commit message:

 Add support for HTML output for the alignment.
 
Package: enhancerHomologSearch
Commit: 5e63aae711eea1d6a06be3de7ed2b5e8c6e7d0aa
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-06-24 10:06:04 -0400
Commit message:

 Add support for multiple alignments for alignment function.
 
Package: beer
Commit: f9968d7d1dc21cd7a181a74bff43ef4cd6f2afe7
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2022-06-27 17:00:20 -0400
Commit message:

 added Bayes Factor helper
 
Package: beer
Commit: 33fb3da140396dfb22678997a94232f5e1628a18
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2022-06-27 13:50:29 -0400
Commit message:

 updated workflow to use magick@7
 
Package: beer
Commit: 1d44780cc5e300ed4b456111dff27cdeaa1f61bc
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2022-06-26 14:09:36 -0400
Commit message:

 Bumped version number
 
Package: beer
Commit: 5d24444f614f73c56a29a6b2fbcad7c8f1400bfe
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2022-06-26 13:16:09 -0400
Commit message:

 Added getExpected plot helper
 
Package: BiocParallel
Commit: dfbfd27a4b7327a7ff6246b043fcc79a9330ac37
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-06-27 16:14:13 -0400
Commit message:

 error more explicitly when mc.cores is not coercible to scalar integer

- minor related code clean-up
 
Package: cytolib
Commit: 7aa37f5fc7386b4cfd39f94a79358a755b10b926
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-27 11:50:22 -0700
Commit message:

 merge
 
Package: cytolib
Commit: d975f4000e1093db239e9925928266db448acde7
Author: Mike Jiang <mike@ozette.com>
Date: 2022-06-27 11:45:37 -0700
Commit message:

 Merge pull request #53 from RGLab/fixed-logical-gate-compute

Fixed logical gate compute 
Package: cytolib
Commit: 4e756fc60513f93e3cbd54c1336c8dd591c9a1d4
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-27 11:19:53 -0700
Commit message:

 fix build
 
Package: cytolib
Commit: ab2febe7e21b1cfcc949c59bce702f494927c858
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-27 10:30:16 -0700
Commit message:

 bump
 
Package: cytolib
Commit: a994a3546c29de9019ddd0c752ade17f67e4c03a
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2022-04-26 15:42:38 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_15 branch
 
Package: cytolib
Commit: 040f8124b6ff893c46789ed1873daceb2b25afe2
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2022-04-26 15:42:38 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
 
Package: cytolib
Commit: 14850d1034a74e40cb1e85a990885d8b9c89ee88
Author: mikejiang <mike@ozette.ai>
Date: 2022-06-27 10:27:46 -0700
Commit message:

 fix logical gate recompute issue
 
Package: densvis
Commit: e2c26deae510631686afe6ca45834dac6a50d962
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2022-06-27 18:55:47 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/densvis
 
Package: densvis
Commit: 2b33f355cb534061e113e300474d632d2b30d494
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2022-06-27 18:49:26 +0100
Commit message:

 Merge pull request #6 from Aurelius333/make-Y-init-work

Make the `Y_init` parameter work 
Package: densvis
Commit: abdb2bf580e5e995b1ba26753a5c284ecf0434e9
Author: Ajai Nelson <22969541+Aurelius333@users.noreply.github.com>
Date: 2022-06-26 01:24:21 -0400
Commit message:

 Make the Y_init parameter work

Before this change, it seems like the Y_init parameter isn't actually
used. This commit does the following:

1. Pass the Y_init parameter to densne_cpp.
2. Tell the DENSNE::run function to skip_random_init when init is true.
 
Package: densvis
Commit: 6d1fe5ffe8daf5ef330e42cd16e22252a61b560f
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2022-03-24 00:36:51 +0000
Commit message:

 Updated and working GHA
 
Package: densvis
Commit: f67324e70160bfceb2735afe6597a3a08bf85629
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2022-03-16 14:54:49 +0000
Commit message:

 Genentech bioc action
 
Package: densvis
Commit: bf064ca0814c93b3d094ad5ff04c8edf62ff35e0
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2022-03-01 15:58:22 +0000
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/densvis
 
Package: densvis
Commit: ffd4b2d0ce05aa96643bdcae5d8503ee2b799dd9
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2022-03-01 13:55:24 +0000
Commit message:

 use bioc action
 
Package: densvis
Commit: a73270d27c52454a12b3f09ee765fd6f9af4d610
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2021-10-15 00:57:41 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/densvis
 
Package: densvis
Commit: 063c7f005fc88c933ad79bf431f1852777ef6165
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2021-10-15 00:56:47 +0100
Commit message:

 v1.1.11; bugfix when passing data to Rtsne normalise fn
 
Package: spbtest3
Commit: e71f373f2091f1982aa5d6eeeb8278be1a2270f3
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-06-27 13:48:45 -0400
Commit message:

 change sleep to sys.sleep
 
Package: spbtest3
Commit: bdf8a707a3b482dd0c9c9748162cd34898e73396
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-06-27 13:45:01 -0400
Commit message:

 make a test that takes a long time
 
Package: DESeq2
Commit: 26fb6f41c28aac7e9b6f099ff379b9a4aa587382
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-24 15:12:26 -0700
Commit message:

 add copy of apeglm function to avoid import
 
Package: DESeq2
Commit: 38bebbe4f48e477f92773367170055026680c969
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-24 11:01:58 -0700
Commit message:

 updating vignette
 
Package: DESeq2
Commit: 0e96aebc544a3fcd3541cf90750156b2397d1400
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-23 08:19:54 -0700
Commit message:

 working on tests
 
Package: DESeq2
Commit: 0f2020b69e87a81ea8073f90243169cff11fd459
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-23 06:48:06 -0700
Commit message:

 working on ashr lfc threshold
 
Package: DESeq2
Commit: d01e24ae125c3598dc7610ddbc39ed57793f5533
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-06-16 09:39:19 -0400
Commit message:

 cleaning up for ashr LFC threshold
 
Package: KnowSeq
Commit: 5470502b2e1f5476c5f78199d82e25123d77df59
Author: Daniel Castillo-Secilla <cased@ugr.es>
Date: 2022-06-27 17:23:08 +0200
Commit message:

 Version 1.11.1
 
Package: KnowSeq
Commit: 8ba5c1f41fb95b00f0f6ee6215a53982331f223d
Author: Daniel Castillo-Secilla <cased@ugr.es>
Date: 2022-06-27 17:21:38 +0200
Commit message:

 Version 1.9.2
 
Package: Uniquorn
Commit: db5cef2f9926ebdd9b8a0d37e0ceb9efb24aab3b
Author: ottoraik <raik.otto@hu-berlin.de>
Date: 2022-06-27 14:43:54 +0200
Commit message:

 update
 
Package: Uniquorn
Commit: d0681b4db9ae27dbf8f961ef68e0682569b9acc6
Author: mftth <mfattohi@gmail.com>
Date: 2022-05-17 12:18:50 +0200
Commit message:

 Merge branch 'master' of https://github.com/RaikOtto/Uniquorn
 
Package: Uniquorn
Commit: ff034d789519b6e42e6d80890e369b838f531944
Author: mftth <mfattohi@gmail.com>
Date: 2022-05-17 12:18:17 +0200
Commit message:

 update
 
Package: CTSV
Commit: 9162e529beb9e26289c2db47b62ec716f12e683b
Author: jinge.yu
Date: 2022-06-27 20:15:44 +0800
Commit message:

 "Bump the version to 0.99.9"
 
</div>
Package: dupRadar
Commit: 9ff29f74eeb9aec0896a14c26d519c55a96ab02d
Author: ssayols <sergisayolspuig@gmail.com>
Date: 2022-06-27 14:13:36 +0200
Commit message:

 merge with bioc devel
 
Package: dupRadar
Commit: 3b8903695446fd3bf2fa783a2d9d540031a7091e
Author: ssayols <sergisayolspuig@gmail.com>
Date: 2022-06-27 14:12:06 +0200
Commit message:

 version bump
 
Package: dupRadar
Commit: 09dc071e5314150077dc6f8ccdc8bee311fd0939
Author: ssayols <sergisayolspuig@gmail.com>
Date: 2022-06-27 14:11:00 +0200
Commit message:

 roxygenize documentation
 
Package: dupRadar
Commit: cadff6e6ef1bc29f02cedb362e608955ec063181
Author: ssayols <sergisayolspuig@gmail.com>
Date: 2021-12-07 09:42:42 +0100
Commit message:

 altmetric badge
 
Package: dupRadar
Commit: 9abae8027e7b9d77e0f716d606ed6ba16a945883
Author: ssayols <sergisayolspuig@gmail.com>
Date: 2021-02-11 16:00:57 +0100
Commit message:

 github pages
 
Package: dupRadar
Commit: ae694c31bb639677f3db9285ea879d0689de51df
Author: ssayols <sergisayolspuig@gmail.com>
Date: 2021-02-11 15:50:03 +0100
Commit message:

 add pkgdown documentation
 
Package: dupRadar
Commit: ab74299e34569ee801ff7aa6b82d325626a71e86
Author: ssayols <sergisayolspuig@gmail.com>
Date: 2020-02-27 11:29:54 +0100
Commit message:

 move project site from Sourceforge to Github
 
Package: rexposome
Commit: f208c75a542e45359768f190e97ae02fd64c169f
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-27 12:56:08 +0200
Commit message:

 bump version
 
Package: rexposome
Commit: a701011a583cff0bc88cf3ed08f646f12c1485f1
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-27 12:52:39 +0200
Commit message:

 added form definition
 
Package: katdetectr
Commit: 4c215611f4f2e8895456d0ec518ff4040bcbb60c
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-27 12:55:47 +0200
Commit message:

 update vignette for omikli, DBS and MBS
 
Package: katdetectr
Commit: 66a3a1438dbbffcc69a205c6ca43fb1b2fd9144b
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-27 10:26:05 +0200
Commit message:

 version bump
 
Package: katdetectr
Commit: 159d17af059b4331dd5d1a426346a14b7c45ca08
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-27 10:25:51 +0200
Commit message:

 replaced BiocParallel::MulticoreParam(workers = 1) with BiocParallel::SerialParam() in tests
 
Package: katdetectr
Commit: 471306178536b30a898607d6efacec5b17c9a3d4
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-27 10:17:55 +0200
Commit message:

 fix typos
 
Package: ASICS
Commit: 151185d9be2305412919c20bbe8dc52853da8293
Author: Gaëlle Lefort <gaelle.lefort@inrae.fr>
Date: 2022-06-27 08:50:48 +0200
Commit message:

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

# Conflicts:
#	DESCRIPTION
 
Package: ASICS
Commit: 7580d74eb0445f8617ade62cbc761eb349ec47af
Author: Gaëlle Lefort <gaelle.lefort@inrae.fr>
Date: 2022-06-27 08:48:56 +0200
Commit message:

 change depreceated parameter from ropls package
 
Package: SingleR
Commit: 59d97fac1a17e86137c0e293f2703d0925f75630
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-26 18:57:17 -0700
Commit message:

 Bumped version and date.
 
Package: SingleR
Commit: 831afa96b8c7ad6d11ff82a0b87191d8ea0d1030
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-26 18:16:04 -0700
Commit message:

 Migrated the classic marker C++ code to singlepp.

Updated the singlepp library. This required updates to the C++ code,
to account for renamed Classifier class and to use the umbrella header.
 
Package: SingleR
Commit: ddae9243078dda45ed75b9818b2ce2b60b4fba6e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-21 15:57:03 -0700
Commit message:

 Minor fixes to the docs.
 
Package: SingleR
Commit: 5bab4c5825343830c551bf06f5b3622eb3c1effa
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-21 15:01:31 -0700
Commit message:

 Parallelize getClassicMarkers for many labels, closes #227.

This involved switching to a C++ implementation with ,
which makes the whole thing a lot faster than intended.
 </pre>
    </div>
  
    
Package: Rsubread
Commit: a88381cd2a73c8eb96b3bc780bbfb4fd1c44bdeb
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-06-27 04:16:42 +1000
Commit message:

 Split the "voting table" data structure into two
 
Package: BioNetStat
Commit: 411fa49db10886cda5137d45ff3fa483e385069a
Author: jardimViniciusC <viniciusjc@gmail.com>
Date: 2022-06-26 13:48:26 -0300
Commit message:

 size loading files
 
Package: MultiAssayExperiment
Commit: 734e96a6d40c12be21d70ce96f4a1e592b9e896a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:47:05 -0400
Commit message:

 update indentation for roxygen
 
Package: MultiAssayExperiment
Commit: cd8c7b12b52231a729d45d4e06309cae30d6dbf4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:42:19 -0400
Commit message:

 version bump, 1.23.2
 
Package: MultiAssayExperiment
Commit: f5e98401df5999d9918bb3daefc2cf0488d48b90
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:42:06 -0400
Commit message:

 update to changes in roxygen 7.2
 
Package: MultiAssayExperiment
Commit: c1aa7d5b9ddb6d5bd9815814d7adca5f7e6b4310
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:41:19 -0400
Commit message:

 update NEWS
 
Package: MultiAssayExperiment
Commit: a240679c1097ab4d5dd3b01aef365946ba065d8a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:39:49 -0400
Commit message:

 update wideFormat documentation, closes #312
 
Package: MultiAssayExperiment
Commit: 2b834b5f15eaad658aa9ccc6bf3593c3b5f41246
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-05-18 12:50:34 -0400
Commit message:

 update GHA
 
Package: OncoSimulR
Commit: 79ffadf37e6924c8fc19d52253d8926b612b931a
Author: ramon diaz-uriarte (at Phelsuma) <rdiaz02@gmail.com>
Date: 2022-06-25 16:24:13 +0200
Commit message:

 3.99.1: interventions, death with fdf, user variables
 
Package: basilisk
Commit: 27244b5ff0d640df0727d20acabba43520889dea
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-25 00:24:24 -0700
Commit message:

 Pin the scipy version to avoid GLIBCXX errors.
 
Package: basilisk
Commit: 18c56ff2aeb6309cb1a3470d354492e5b90c6346
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-23 22:12:35 -0700
Commit message:

 Commented onexpectations around basilisk.R.
 
Package: basilisk
Commit: 6a25e1d864ccd825b375812376f77f8b3e4088ab
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-23 20:41:43 -0700
Commit message:

 Exported utility to get the path to a BasiliskEnvironment.
 
Package: basilisk.utils
Commit: 2044ccf86f172c55c9ea647b0aca49829d4d020a
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-25 00:23:49 -0700
Commit message:

 Try harder to find a good port when activating the environment. (#5)

 
Package: crisprDesign
Commit: df73c83eb0a506cecc50ee2e94145e9f7a5a1487
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-24 12:37:48 -0700
Commit message:

 Fixed bug in ops
 
Package: crisprDesign
Commit: c43f940d6d947082170ce5fb47ced32f4db063c3
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-24 12:28:02 -0700
Commit message:

 Fixed ops code
 
Package: crisprDesign
Commit: 6489b51a1cff7092f7ff6059e5a9037f800a6873
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-16 09:01:09 -0700
Commit message:

 Done with creating add functions for PairedGuideSet
 
Package: crisprDesign
Commit: 658a433141855d4703cd5f91748f08a1cef493cc
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-16 08:12:56 -0700
Commit message:

 Added generic for addOffTargetScores
 
Package: crisprDesign
Commit: 71f770d5dcc01d9a1205159e7d30a99040436f52
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-16 08:06:51 -0700
Commit message:

 addgene and addtss have now dispatch methods
 
Package: crisprDesign
Commit: f9a5bd6270505bcd80a0753a37f58378eb2ac064
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 16:58:17 -0700
Commit message:

 Ready to merge with master
 
Package: crisprDesign
Commit: f564487935db1f839b1711f6243fc2b850a0dd15
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 16:56:03 -0700
Commit message:

 Done for today
 
Package: crisprDesign
Commit: 5c32c869915dd2a23d91fbfc457f02c4ffd2f68e
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 16:50:22 -0700
Commit message:

 Added addRepeats
 
Package: crisprDesign
Commit: 410289524478c638f5277db53697646d019a05d7
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 15:58:45 -0700
Commit message:

 Creating more generics for handling PairedGuideSet
 
Package: crisprDesign
Commit: 7634d6bc35823369cf7004f933705036ec7ec320
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 15:44:53 -0700
Commit message:

 Documented PairedGuideSet
 
Package: crisprDesign
Commit: 2f118e7724151d7845e898c33021ef1d325e313b
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 14:26:30 -0700
Commit message:

 Merge branch 'master' into paired
 
Package: crisprDesign
Commit: 002b9d7e3681f6d6e8439a678908a2c188383ec7
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-14 21:27:43 -0700
Commit message:

 Added generic for on-target
 
Package: crisprDesign
Commit: b767ffe2f212e950f341c32c4e975e0a7ed07471
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-14 21:12:10 -0700
Commit message:

 Merge branch 'paired' of github.com:Jfortin1/crisprDesign into paired
 
Package: crisprDesign
Commit: 3f38e23908dcfcb65680ded1cdd7ef305f4424de
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 17:48:21 -0700
Commit message:

 Done for today
 
Package: crisprDesign
Commit: 300d592f219d2a37dbc613903a2a350ff01d390d
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:18:01 -0700
Commit message:

 Added imports for first<- and second<-
 
Package: crisprDesign
Commit: 1d258ea12038f229635380a2907dad4633c0b63a
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:17:12 -0700
Commit message:

 Formatted file
 
Package: crisprDesign
Commit: a512d049bacc68e7b5702424afdfab035c3c8bfc
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:15:50 -0700
Commit message:

 Started adding internal functions to add annotations to PairedGuideSet
 
Package: crisprDesign
Commit: 32e4b6758d5714b2e3321c1ed751fa5cef4fd254
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 17:48:21 -0700
Commit message:

 Done for today
 
Package: crisprDesign
Commit: 1249f127227890ee3cbaae2166f9ced17095eb35
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:18:01 -0700
Commit message:

 Added imports for first<- and second<-
 
Package: crisprDesign
Commit: b6a2438cf7f00b73ebaa044e03bdaaa16967a78f
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:17:12 -0700
Commit message:

 Formatted file
 
Package: crisprDesign
Commit: 2565ad3ab70217eac2e6b2aa40c91ead5c097604
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:15:50 -0700
Commit message:

 Started adding internal functions to add annotations to PairedGuideSet
 
Package: crisprScore
Commit: 6f2475d61a0623b7dd82df77d6bfbbf88c5c6daf
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-24 12:08:17 -0700
Commit message:

 Updated doc, and added crisprRater
 
Package: crisprScore
Commit: a1fef447884bd1dde5e7824998aa4d21258809be
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-23 07:20:41 -0700
Commit message:

 Merge branch 'crisprater' of github.com:Jfortin1/crisprScore into crisprater
 
Package: crisprScore
Commit: 9b7c8a0002d3a54f27aaf731cd6ab35522322790
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-22 14:34:48 -0700
Commit message:

 Started integrating crisprRater
 
Package: crisprScore
Commit: 65fcd2909fb08964b13249e3d164180dee417fe8
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-22 14:34:48 -0700
Commit message:

 Started integrating crisprRater
 
Package: RiboDiPA
Commit: 6cb8b3fe468a76717799f9ce6826c58f97edad3d
Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu>
Date: 2022-06-24 12:54:23 -0500
Commit message:

 bug fix for parsing gtf
 
Package: RiboDiPA
Commit: 6ff6cbe6a4e08d5135851c76e8242d023259e1ff
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2022-04-26 16:12:25 +0000
Commit message:

 bug fix for parsing gtf
 
Package: msa
Commit: d6f4b25eda7b0599135cd6a38754f96a0b1fb570
Author: UBod <ulrich@bodenhofer.com>
Date: 2022-06-24 19:41:17 +0200
Commit message:

 fix in texshade.sty as suggested on TeXshade homepage at CTAN; version number bumped to 1.29.2
 
Package: signeR
Commit: d44a81f1a3f48c28fa45ad51e2a34f4de62adcd4
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2022-06-24 14:31:38 -0300
Commit message:

 signerflow
 
Package: katdetectr
Commit: 6af9c8a88199b352f276aa07d465b757dcad1b2a
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:50:03 +0200
Commit message:

 replaced @ symbol with corresponding getter functions in tests
 
Package: katdetectr
Commit: aab65207a09839102af692b3d0f62eaa86037761
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:49:38 +0200
Commit message:

 removed github installation procedure from vingette and add toc:TRUE
 
Package: katdetectr
Commit: 7719a49c0f5abd992e6f53a0693fa30cc4da0715
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:49:02 +0200
Commit message:

 replaced BiocParallel::MulticoreParam(workers = 1) with BiocParallel::SerialParam()
 
Package: katdetectr
Commit: 4d5d362add87ca9e4ce54a562da94ae1933a7a34
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:48:42 +0200
Commit message:

 removed installation from github explantation and browsevingette() suggestion
 
Package: katdetectr
Commit: dd3145ca6add8c473567a3f3e9b8818b79c12aa4
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:48:12 +0200
Commit message:

 add correct link to issues page and version bump
 
Package: ANCOMBC
Commit: ceb5ad5f595e91630055eb030fcd44caea58c41d
Author: Huang Lin <huanglinfrederick@gmail.com>
Date: 2022-06-24 11:17:48 -0400
Commit message:

 Author list change and bug fix
 
Package: MetNet
Commit: efc1ef44e8838a305157005ac0ccbd3e10890682
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-06-24 11:31:55 +0200
Commit message:

 implement corpcor package, bump to version 1.15.3
 
Package: Rbowtie2
Commit: c96aa6e06b37827c4ca7397221c352819ebc62de
Author: wzthu <wzweizheng@qq.com>
Date: 2022-06-24 15:55:46 +0800
Commit message:

 version bump
 
Package: Rbowtie2
Commit: deccc7c2e63f26998d2e3693f29c991b7f7a3c2c
Author: wzthu <wzweizheng@qq.com>
Date: 2022-06-24 15:54:12 +0800
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/Rbowtie2
 
Package: Rbowtie2
Commit: 6cee528c8a06fe1ff8e2b90474246708e2509b9f
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2022-06-24 15:50:57 +0800
Commit message:

 Merge pull request #5 from jsun/master

escape file path to bt2index. 
Package: Rbowtie2
Commit: 0af53695553899281686238231f03b5abcd204fd
Author: jsun <sun@aabbdd.jp>
Date: 2022-06-24 11:17:17 +0900
Commit message:

 escape file path to bt2index.
 
Package: omada
Commit: c1ad01731d9d66a843fdab0132bdc8dd9093859f
Author: Sokratis Kariotis <sokratiskariotis@gmail.com>
Date: 2022-06-24 09:23:31 +0300
Commit message:

 bumping version for new build
 
Package: MatrixGenerics
Commit: ab97ac048888e497731883715f48bdb2bdb9dfd8
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2022-06-24 11:25:30 +1000
Commit message:

 Update NEWS
 
Package: MatrixGenerics
Commit: ace5cf69d4888c938d8ac62247ce3391e602cc89
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2022-06-24 11:08:15 +1000
Commit message:

 Version bump
 
Package: MatrixGenerics
Commit: f7dca54132adfd4e2c503e0d559876719c895327
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2022-06-24 11:08:03 +1000
Commit message:

 Make R CMD check happy by adding Matrix to Suggests
 
Package: MatrixGenerics
Commit: ca52284150533933bf1ed98e449c7df05af9e425
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2022-06-24 11:03:06 +1000
Commit message:

 Update roxygen version
 
Package: MatrixGenerics
Commit: 53aa2271782f3569aaa6deeedea92b4bf9fa0813
Author: const-ae <artjom31415@googlemail.com>
Date: 2022-06-11 15:14:58 +0200
Commit message:

 Add test to check that dynamic loading works
 
Package: MatrixGenerics
Commit: a7bcbc077a43721c2892c817352574c24ffad4a9
Author: const-ae <artjom31415@googlemail.com>
Date: 2022-06-11 15:06:25 +0200
Commit message:

 Override the [row|col]AvgsPerColSet ANY generics to match the arg names
 
Package: MatrixGenerics
Commit: dce305f97a84af9f34b8b28b7f6ffa4b28dd30e9
Author: const-ae <artjom31415@googlemail.com>
Date: 2022-06-03 19:34:39 +0200
Commit message:

 Fix #28

Unlike most other functions rowLogSumExps first argument is called `lx`
instead of `x`. This caused `make_default_method_def("rowLogSumExps")`
to generate erroneous code. To fix the issue I inline the correct code
manually.
 
Package: katdetectr
Commit: 06b1334b6b04cfcf5f6f31785d737cd442e95c24
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-23 22:24:12 +0200
Commit message:

 Fix warning due to reference in documentation
 
Package: katdetectr
Commit: 399c4659b896978b2e9b416054dd87ee823514a9
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-23 19:28:29 +0200
Commit message:

 version bump
 
Package: katdetectr
Commit: 7a495f92d96f8cc5c59647797c46c7c1dbb598da
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-23 19:08:15 +0200
Commit message:

 build document
 
Package: katdetectr
Commit: 337b35e80960d83450d4cbd3992c186b17fdd32c
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-23 19:07:13 +0200
Commit message:

 added manually calculating mutation rate for chromosomes with less than 5 variants
 
Package: katdetectr
Commit: 4ea46ce04dc41270d6a22d13452b9f3a0fff3574
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-21 16:48:06 +0200
Commit message:

 implementing comments from bioconductor reviewer
 
Package: katdetectr
Commit: 8e5239c68f7f66240ec1cbb047a284a5e43bbcd7
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-20 18:54:45 +0200
Commit message:

 comment out General overview for testing
 
Package: katdetectr
Commit: 24749da4eaf99d2ce4d87fb62d4056039f47cd4a
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-20 18:48:50 +0200
Commit message:

 update gitignore
 
Package: katdetectr
Commit: 0bea3ca722b7981a99dbf4f03edd06a868bcc262
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-20 18:48:37 +0200
Commit message:

 update documentation rainfallPlot()
 
Package: PharmacoGx
Commit: f6800889523eb97aac35a46b3405cf19e6ef9a82
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-23 12:32:14 -0400
Commit message:

 Fix mismatched quotation in CreatingPharmacoSet vignette
 
Package: BiocCheck
Commit: 620c128fc4c1a81e6b79c38a5c6d900fd9d17292
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-23 12:16:15 -0400
Commit message:

 version bump, 1.33.10, closes #161
 
Package: BiocCheck
Commit: 4711b2f0061504b5a0a1f5b1f46c0a105d51cafc
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-23 12:15:50 -0400
Commit message:

 update NEWS
 
Package: BiocCheck
Commit: 715b68f50cf6c907830f06ff24b2b7f25806c083
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-23 12:12:03 -0400
Commit message:

 add single char lookback to remove list$F matches in T/F use Warning
 
Package: BgeeDB
Commit: f52f54e153216eb2131ebbe101b72689bc312134
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 16:34:36 +0200
Commit message:

 bump version
 
Package: BgeeDB
Commit: 3d6d9dd11d58419a54eabdd22e41a407b2b48f26
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 16:33:55 +0200
Commit message:

 update how data are uncompressed
 
Package: spbtest3
Commit: 8c0f1ef496fada235b98528c106ba3d27b1a946f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-06-23 09:55:52 -0400
Commit message:

 Bump version in description to trigger build
 
Package: sSNAPPY
Commit: b5a52b7b69c7e488b52ec83fba07b06f583d8d65
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 22:32:17 +0930
Commit message:

 fixed typo in description
 
Package: sSNAPPY
Commit: d44f0cb1831bf77e148e58188fb1be67d7149fab
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 22:29:43 +0930
Commit message:

 fixed typo in description
 
Package: sSNAPPY
Commit: 1b119d523ad802fe28efba5940d0db3ee91246dc
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 17:39:14 +0930
Commit message:

 fixed conflict
 
Package: sSNAPPY
Commit: 8c694f714583ef5f548e226d109f166f5d54dff0
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 16:54:55 +0930
Commit message:

 fixed typo in descrip
 
Package: rexposome
Commit: c9bb6d47fffe04be9388b6e90ed3f7dfabfbe6fa
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:45:45 +0200
Commit message:

 solve merge conflicts
 
Package: rexposome
Commit: 8ad0a2ebf8b16164c5b9eef3282825040adda36a
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:41:52 +0200
Commit message:

 bumped version
 
Package: rexposome
Commit: 20bc7bec7c118e337855be5c747f88c46b731dff
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:41:31 +0200
Commit message:

 fixed standardize bug
 
Package: rexposome
Commit: ce3fe79d3399cd2a41a1a05763fe6c9963bd1f70
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:41:07 +0200
Commit message:

 fixed exwas bug
 
Package: rexposome
Commit: 6e6f0285b2c677799b1be3352cb47a142d296be5
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:28:26 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: rexposome
Commit: 49e1dbde53c66247b981317cd76d8c09d1ad3fef
Author: Xavier Escribà Montagut <xavier.escriba.montagut@gmail.com>
Date: 2021-12-17 18:21:49 +0100
Commit message:

 put 0 in numeric test data 
Package: fastreeR
Commit: e574c5b2c8b6a0f5d3edab2b857e5e92f930e882
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2022-06-23 12:33:39 +0200
Commit message:

 Update vignette minor bug.
 
Package: BgeeDB
Commit: 31b91658febccdfb6f9c1c1ca9a3bdcce41c8129
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 12:27:30 +0200
Commit message:

 Merge branch 'RELEASE_3_15' into BIOC_master
 
Package: BgeeDB
Commit: 04c89fd9d42003fc852acc1121fe999742c97edb
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 12:11:18 +0200
Commit message:

 bump version
 
Package: BgeeDB
Commit: 2594ccafe82690a76d1100d9e42f12e046fc32f3
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 12:10:51 +0200
Commit message:

 update documentation
 
Package: BgeeDB
Commit: 6ca006d8b317257d23ffe59795c8fdd82bc72784
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-16 14:22:59 +0200
Commit message:

 bump package version
 
Package: BgeeDB
Commit: 5eb6602da2b01adc8558082e855e1b2b11891bcb
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-16 11:49:20 +0200
Commit message:

 allows user to define its own download timeout when using webservice for topAnat
 
Package: BgeeDB
Commit: 23e9a901dfa37bad22e7fbb89f96997a9cba04be
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-05-06 16:22:52 +0200
Commit message:

 update citation
 
Package: BgeeDB
Commit: 0af86025f90c8b3724bd9d1cdd76d3805a799c78
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-05-06 16:19:19 +0200
Commit message:

 update example and timeout value to avoid timeout
 
Package: imcdatasets
Commit: 42cb2dc918b0fa87099467a8be7948a4dda1a7d3
Author: Nicolas Damond <nicolas.damond@gmail.com>
Date: 2022-06-23 09:30:03 +0000
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: imcdatasets
Commit: f28e240b3a9329a881608bc809cae799774f26f1
Author: ndamond <nicolas.damond@gmail.com>
Date: 2022-03-22 16:44:34 +0000
Commit message:

 Merge branch 'master' of ssh://github.com/BodenmillerGroup/imcdatasets
 
Package: imcdatasets
Commit: 0062fdee24ef6bc699866f8df54de638fccb2f8c
Author: Nicolas Damond <nicolas.damond@gmail.com>
Date: 2021-10-27 10:40:23 +0200
Commit message:

 Merge pull request #12 from BodenmillerGroup/RELEASE_3_14

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch 
Package: zellkonverter
Commit: 280620b25e5b99b4d7572c5e52253def86671995
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2022-06-23 10:15:48 +0200
Commit message:

 Merge branch 'RELEASE_3_15'

* RELEASE_3_15:
  Move verbose from zellkonverterAnnDataEnv()
 
Package: zellkonverter
Commit: 437ff0219ea4e2e59c7c0d291db4f42aab14cc98
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2022-06-23 10:13:26 +0200
Commit message:

 Move verbose from zellkonverterAnnDataEnv()

Needs to be able be directly sourced by {basilisk}
 
Package: sSNAPPY
Commit: 2df5dc6f01ceb9b8c60bea3f498758a1b89edeef
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 17:35:31 +0930
Commit message:

 fixed a typo
 
Package: sSNAPPY
Commit: 9195e45e68e03bdf28d1233f9c37f4cf6a0c7471
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 16:54:55 +0930
Commit message:

 fixed typo in descrip

"rebasing"#
 
Package: rGREAT
Commit: 8c09b897ba41521cc48119e6ae83d1685a1fb368
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2022-06-23 09:45:12 +0200
Commit message:

 fix a problem of par()
 
Package: rGREAT
Commit: 11bc42393f3c7f7cc224a3db126c2efdbc98b522
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2022-06-23 08:06:19 +0200
Commit message:

 version bump
 
Package: rGREAT
Commit: 9e9155ad2678027ae4cf5b41cf204896f391c5b6
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2022-06-23 08:01:03 +0200
Commit message:

 use gzfile()
 
Package: PharmacoGx
Commit: 056b3444c2919dedaa1b6f3db167fed2b059c06e
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-23 01:01:55 -0400
Commit message:

 Version bump for Bioc push
 
Package: PharmacoGx
Commit: 7a0010fc1a3764b24fe14e8b75670081d5cac6d6
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2022-06-23 00:54:50 -0400
Commit message:

 Merge pull request #119 from bhklab/development

Basic synergy metrics 
Package: PharmacoGx
Commit: 68b885e5791dbd124a9aad70f1f5eb4708717e41
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-23 00:33:40 -0400
Commit message:

 Debug BiocCheck to false positive T/F usage in geneDrug*.R files
* There is already an issue open https://github.com/Bioconductor/BiocCheck/issues/161
 
Package: PharmacoGx
Commit: b17985ea91a72a37794fa6b9dfe5ca45d5a93a4a
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 23:55:06 -0400
Commit message:

 Renamed some files; added more examples to appease BiocCheck
 
Package: PharmacoGx
Commit: 27623c243a95f0e75991eb6b2a3c90184883b2e8
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 22:53:23 -0400
Commit message:

 Added BiocStyle to SUGGESTS to allow vignettes to build
 
Package: PharmacoGx
Commit: 58bcaecb6df8182b4821c65d48b55c14f5211580
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 22:03:57 -0400
Commit message:

 Resolve conflicts with master
 
Package: PharmacoGx
Commit: a51668e3b281fc167a19b6054c79c9cd04e420e3
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 22:02:37 -0400
Commit message:

 Fix some minor NAMESPACE issues; add Fei as author
 
Package: PharmacoGx
Commit: c9f8f03e418a716cd618c9987d52c4b628673a07
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 21:41:57 -0400
Commit message:

 Convert vignettes to HTML so I (hopefully) never have to debug a LaTeX error again
 
Package: PharmacoGx
Commit: e6b095b294a27563acc66fcf0157d60b3c73e29d
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2022-06-21 17:53:25 -0400
Commit message:

 Merge pull request #118 from bhklab/fix_sProfiles

fixed bugs related to using sProfiles in drugSensSig 
Package: PharmacoGx
Commit: 0d23aca75c0576f7e2fadf6912d1d3fd50b99e2e
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2022-06-21 17:51:35 -0400
Commit message:

 fixed bugs related to using sProfiles in drugSensSig
 
Package: PharmacoGx
Commit: 9e6fb691b4a63e2ad91195f24d5e45ecab8e7bbc
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 15:37:14 -0400
Commit message:

 Fix PharmacoGx build to allow bioc2022Workshop to build
 
Package: PharmacoGx
Commit: 3d3e7e60240806040bdd21e7be2742236b2b8175
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-06-21 14:34:14 -0400
Commit message:

 Loewe methods added
 
Package: PharmacoGx
Commit: 76e1aa6c5c5168074ceed6f36e6ee95bec931099
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-18 13:51:19 -0400
Commit message:

 Fix wrong argument name in .PharmacoSet for PharmacoSet2 constructor
 
Package: PharmacoGx
Commit: 9d525702809927cb1af9335415b0d6585b970efa
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-07 12:41:31 -0400
Commit message:

 Update sensitivitySlot to treatmentResponse method to match new package nomenclature
* Aliased treatmentResponse to sensitivitySlot in CoreGx for backwards compatibility
 
Package: sesame
Commit: caa961ec756edb4560d067d339086adea8821b47
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-06-22 22:03:46 -0400
Commit message:

 bump to 1.15.3
 
Package: sesame
Commit: 0a094f87c3848d3f26af7e0d883c1fb82372626a
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-06-13 11:20:00 -0400
Commit message:

 update to summaryExtractTest
 
Package: sesame
Commit: 0275992120346b70ec5a479dc9d838fdcbaee89c
Author: Zhou <zhouw3@c7d363v6qq.chop.edu>
Date: 2022-06-08 13:09:25 -0400
Commit message:

 fix singularity case in DMR
 
Package: CoreGx
Commit: 6c7e434d35b7beab564cda8b24da69502aeae4f7
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 20:43:48 -0400
Commit message:

 Version bump for Bioc push; add Fei as contributor (thanks for unit tests)
 
Package: CoreGx
Commit: 2642c2f330f585c1a4abc4a74880e58eb0ee0b5d
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2022-06-22 20:36:53 -0400
Commit message:

 Merge pull request #150 from bhklab/development

Finally passing the checks. R NAMESPACE errors are the worst. 
Package: CoreGx
Commit: 9126239d0314cf4a305e3625c358255bc5e31564
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 20:22:44 -0400
Commit message:

 Passing rcmdcheck with only notes finally
 
Package: CoreGx
Commit: 3b494e11b5dc18a49f978c0dc74fa0419b37ec1a
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 19:38:23 -0400
Commit message:

 Debugging NAMESPACE related warnings in rcmdcheck
 
Package: CoreGx
Commit: 5a8b70216624533aa932c0241a29b6cba155c2af
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 19:15:52 -0400
Commit message:

 Fix sensitivityRaw assignment
 
Package: CoreGx
Commit: d0a0faa8308509aa0f1a47b59b7a5c5991a65839
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 18:28:25 -0400
Commit message:

 Fixed tests after modifying assay,LongTable-method for summary assays
 
Package: CoreGx
Commit: 7fbcf571837f8d54e77029763a7461735b1c113c
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 16:24:34 -0400
Commit message:

 Added summarize argument to assay which only returns columns mapping 1:1 with the assayKey when TRUE
 
Package: CoreGx
Commit: 42e83ba2aec42ab00d64fbf6f2359189562eac64
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 15:37:44 -0400
Commit message:

 Update CoreGx to allow bioc2022Workshop to build
 
Package: CoreGx
Commit: 5e6921ae6b4e32ab880c03a06e4986e930a3b022
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 15:34:38 -0400
Commit message:

 Debugging endoaggregate method
 
Package: CoreGx
Commit: e4b26409a157a9879e0c4e3daafe4b0b3f21d06c
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 14:09:57 -0400
Commit message:

 Fix #155 by adding by=.EACHI to cartesian join to prevent allocating the entire table as once, but this has slowed down assignment significantly
 
Package: CoreGx
Commit: e66ffb6a7a10a98b212b6d2627b063c76b301393
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 12:07:06 -0400
Commit message:

 Fix #154, was being caused by failure to import bpprogressbar<- and bpworkers<- in aggregate file
* Resulted in hasMethod for these two generics to always return FALSE, since they weren't available in the local environment
 
Package: CoreGx
Commit: 53d332c5667373e1147bc305762192a2e44eded9
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 11:27:56 -0400
Commit message:

 New endoaggregate method working for assigning new assays; testing for updating existing assays
 
Package: CoreGx
Commit: 5813df334fd63f027b2b76d3a094de5f5a5936d8
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-20 20:04:45 -0400
Commit message:

 Fix molecularProfiles bug caused by name clash between function argument and assay function call
 
Package: CoreGx
Commit: 3e85b8dbb296ee1c5002f3444c0da5085939e6a6
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-20 00:48:16 -0400
Commit message:

 Merge branch 'development' of github.com:bhklab/CoreGx into development
 
Package: CoreGx
Commit: 2d0a1f3388701d0e71c3dc8caa8c7811a48262ee
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-19 19:05:57 -0400
Commit message:

 Update .Rbuildignore and NAMESPACE
 
Package: CoreGx
Commit: ca41d7da827c3691bdf9fac29b1b821511e95f39
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-18 19:51:32 -0400
Commit message:

 Add summarized of synergy metrics via mean
 
Package: CoreGx
Commit: 21a419de5c7b2541388610862521fd7e32acfc89
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-18 12:39:42 -0400
Commit message:

 Update man and NAMESPACE to fix sensitivitySlot method issues
 
Package: CoreGx
Commit: 50bce1aea1905b02a9f5bc103bf7d4cade7bc9ef
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-06-18 01:31:12 -0400
Commit message:

 Merge branch 'development' of https://github.com/bhklab/CoreGx into development
Merge pull w/ local
 
Package: CoreGx
Commit: 3f2a6839fd87113ef25213c31b038c028e990d40
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-06-18 01:22:21 -0400
Commit message:

 Added testing code for calculating Loewe CI in aggregate-method.R
 
Package: CoreGx
Commit: 5321c36be6fe719749d6433807b594ca06fe8c63
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-18 00:38:11 -0400
Commit message:

 Fix bug in .rebuildProfiles by summarizing values in sensitivityProfiles if they map to dose
 
Package: CoreGx
Commit: ec1a88c6e4b07df396b777ee11dc37f0e68c2b5b
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-06-15 13:40:26 -0400
Commit message:

 Method for grouping monotherapy and drug-combination responses within an assay table added to utilities.R
 
Package: CoreGx
Commit: 30ac4abd5ec26953067fb53da9cba692a174513a
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-15 15:44:21 -0400
Commit message:

 Add testing code for drug combination modelling in aggregate-method.R file
 
Package: CoreGx
Commit: 41bf8d4b29b9d374a46861bfbb413a66a498d18b
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-13 18:04:32 -0400
Commit message:

 Fix #151 by swapping all.equal for .table_is_subset inside assay<-,LongTable,character-method
 
Package: CoreGx
Commit: 5aefb199eeb63d9351d3369558c68c5415032fac
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-07 18:41:33 -0400
Commit message:

 aggregate2 and aggregate,TreatmentResponseExperiment-method now work with enlist=FALSE argument, which evaluates closer to raw data.table group by
 
Package: CoreGx
Commit: 9ec789baa3429d1c7fed4fd5d57ed1c90bca8e27
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-07 12:42:07 -0400
Commit message:

 Renamed method sensitivitySlot to treatmentResponse, aliased back to sensitivitySlot for backward compatability
 
Package: CoreGx
Commit: 4b76feee0cf1eb00bcc4525d84a3c2fcc8550898
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 18:01:31 -0400
Commit message:

 Fix aggregate2 method so it only tries to set bpworkers for BPPARAM classes which define that method
 
Package: CoreGx
Commit: bbf7dce64133790932691a246a6043b54cb60196
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 17:44:38 -0400
Commit message:

 Merge branch 'main' into development
 
Package: CoreGx
Commit: 3a2d42906431051ad14ca1a2c421f2367706f883
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 17:42:13 -0400
Commit message:

 All unit tests passing
 
Package: CoreGx
Commit: b4564b0760d82ecec4210dff6f5e3f5fe1574ced
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 16:37:45 -0400
Commit message:

 Updated comments for .subsetByIndex
 
Package: CoreGx
Commit: 29f8f9326f8a98269ffdd65e71b374ba483dd406
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 16:00:30 -0400
Commit message:

 Update .subsetByIndex to apply unique to each assay data.table before assigning back to the TRE object; this fixes #149
 
Package: CoreGx
Commit: 3afb956a4099978737e5ea74f12f3906f7dbd960
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 18:19:51 -0400
Commit message:

 Debugging issue with assignment of summary assays
 
Package: CoreGx
Commit: 318aeb59ae33dbfda5b94c9c2934c5ac3fe037d1
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 17:31:02 -0400
Commit message:

 Add tests to ensure assignment of summarized assays works correctly; fix #147; add test case for #147
 
Package: CoreGx
Commit: 092f09849a901748fa24070521c01bc77cef5f8b
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 17:08:52 -0400
Commit message:

 Add test to ensure that automatic column name generation works in aggregate2 and aggreagate,LongTable-methods
 
Package: CoreGx
Commit: d26babf0642a484639a96dc09d3f87e4ff185bc6
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 15:53:10 -0400
Commit message:

 Add test to ensure aggregate,LongTable-method is equivalent to data.table aggregation of the associated assay
 
Package: CoreGx
Commit: 9197a4a666abbc5a7dbc17c0e6ab6a9aabe027e2
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 15:41:06 -0400
Commit message:

 Add tests to ensure aggregate2 results are identical to data.table aggregation
 
Package: CoreGx
Commit: dcfbeb2332fed6715697dbd018ea2c2f9df12b29
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 15:09:14 -0400
Commit message:

 Fix bug in aggregate2 causing default name parsing to fail when no aggregation calls have names
 
Package: CoreGx
Commit: a98a408fb52979248c5a9bb4d9af453b0388efbb
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 14:38:38 -0400
Commit message:

 Forgot to git add some stuf f in last push
 
Package: CoreGx
Commit: be619223d787f26a5a6a61c97e0c5ed90e94567d
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 14:38:02 -0400
Commit message:

 All unit tests now passing with modified subset,LongTable-method algorithm
 
Package: CoreGx
Commit: 7ac7ca0784a2112d9f5f8a0681009b1d7ab845c5
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 13:15:05 -0400
Commit message:

 Update unit tests to account for change in how subsetting a LongTable works
 
Package: CoreGx
Commit: 070cecc0e274ca23a59b9ce8c736436a96a25186
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 12:39:25 -0400
Commit message:

 Fix unit tests for subset,LongTable-method to account for the fact that additional row or colKeys may get dropped when there are no observations remaining in the table
 
Package: CoreGx
Commit: 33f9dc4ba761340a42caf4aedd50b77a7f1442d7
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 12:33:26 -0400
Commit message:

 Add .table_is_subset utility for use in unit test
 
Package: CoreGx
Commit: 9341ac135e31d479f0696a47e5a55b37fd297128
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-03 09:24:10 -0400
Commit message:

 Debugging LongTable/TRE unit tests
 
Package: CoreGx
Commit: 9fbfa79ee0d58bb5a87ee2e61de6063c4fe1e3b2
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 18:48:02 -0400
Commit message:

 Merge branch 'development' of github.com:bhklab/CoreGx into development
 
Package: CoreGx
Commit: fe497df9f92e090a63a3510a24f801c575cce173
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 18:46:35 -0400
Commit message:

 fix #148 by feeding back rowKeya nd/colKey from assays to index after subset
 
Package: CoreGx
Commit: 783617bc70efd25a75deeaf118116605dfe270e2
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 18:46:35 -0400
Commit message:

 Fix #148 by feeding back rowKeya nd/colKey from assays to index after subset
 
Package: CoreGx
Commit: 496ba7fa2299ec1b22254b73d17a590ecd1607e5
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 17:29:42 -0400
Commit message:

 Refactored row and colData<-,LongTable-method to use a shared helper method
 
Package: CoreGx
Commit: 9e33136f691caadd0fafb4503c8b279438bca50c
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 13:06:47 -0400
Commit message:

 Basic aggregation of TreatmentResponseExperiment now working
 
Package: CoreGx
Commit: 26a37b9cc0ecd8bf388025d17ea9a36427a3568b
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 12:36:33 -0400
Commit message:

 Revert "Revert "Revert "Update issue templates"" to fix accidental push to main :sunglasses:"

This reverts commit 69fbee5002276a080190bb21f7a6c8f996c3e8e8.
 
Package: CoreGx
Commit: 59a85888a1e012e447d048caa9ff3ddac722a322
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 12:35:44 -0400
Commit message:

 RE fixing #146, merge with main reverted it apparently
 
Package: CoreGx
Commit: 69fbee5002276a080190bb21f7a6c8f996c3e8e8
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 17:52:07 -0400
Commit message:

 Revert "Revert "Update issue templates"" to fix accidental push to main :sunglasses:

This reverts commit 5532ca4ecd2abdee0dcfb558d1e36ddd0549ca52.
 
Package: CoreGx
Commit: 164a94ddf6ff86e5cc5012fefe8753bbbeafb3c0
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 17:51:39 -0400
Commit message:

 Merge branch 'main' into development
 
Package: CoreGx
Commit: 460f3da9f1a8f9c838de0679b57a16eb79223fd3
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 17:51:24 -0400
Commit message:

 Still accidentally commiting to main instead of development :cry:
 
Package: CoreGx
Commit: 2be9809f03513a670a8df1a4a867fb2737e85ce8
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 16:07:41 -0400
Commit message:

 Added some benchmarking code to test aggregate2 performance across different parallelization backends
 
Package: CoreGx
Commit: 5532ca4ecd2abdee0dcfb558d1e36ddd0549ca52
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 14:20:40 -0400
Commit message:

 Revert "Update issue templates"

This reverts commit 23ba0a3ed9d6091141cd296eaeca277634efdd2d.
 
Package: CoreGx
Commit: 299b38abbcfcf964cb274c83fb750352ca625228
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 14:14:44 -0400
Commit message:

 Merge branch 'development' of github.com:bhklab/CoreGx into development
 
Package: CoreGx
Commit: 267dbd3f6aade6674b0d34c7d622144fb3c2d965
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 14:13:56 -0400
Commit message:

 Merge accidental push to main into development :joy:
 
Package: CoreGx
Commit: 8f780b95d0bb2c42c7b1cce973768b8797c8c99c
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 14:12:36 -0400
Commit message:

 Added benchmarks to aggregation with computeAUC; accidentally pushing to main :sadface:
 
Package: CoreGx
Commit: 917e753cb71ea935cab622d020c4243279f41cbc
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 13:56:18 -0400
Commit message:

 Parallelization working in aggregate2 data.table method
 
Package: CoreGx
Commit: b5120758e69579e6bfcc4676342f12cf8e7fffa1
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-31 19:13:08 -0400
Commit message:

 Add basic function documentation for aggregate2 function
 
Package: CoreGx
Commit: 1782513e00e2a6dd5ad0d1d1dddfd900f64b9659
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-31 19:00:50 -0400
Commit message:

 Add draft of aggregate method for data.table, to be used in TRE aggregate method
 
Package: CoreGx
Commit: 97abebb4c2665455da70ef0e2be65e75752b30d3
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-30 17:01:04 -0400
Commit message:

 Split unit tests by .R files.
 
Package: CoreGx
Commit: 52b0cde46600f4c2a5047fb81d71f38c067b9be9
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-30 16:17:52 -0400
Commit message:

 resolved merge conflicts
 
Package: CoreGx
Commit: d1937eebecaad8d9c6c6ed26ff85b47039b6fd9e
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-30 16:08:27 -0400
Commit message:

 New subset() tests added. Compressed test dataset. Added missing colData param check for LongTable consturctor.
 
Package: CoreGx
Commit: 23ba0a3ed9d6091141cd296eaeca277634efdd2d
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2022-05-30 12:11:13 -0400
Commit message:

 Update issue templates 
Package: CoreGx
Commit: 51f850883594d7a799d5ea0d6df8ad0e9625777a
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-30 11:33:38 -0400
Commit message:

 Add GHA CI/CD for release branch
 
Package: CoreGx
Commit: d394583fa5a4593a3b8d8e4b5ec94124d8f3afb5
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-30 11:20:03 -0400
Commit message:

 Fix duplicated detection in rowData method
 
Package: CoreGx
Commit: 644c8cee299a88cf5cfb4365586d199c2ee10b16
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-26 20:44:41 -0400
Commit message:

 Added NCI-ALMANAC TRE subset to the package.
 
Package: CoreGx
Commit: 3de48780f9cbfc45edbacab7aa76bf57f929d356
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-26 19:57:52 -0400
Commit message:

 New test cases for subset method and TRE class added
 
Package: CoreGx
Commit: 3793f60e8be91ffbc4e11afc2ab8f650b6c28d55
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-26 12:34:17 -0400
Commit message:

 Add warning for duplciated idColumns in rowData assignment method; stil need to propogate change to colData
 
Package: CoreGx
Commit: a1aabd6112ef05ad4faaf4252305c73abbf8726b
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-26 11:19:14 -0400
Commit message:

 Renamed all instances of lt to tre in tests to represent updated package nomenclature
 
Package: CoreGx
Commit: 957fe2c2e89662f6800d7d783cccf8a6c95a6253
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-25 14:53:51 -0400
Commit message:

 Fix #146: join on wrong index in reindex,LongTable-method was failing to update the assayIndex row and colKeys
 
Package: CoreGx
Commit: b8aaad5f1d0ff15f31bde01a714ed6c916b80dc6
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-20 18:50:47 -0400
Commit message:

 Minor fix: subset i rowname length check works now
 

</div> </div>

Source Code & Build Reports »

Source code is stored in Git.

Software packages are built and checked nightly. Build reports:

 

Development Version »

Bioconductor packages under development:

Developer Resources: