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GIT Logs

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Package: flowWorkspace
Commit: c480890fb1e9156098febcb3e73acec2e7ddafe0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-19 12:26:41 -0800
Commit message:

 bump
 
Package: cytolib
Commit: a08b61fe6e5adc09605c2d378781ff4ce0aaa462
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-21 11:36:31 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: cytolib
Commit: 0b7da452b2b5f6adbc831f052ed970a8707f1b3f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-18 14:31:04 -0800
Commit message:

 skip libboost_fs.a for win build since it didn't work
 
Package: cytolib
Commit: 472de4350df058e77a5dfeed9b02af121db8fddb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-18 12:37:23 -0800
Commit message:

 update c files by protoc3.10
 
Package: RProtoBufLib
Commit: 30d7aae962c279a0ab188eae1a7776c45bcf29f1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-21 11:33:54 -0800
Commit message:

 rm libprotobuf-lite.a to pass bioc size limit
 
Package: RProtoBufLib
Commit: 6fa749142bc0ae1354877e3ea4680d72bd3b78cf
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-21 11:31:32 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: RProtoBufLib
Commit: cf21041915bd4a875ea70cc3428fbb8d16b5678b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-19 12:54:13 -0800
Commit message:

 up x64/libprotobuf-lite.a
 
Package: RProtoBufLib
Commit: 000664bf45c791130cdd019a51ca0103c49de819
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-19 12:21:50 -0800
Commit message:

 up INSTALL
 
Package: RProtoBufLib
Commit: 8053912f6d7df523d506152ef72bd0d5ab4a3153
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-18 16:33:54 -0800
Commit message:

 up header for win
 
Package: RProtoBufLib
Commit: 7ed6664b1927870085eb93f6a8cc833306055bb2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-18 16:22:37 -0800
Commit message:

 up i386/libprotobuf-lite.a
 
Package: RProtoBufLib
Commit: c15d39ded6df80ef42d057abd58b99dd75e029d7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-18 12:26:34 -0800
Commit message:

 up protobuf to 3.10 #8
 
Package: CytoML
Commit: 138ca2acfd9b8c4fce4ea70ecec50d91eb2ac62c
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-21 10:52:25 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: CytoML
Commit: 342927e4a6aa21eb51281ffca8246de70217ace8
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-21 10:48:51 -0800
Commit message:

 bump
 
Package: CytoML
Commit: bc5ae5ae13c0517f349ed000975302cc262990f4
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-21 10:48:29 -0800
Commit message:

 Fix arg references in gating_graphGML
 
Package: CytoML
Commit: 25819126bf874bb3776a4d80a2a947f886f1915e
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-21 10:32:00 -0800
Commit message:

 Merge branch 'cytoset' into trunk
 
Package: CytoML
Commit: bd9e88fe61a49c744366e79fdc6172f9d6ee3103
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-20 15:54:48 -0800
Commit message:

 rename gating to gating_graphGML RGLab/openCyto#204
 
Package: CytoML
Commit: 25d353e2079d5a5c07abc254daf39d05d4e9f9b3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-20 15:51:32 -0800
Commit message:

 switch to boost::fs
 
Package: CytoML
Commit: be305d88e690e7a7391ff3b155058f3e126ef454
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-04 12:34:37 -0800
Commit message:

 Fix cytobank_to_gatingset arg reference
 
Package: CytoML
Commit: 8674a6b83ed97c37d76e5a162347af33bbaa3d70
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-04 12:30:17 -0800
Commit message:

 pkgdown updates
 
Package: CytoML
Commit: f729ebbe0694c91a7c0654d6148464bfbb46938f
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-04 12:29:55 -0800
Commit message:

 Doc cleanup/consolidation
 
Package: CytoML
Commit: f974eac38a581bbb8edf7da0fd564d30c978cfc3
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-04 12:27:39 -0800
Commit message:

 Add cytolib and RcppParallel to imports for R CMD check
 
Package: CytoML
Commit: 7a53f9dec034dc1a564d3e264f853a6d8155897c
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-01 16:42:20 -0700
Commit message:

 Fix typo in namespace
 
Package: CytoML
Commit: 1d72e550a81952662e5159a4b10fea7ee0e6e6c5
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-01 16:41:16 -0700
Commit message:

 fix typo
 
Package: CytoML
Commit: 2dac67c8f4ea383ba97ebdd8faa39fc14080cbde
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-01 16:42:20 -0700
Commit message:

 Fix typo in namespace
 
Package: CytoML
Commit: 246157d7d6ccecaa6e105499c32caba72d52684a
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-01 16:41:16 -0700
Commit message:

 fix typo
 
Package: CytoML
Commit: 6a8e7c1e0092b02d3a6fec706bfce1d97aedb5ab
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-01 16:16:00 -0700
Commit message:

 Minor fix to ce_get_panels
 
Package: CytoML
Commit: 1d9751979abc3f25ee0d8b01f27bc3ee32e5635d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-11-01 16:16:00 -0700
Commit message:

 Minor fix to ce_get_panels
 
Package: CytoML
Commit: a04a8e0d4a56cede9a0d7a38307ce0a15355584d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-23 14:55:17 -0700
Commit message:

 #64: Allow application of compensation matrix from xml
 
Package: CytoML
Commit: 69d96258fac8a09354aff4a1d388059b45c01c8f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-01 10:40:42 -0700
Commit message:

 mv schema folder to inst
 
Package: CytoML
Commit: b930bdfbb4c905ea54c2b5db97d1f39ae78a599c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-01 10:40:42 -0700
Commit message:

 mv schema folder to inst
 
Package: CytoML
Commit: fde0ee9f40510030192bfe05a100e310c6939e6a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-01 10:38:22 -0700
Commit message:

 update doc
 
Package: CytoML
Commit: 4a75102cfe38d6c0c825b2d33366387e678ef544
Author: whitews <whitews@gmail.com>
Date: 2019-10-31 16:57:03 -0400
Commit message:

 add CytoML XSD
 
Package: CytoML
Commit: 33f7f1bffdd6615c63402d37ac2932bf31fcdac0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-30 16:41:53 -0700
Commit message:

 filter samples by panel when parsing cytobank_experiment  #73
 
Package: CytoML
Commit: 5bf62bc13e31b96f1c5756e4e7aad4310a421188
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-30 11:54:18 -0700
Commit message:

 fix some bugs for cytobankExperiment parser. close #48
 
Package: CytoML
Commit: e5faa0082ca49a76fafb5996b31cb615e761b8de
Author: whitews <whitews@gmail.com>
Date: 2019-10-29 10:57:26 -0400
Commit message:

 add attribute namespaces for modified tags
 
Package: CytoML
Commit: 1edcb4c278db7b6da1e6ee8e76d3f2843304d1e8
Author: whitews <whitews@gmail.com>
Date: 2019-10-29 09:29:24 -0400
Commit message:

 export cytobank ML with attribute namespaces
 
Package: CytoML
Commit: 0e3bd0b33b92a8596744a52d8e5b8a26c5ba44b6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-23 10:28:49 -0700
Commit message:

 pass dots to fcs parser. #68
 
Package: CytoML
Commit: 44d396e291a7231e04e4cbecfe8c3fb4e6e8384d
Author: Mike Jiang <wenxin.jiang@gmail.com>
Date: 2019-11-01 10:23:01 -0700
Commit message:

 Merge pull request #74 from whitews/trunk

Adding new CytoML XSD 
Package: CytoML
Commit: 5f4d8bb9f6c5a9eb697c18c1e9eac7e76be1ce8a
Author: whitews <whitews@gmail.com>
Date: 2019-10-31 16:57:03 -0400
Commit message:

 add CytoML XSD
 
Package: CytoML
Commit: 76eb0b6bf7a55a53750a02bcfd4d1cf52a56be82
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-30 16:41:53 -0700
Commit message:

 filter samples by panel when parsing cytobank_experiment  #73
 
Package: CytoML
Commit: 4bf759ccf11333b75b3feebc03b47b17632e7352
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-30 15:25:35 -0700
Commit message:

 Merge branch 'trunk' of github.com:RGLab/CytoML into trunk
 
Package: CytoML
Commit: 65893cf89381fbea173ba8bfb914e32ee6a5c412
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:41:47 -0400
Commit message:

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 
Package: CytoML
Commit: a45b90d45d2db964eb21bc81ffcfb7e3d86b33cc
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:09:50 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 
Package: CytoML
Commit: f98857bf04a20f54ce7a55165fb89fbca9f40fdb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-30 11:54:18 -0700
Commit message:

 fix some bugs for cytobankExperiment parser. close #48
 
Package: CytoML
Commit: b99c08e106bed1c1c925c4d2fd5e234e466f7abb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-29 10:48:43 -0700
Commit message:

 Merge branch 'trunk' into whitews-trunk
 
Package: CytoML
Commit: d5082112f1d77bb863f82a2af8e42f3b2cdab9c8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-29 10:40:28 -0700
Commit message:

 run roxygen
 
Package: CytoML
Commit: 179a2ca2255da435d3461a620602e26033df4ba1
Author: whitews <whitews@gmail.com>
Date: 2019-10-29 11:14:31 -0400
Commit message:

 Merge branch 'trunk' of https://github.com/rglab/cytoml into trunk
 
Package: CytoML
Commit: 431d250ed917b319848df018c849aa2ae5c9a6a9
Author: whitews <whitews@gmail.com>
Date: 2019-10-29 10:57:26 -0400
Commit message:

 add attribute namespaces for modified tags
 
Package: CytoML
Commit: b8a67898390eccc1ebd23d94381d04e30c1e8311
Author: whitews <whitews@gmail.com>
Date: 2019-10-29 09:29:24 -0400
Commit message:

 export cytobank ML with attribute namespaces
 
Package: CytoML
Commit: 71ccddc2c340f60933597e373fb77d7465a312c5
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-28 11:12:58 -0700
Commit message:

 Update docs and README to get Cytobank xml from acs experiment file
 
Package: CytoML
Commit: a35170a52a1f25f4f33a0ab12289756ba2da39f7
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-11 12:37:49 -0700
Commit message:

 Fix diva_to_gatingset gate scaling issue
 
Package: CytoML
Commit: 99999b1a709da3fbca623ae9da0939e9006c6c52
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-09 15:51:31 -0700
Commit message:

 parse quadgate
 
Package: CytoML
Commit: ab45174c020cadffde374f8f9fff882dce6d217c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-26 14:35:57 -0700
Commit message:

 update diva test case
 
Package: CytoML
Commit: b4d8af3fe0f8b27869733d5b1a0d2325a5bdecf4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-26 14:31:49 -0700
Commit message:

 guard against unsupported trans being added to gs during diva parsing
 
Package: CytoML
Commit: f9a98259dcbfa67c6ddfd59c713fbd2ef4e3e602
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-26 13:44:48 -0700
Commit message:

 lower tolerance due to the lower digits
 
Package: CytoML
Commit: 642ffc0304e85492c5ac1abab5bc65641c8f60b3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-26 12:44:28 -0700
Commit message:

 switch to flowJo_log for diva
 
Package: CytoML
Commit: ae7bca3215cc23fb7c8c05469771bdf9e9f4da35
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-25 16:21:19 -0700
Commit message:

 fix test case related to flog
 
Package: CytoML
Commit: 6851b5e3beeae2c364d2e111bfd3f0982f909f19
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-25 14:50:20 -0700
Commit message:

 update according changes in cytolib
 
Package: CytoML
Commit: 2d943ce392a9e9a63e437e625b04533c2acd50c7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-25 14:30:45 -0700
Commit message:

 bump
 
Package: CytoML
Commit: a3722298d16f52c267e6f4c92173c23c2f13a47f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-16 16:31:43 -0700
Commit message:

 fix digits
 
Package: CytoML
Commit: 2018dfe9e11406e85dfeb89ba3126a6228759433
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-12 11:26:57 -0700
Commit message:

 use round to set precision for format_float
 
Package: CytoML
Commit: 4a7ea38bd138f6909b42ad93e1074a476074e68a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-11 15:12:06 -0700
Commit message:

 fix range for DerivedParameterNode
 
Package: CytoML
Commit: cd6d16f0b01b5b2427e63fab3acb3fcb9175c917
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-11 15:08:16 -0700
Commit message:

 format_float(gain)
 
Package: CytoML
Commit: 5c43d27a0e0ebbcefe6c20f8a11a99baaa64c04c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-10 12:43:29 -0700
Commit message:

 lower digits for transformationNode
 
Package: CytoML
Commit: acedcb2525ae0d25c77686dbab5c710fb13c40e2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-04 13:35:41 -0700
Commit message:

 lower precision for format_float
 
Package: CytoML
Commit: 67526e3c5d517dc6bed428c8fd7b219aed9ebf0c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-23 13:51:54 -0700
Commit message:

 bump
 
Package: CytoML
Commit: bb548e660a34b7741ce66dea7a74927c5ef7d3cf
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-23 13:45:09 -0700
Commit message:

 add test case for flog
 
Package: CytoML
Commit: e971e5349d5d21703425d6073f52202bb7e4eca3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-20 13:41:22 -0700
Commit message:

 attach DerivedParametersNode after sampleNode to be consistent with c++ code
 
Package: CytoML
Commit: cb2301b209851a50180f27d0e973d69643f4279d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-08-20 10:54:35 -0700
Commit message:

 Strip name from value resulting from `format_float` calls
 
Package: CytoML
Commit: b8fc14427032d6ddc0a04ae4d132664b8ed4eaea
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-19 15:51:08 -0700
Commit message:

 skip inf dims for rectangleGate to be consistent with c++ code
 
Package: CytoML
Commit: c3b3b1b85f7dcde7c1c0472cad25a961d031adda
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-16 14:51:17 -0700
Commit message:

 add format_float to customize precision(increase default 15 to 17) for double to match up to pugixml behavior
 
Package: CytoML
Commit: 963815d4c15ec5ca27c74e4aa3f0f67900c9939b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-16 11:49:27 -0700
Commit message:

 fix xmlTag R API to enable self-closing tags
 
Package: CytoML
Commit: 96727a76189c3c42f1a6c77f92aafd4d216022ea
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-08 13:51:13 -0700
Commit message:

 gate * to smart ptr
 
Package: CytoML
Commit: b28a7e09a9c4950746a4366640ecfbebc41e52ae
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-22 13:35:52 -0700
Commit message:

 update according to the refactored cytolib
 
Package: CytoML
Commit: e80fb6b91c32df1f90fac706d013359f41fd6626
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-19 11:58:00 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/CytoML into cytoset
 
Package: CytoML
Commit: 9c01bae371301982703498e9b578a66e3b068f6e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-19 11:45:15 -0700
Commit message:

 add the missing code from merging trunk to cs #289
 
Package: CytoML
Commit: 24e56d04936122db7d4253e87c7fb75800928499
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-17 16:37:27 -0700
Commit message:

 use non-header-only version of cytolib
 
Package: CytoML
Commit: 9e7224d0228cb3f0817042cce32d7ec77d5543e3
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-07-17 11:45:02 -0700
Commit message:

 Update for FredHutch/cytolib@52ca5ec
 
Package: CytoML
Commit: e8a36df123880cb3034db91d3a310fdbc94d4670
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-12 14:13:15 -0700
Commit message:

 load flowCore in tests
 
Package: CytoML
Commit: b106ad3e330d644db9e4950df2ee1f9799942218
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-11 14:51:09 -0700
Commit message:

 remove merging contaminants
 
Package: CytoML
Commit: d88d61d7f144ebc59438aef8ce4e54b3f06bbe63
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-02 10:19:03 -0700
Commit message:

 merge trunk
 
Package: CytoML
Commit: 6d15ecdbf1d71ee15dba51fbcd9b28fc95b8353e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-11 15:42:30 -0700
Commit message:

 add test-internal-suite
 
Package: CytoML
Commit: dac3ee97fbabb6f258ac12ccc3bfe734d84c420d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-11 14:49:09 -0700
Commit message:

 bump
 
Package: CytoML
Commit: 44bd94a8990ea3c97e200a1c40a3440f40468792
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-10 14:27:25 -0700
Commit message:

 call scale_time_channel separately
 
Package: CytoML
Commit: e1bf311745020a65c2c5621413c86a637fd8325c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-07 10:44:52 -0700
Commit message:

 run roxygen
 
Package: CytoML
Commit: 7b17c915f8cdcb1b78d1fd09a6db9b6b7661420a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-06 14:57:59 -0700
Commit message:

 close #58
 
Package: CytoML
Commit: f0b3370654f877df9aa7606ce156d23405abf97a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-04 16:29:35 -0700
Commit message:

 load ncdfFlow
 
Package: CytoML
Commit: 328101fabaf195d65bdcc778b9adf823e5923389
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 13:44:27 -0700
Commit message:

 fix references to legacy gs archive
 
Package: CytoML
Commit: adef9ac14f5692e34d30fbb648b93b68f1aa6bd0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 13:39:14 -0700
Commit message:

 fix test case for Inverse function of flog
 
Package: CytoML
Commit: 7e2efc655045dcb53abcf48b543b3c5d0c0263aa
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 13:31:28 -0700
Commit message:

 fix folder name for duplicatedSampleID test case
 
Package: CytoML
Commit: c0abdc0c301c5a0c49ec8519fb6b240a533901e4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 12:13:17 -0700
Commit message:

 getSampleGroups --> fj_ws_get_sample_groups
 
Package: CytoML
Commit: d227d7e569ac73852c0d5c5c49fa2fadf3e93c87
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 12:09:12 -0700
Commit message:

 rbind2 --> gslist_to_gs
 
Package: CytoML
Commit: 4be0efb85a6a08a10ec713b0e779c3593e2794e9
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 12:07:55 -0700
Commit message:

 fix diva_workspace class
 
Package: CytoML
Commit: bb53f54b85e0efe868bbb5ad0723118dc2a93ecc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 12:01:57 -0700
Commit message:

 fix fj_ws_get_keywords
 
Package: CytoML
Commit: 5e8ec84a47ac53a3eec21132490ccadb8c581961
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 11:31:46 -0700
Commit message:

 getCompensationMatrices --> gs_get_compensations
 
Package: CytoML
Commit: 891d6ecd1b784b8036d9c560fda9b2eaefc221c4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 11:28:19 -0700
Commit message:

 getData --> gs_pop_get_data
 
Package: CytoML
Commit: 1da2892bbf7d9e61caac25403b2c1408eac4bbbb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 11:24:56 -0700
Commit message:

 getSampleGroups --> fj_ws_get_sample_groups
 
Package: CytoML
Commit: 83421460cf470b95a1fd889450e8b2091cd3ea1d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 11:21:18 -0700
Commit message:

 merge trunk
 
Package: CytoML
Commit: d779c124f599664ac600e1aa90064556fca60aff
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-28 14:04:05 -0700
Commit message:

 Merge branch 'trunk' into cytoset
 
Package: CytoML
Commit: 4e53a0a88be46af3beae27ad28e3fa5cb78f1511
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-21 10:23:23 -0700
Commit message:

 update
 
Package: CytoML
Commit: 2e816ffaeb589e86eeb783f12e6fb6dd58032a74
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-20 11:34:26 -0700
Commit message:

 merge cytoverse/trunk
 
Package: CytoML
Commit: aa0d5ff7d7e50ce838699e2a2da817c20d778142
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-22 14:02:35 -0700
Commit message:

 add flowjo parser
 
Package: CytoML
Commit: 8822aa28d78fe337bbd7f98080539a8832b53158
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-11 11:51:32 -0700
Commit message:

 merge trunk
 
Package: CytoML
Commit: 11d0afe48cf36ac0a41987faca7cac6efa2600d1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-11 11:43:39 -0700
Commit message:

 Merge branch 'trunk' into cytoset
 
Package: CytoML
Commit: a31bd1e598b8669613fd91a82378094b5853779b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-08 15:04:44 -0800
Commit message:

 fix tests
 
Package: CytoML
Commit: fa9ce9d5c209084ffab51afb0e72fe6413b11aff
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-07 15:12:46 -0800
Commit message:

 cytobankExperiment
 
Package: CytoML
Commit: 6c87ac40b540a82795bb2b14988d132488c4323d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-26 16:54:18 -0800
Commit message:

 Merge remote-tracking branch 'origin/cytoset' into cytoset
 
Package: CytoML
Commit: 3d495cbebedf0f84fe4efbbdd11e66aa4abdc93a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-26 16:50:48 -0800
Commit message:

 export parseWorkspace s3 generic
 
Package: CytoML
Commit: ea892110e9eb1819abdaa6decdd3736c2754b82f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-23 22:02:01 -0800
Commit message:

 fix #49
 
Package: CytoML
Commit: 0295ed51bce8bf6f5cc7b2a069865e60db75dbe4
Author: gfinak <greg.finak@gmail.com>
Date: 2019-02-15 11:42:13 -0800
Commit message:

 udpate
 
Package: CytoML
Commit: f2c4e2824178e25e437da9f37b25c8db7bb802b6
Author: Greg Finak <greg.finak@gmail.com>
Date: 2019-02-15 11:38:23 -0800
Commit message:

 Update DESCRIPTION 
Package: CytoML
Commit: 88d1ab6d04c773b3a0a4f981cf53ed4e086041dd
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-30 16:02:44 -0800
Commit message:

 bump to 2
 
Package: CytoML
Commit: 026f3385fbef9861a74ed0662cd0aff32f556daa
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-30 14:53:23 -0800
Commit message:

 Update calls to ggcyto::transform_gate() to renamed ggcyto::rescale_gate()
 
Package: CytoML
Commit: ba4843c3610ec39bbd5254a0b454a8e47c60ccbe
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-30 14:49:56 -0800
Commit message:

 update
 
Package: CytoML
Commit: 4dc536fab39b7a8b7b2f5f34f5a3524ac010e13f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-23 15:03:52 -0800
Commit message:

 use cytoset in diva parser
 
Package: CytoML
Commit: f9f41aef8ccecad7b55aa9da968376ab1b802c1a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-15 14:50:43 -0800
Commit message:

 unlock gs temporarily in GatingSet2flowJo
 
Package: CytoML
Commit: 236506290c5a412d2fcf7929e05cf82f5fd98eeb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 14:57:40 -0800
Commit message:

 use S3 for getSamples
 
Package: CytoML
Commit: f27cf7ce7b76257d3da37062f32e9cb98380f18a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 13:33:33 -0800
Commit message:

 fix diva parser for cytolib2
 
Package: CytoML
Commit: 856e5d5a6d14fd78633c20150ab9ba43489f9a88
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 12:49:36 -0800
Commit message:

 update according to the latest changes in cytolib2
 
Package: CytoML
Commit: 2cebfe13e6797bfda2730a526c19464f4052b58b
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-09 12:11:34 -0800
Commit message:

 Convert parseWorkspace for divaWorkspace objects to S3 Method
 
Package: methylGSA
Commit: 56ef0e8784bb617edba0f7ab16892ef7c561f56e
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2019-11-21 11:53:33 -0500
Commit message:

 updated
 
Package: BioQC
Commit: 423017c491aa0d98aec9fc961bc7b2754285468c
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-21 16:41:44 +0100
Commit message:

 much faster readGmt files thanks to turning off the isValidity check
 
Package: BioQC
Commit: 15d445e019853155f713147485d6e4afc271a710
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-21 16:41:20 +0100
Commit message:

 export isValid functions
 
Package: BioQC
Commit: 3438683df2ab534d02ca9118180a1f33466d1772
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-21 16:36:24 +0100
Commit message:

 turn off setValidity by default, export the functions so the users can check when they wish
 
Package: BioQC
Commit: eebd7a7f87efa0101e686ebe749ad2052541f2a7
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-21 16:36:01 +0100
Commit message:

 add isValid functions
 
Package: BioQC
Commit: e30fb79d6f2922f1994a4da7c9c9c0b38e294b6f
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-21 16:35:50 +0100
Commit message:

 return a plain list from readSingleGmt
 
Package: BioQC
Commit: f68e4e03f97d0ba1149f0d76418acc821b27d9bc
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-21 16:08:18 +0100
Commit message:

 using Roxygen 7.0.0, and version bump thanks to improved error message in readSingleGmt
 
Package: BioQC
Commit: 1578fd67a9e65c6c022b7015912e87c9db52267c
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-21 15:57:24 +0100
Commit message:

 in case a gmt file does not exist, print its name for easier debugging
 
Package: phantasus
Commit: 5d2cf021ab7c15563b9e666e5d9bb18dfa2c9779
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-11-21 12:49:38 +0300
Commit message:

 version bump
 
Package: phantasus
Commit: 24006828babe7889b7b0a6bac621f1a3b96c6131
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-11-21 12:49:23 +0300
Commit message:

 support for hierarchical preloaded folder
 
Package: phantasus
Commit: a9620dd90035eec9b8fe5e5edd1008619317fd19
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-11-21 11:57:56 +0300
Commit message:

 Fixed direction in DESeq2
 
Package: phantasus
Commit: 604085f3236126e20ad8a7df1242483642d8f4b3
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-11-21 11:52:12 +0300
Commit message:

 Merge branch 'develop'
 
Package: phantasus
Commit: 078c2f0b7a3f265a081a937c461abc44c4569140
Author: Vladislav Kamenev <vlad.kamenev96@gmail.com>
Date: 2019-11-19 20:26:13 +0300
Commit message:

 Update JS
 
Package: phantasus
Commit: 4c76376aab0889cb916d41b5ea34209449fde030
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-11-19 18:58:35 +0300
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/phantasus
 
Package: phantasus
Commit: de8eb3600b43dca6cbcb1b6368650caa60988e5d
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-22 13:41:43 +0300
Commit message:

 Volcano graph
 
Package: phantasus
Commit: 42e0e7e39e87f3267385ba63b71571ac855334eb
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-22 13:41:00 +0300
Commit message:

 GEO: Safer brief data downloader
 
Package: phantasus
Commit: 48cbc7b1cfaebc37e3d5a2a5f5cce280a7ebe1e3
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-13 00:51:50 +0300
Commit message:

 ARCHS4: safe column adder
 
Package: phantasus
Commit: f17b4cbe22c18447ddc24bc5d6eb192e740d3c9b
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-11 17:22:40 +0300
Commit message:

 NGINX: revalidate frontend cache
 
Package: phantasus
Commit: 040b6f90fbb723ed253a66ad9f712d5a36b70411
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-11 06:13:15 +0300
Commit message:

 Brief data fail-safe improved
 
Package: phantasus
Commit: 285bf324f517cd9532a892b51ed51aeee75025ec
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-10 19:00:03 +0300
Commit message:

 TRAVIS: remove specific fgsea version
 
Package: phantasus
Commit: 515773ffa958b3d72fc5221c51e87524922eb66a
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-10 18:46:11 +0300
Commit message:

 DESeq: finalisation
 
Package: phantasus
Commit: 2855eac580666625dbfcef8f0aee1f510a3aa671
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-04 07:29:17 +0300
Commit message:

 Typo fixes
 
Package: phantasus
Commit: 5eda2a55c4a23f99679d16c4cbaa6d9819ec62cd
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-04 07:25:06 +0300
Commit message:

 ARCHS4: populate test h5 file
 
Package: phantasus
Commit: 04f5c8897a8c3bd207ca9107a4cb92f65ec6cdd7
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-09-04 07:18:36 +0300
Commit message:

 GEO: support for experiment type checking
 
Package: phantasus
Commit: f3ef1d1d0b345b08132a9574ddc7ccab361a1ae5
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-08-22 16:57:33 +0300
Commit message:

 ARCHS4: metadata population
 
Package: phantasus
Commit: c6e7a2ac0bfb065f36340d2096bf751a7b816f32
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-08-22 16:51:43 +0300
Commit message:

 DESeq: Results -> lfcShrink
 
Package: phantasus
Commit: ba7ccd758c0c570a39e2ad9e538e2929ef5803b0
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-08-19 06:53:46 +0400
Commit message:

 Limma test fix
 
Package: phantasus
Commit: f4239e049c2b5176adeebfc95e35786c8c361af3
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-08-19 05:05:26 +0300
Commit message:

 Fail-safe binary creation for loadGEO
 
Package: phantasus
Commit: ee858b2ec74ae2f32654dd4544bee47a2505118a
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-08-19 05:04:59 +0300
Commit message:

 Update JS. DESeq2
 
Package: phantasus
Commit: 1213956817f73f8bf82d17dc9824b1aaee0f0242
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-08-19 05:04:44 +0300
Commit message:

 DESeq2
 
Package: phantasus
Commit: c51bc9ecb7dd14ed5867380ee3c7649a82e25736
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-09-06 13:41:21 +0400
Commit message:

 FGSEA: use BioC version
 
Package: phantasus
Commit: 4a39c05b95e735c640ac8ce90ea9e6e10d3ea30a
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-08-19 14:58:55 +0300
Commit message:

 OpenCPU folder missing ind Dockerfile
 
Package: phantasus
Commit: 0e730f3f21af2bcb94d162755fa71c6acb15babe
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-07-19 16:00:20 +0300
Commit message:

 Merge pull request #133 from ctlab/develop

New gpl loader. Example dataset  
Package: phantasus
Commit: d7d45536073dbe2db0c45906a17ff17f5a140e2f
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-07-19 13:37:48 +0300
Commit message:

 Update JS. Example dataset
 
Package: phantasus
Commit: 0005ba3af07560511a586992e649d3f25fb4d821
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-07-19 13:32:09 +0300
Commit message:

 New GPL loader
 
Package: phantasus
Commit: 5bfe49cd5b3f50ddb61aae141c501dc2bea4472b
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-07-19 13:24:31 +0300
Commit message:

 Revert "New GPL loader"

This reverts commit e85d77a39d90917fcc9126958b24c11d660ca5ad.
 
Package: phantasus
Commit: e85d77a39d90917fcc9126958b24c11d660ca5ad
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-07-19 13:23:31 +0300
Commit message:

 New GPL loader
 
Package: phantasus
Commit: 31799acf1a273ffcdbd78cc662796ba12fc24f46
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-28 09:23:39 +0300
Commit message:

 Update tutorial
 
Package: phantasus
Commit: 49c0a1a175e95bf722b2e931b2acb2effd61a381
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-28 09:18:04 +0300
Commit message:

 Update JS. Hide reproduce code
 
Package: phantasus
Commit: 3e3c209b70967b81874e90bbb14d087b1a2d1c82
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-27 16:57:55 +0300
Commit message:

 GSEA plot tutorial fix
 
Package: phantasus
Commit: 6953b28d1f40991f69aeac2cf95365549667711a
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-06-26 21:07:03 +0300
Commit message:

 fgsea database example with eval and symbols
 
Package: phantasus
Commit: 282cc9d8b488f1cca3e5e08899001f7540b16f38
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-26 16:43:30 +0300
Commit message:

 Phantasus tutorial final draft
 
Package: phantasus
Commit: b9961f70c3fa2b387453b0181e8be916b239be68
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-06-25 13:23:20 +0300
Commit message:

 Added citation info
 
Package: phantasus
Commit: 78e4ae95aba4336fdd281b1baec7022359f5bdbe
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-06-25 00:17:04 +0300
Commit message:

 tutorial fixes
 
Package: phantasus
Commit: b842c8decfcaa2f00484759843f0563c327696a2
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-24 19:04:45 +0300
Commit message:

 Tutorial typo
 
Package: phantasus
Commit: db827317cab581aa01fe7a6b79f708469c9f860b
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-24 18:24:02 +0300
Commit message:

 Missing files
 
Package: phantasus
Commit: 225592656e88dc5fa1c1e41790387c3c2167443a
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-24 17:20:43 +0300
Commit message:

 New tutorial
 
Package: phantasus
Commit: 4137063c9e2fcbec50c50efffb5946cbca69ef00
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-21 16:11:12 +0300
Commit message:

 Update JS
 
Package: phantasus
Commit: cc8a30d8bcabbd2704338d01ef03d299156b7254
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-21 16:10:10 +0300
Commit message:

 Omit unannotated removes NA aswell
 
Package: phantasus
Commit: c81f40f10e1e8f67c4ba7731cdff6a87e28dd666
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-20 15:22:53 +0300
Commit message:

 Pattern fix
 
Package: phantasus
Commit: 30a15f12e35da6779ec4f5565096b81e9dbf57dd
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-19 15:57:07 +0300
Commit message:

 AnnotationDB confusion fix
 
Package: phantasus
Commit: 495ad23902412a1daae6ad01a8b5a4cecd93a24c
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-19 15:56:44 +0300
Commit message:

 Fix Docker build
 
Package: phantasus
Commit: 8499e74a57ac9b2363de2440ce59e6da4e8b4ba6
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-19 15:02:59 +0300
Commit message:

 Travis fix
 
Package: phantasus
Commit: 3b3018d01436a45eb20ad1f26fd00d7b8147f6f0
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-06-17 17:44:16 +0300
Commit message:

 Fix non-validated cache for static
 
Package: phantasus
Commit: f719054645e1563cfb03ca53bea1096aa3c988cd
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-06-03 19:06:17 +0300
Commit message:

 Update JS
 
Package: phantasus
Commit: 3de0c016497e3033015098c950faa5a935adc207
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-06-03 19:05:41 +0300
Commit message:

 Reproduce tool
 
Package: phantasus
Commit: e561ff25e39799804db2dfe90bebb688da823a33
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-20 18:20:10 +0300
Commit message:

 Update JS. Minor interface revamp
 
Package: phantasus
Commit: 31de96909bec18a03e03726578422166ec665ce1
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-16 16:12:19 +0300
Commit message:

 Update JS. HeatMap JSON loaing
 
Package: phantasus
Commit: 072c8400c2085522903eace711b6a0ca3f305bbc
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-16 15:59:25 +0300
Commit message:

 HeatMap JSON view
 
Package: phantasus
Commit: 155fcfae73739855d34adb642fbaea167c99450d
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-13 19:08:37 +0300
Commit message:

 Update JS. Title fix
 
Package: phantasus
Commit: 7dbf43289e8f4f427f24aca1f317523e713db794
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-13 16:36:24 +0300
Commit message:

 Add phantasus to opencpu preloaded packages?
 
Package: phantasus
Commit: 364fe3d7c445929a1e2a8674c92736176bc8491d
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-13 16:35:38 +0300
Commit message:

 Forbidden all packages but phantasus. Related #117
 
Package: phantasus
Commit: 59687962c4d3906337481084601fa2c7a16ac38f
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-22 10:56:23 +0300
Commit message:

 Use hotfixed GEOquery version. 
Package: phantasus
Commit: 7f59e035689c520889623f46199397601cf4959b
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-05-21 21:39:36 +0300
Commit message:

 hot fix for hanging on empty annotation file
 
Package: phantasus
Commit: 5427f58f6d9ea864371e8e3664f9714146178c6d
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-05-21 12:21:59 +0300
Commit message:

 verbose selfCheck
 
Package: phantasus
Commit: e8d0803a63bc0d0f6ccdfd22c4bfcaa68349e5b6
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-13 10:07:11 +0300
Commit message:

 Update Dockerfile

Temporarily fix #121 
Package: phantasus
Commit: 0d38506dd00bb0751dc6cad0cea78cb80c117a95
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-05-10 00:04:47 +0300
Commit message:

 Update JS
 
Package: phantasus
Commit: 5621ded660bf1b2a5091d85d8dbbcebb3f39784e
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-08 17:04:38 +0300
Commit message:

 Temporary duplicate OCPU location
 
Package: phantasus
Commit: 27d3fc866a311fce403b149171d4fd5152421636
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-08 13:51:04 +0300
Commit message:

 Merge pull request #122 from ctlab/develop

Develop 
Package: phantasus
Commit: fbe2266cce96bac7aa95e8c9996bd759929ac933
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-05-08 13:50:35 +0300
Commit message:

 Update JS. Decreased number of requests to OCPU
 
Package: phantasus
Commit: 1f71871cd5db0d679e9c02f11a14ca71727d6ceb
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-04 16:45:22 +0300
Commit message:

 Update JS. Chart warning message revised
 
Package: phantasus
Commit: 2ca6f3c0815037cadb541d3fc61484dbe73c84cb
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-04 16:38:07 +0300
Commit message:

 Phantasus self-check before serving
 
Package: phantasus
Commit: 9744c384fb3d902e2269c01561d06704459458d2
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-04 15:34:38 +0300
Commit message:

 Update JS. Charts performance concerns
 
Package: phantasus
Commit: 543188351cfade17eede2c055975bd89b84c58ea
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-03 17:04:12 +0300
Commit message:

 Update JS. Tools reorganization
 
Package: phantasus
Commit: 7690f1f9b574af33ab0a3714ac16752f86539444
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-03 16:55:33 +0300
Commit message:

 Update JS. PCA plot enchancement. Linked dataset notice
 
Package: phantasus
Commit: b0310600e3bbcc0fa9771024092ccd5e6d57886d
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-03 16:04:21 +0300
Commit message:

 Remove versions from ENSEMBL
 
Package: phantasus
Commit: f56bbb2fcbe917db4b3bdf9f5c6b629109717553
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-03 00:12:49 +0300
Commit message:

 Add cairo package on OS X
 
Package: phantasus
Commit: d0bf13f1515709d4bc18c8205e4fafab44bd3f54
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-02 21:47:36 +0300
Commit message:

 Biocheck error fix
 
Package: phantasus
Commit: e1e663c5d295e59c226e1cd3273e7482aa200e6b
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-02 21:15:15 +0300
Commit message:

 Named linked datasets
 
Package: phantasus
Commit: c3e232858ae5291ff12de971f82d8e841c3353e9
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-05-08 11:22:55 +0300
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/phantasus
 
Package: phantasus
Commit: 5f43e6e574007b83890148fab807d98f2df47271
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-29 20:57:34 +0300
Commit message:

 Update JS. Old browser warnings + default library path
 
Package: phantasus
Commit: b3cd3f7a67bbb12411ae2f2a06868f5fa38c3789
Author: Vladislav Kamenev <mazahakaforever@ya.ru>
Date: 2019-04-29 19:04:01 +0300
Commit message:

 Fix reparse error
 
Package: SpidermiR
Commit: cf4795e3b053dd88247d32dbf4d318cf6f5bc59c
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-21 10:32:01 +0100
Commit message:

 update_21nov2018_SECOND_MASTER
 
Package: SpidermiR
Commit: 976c6a7394aa4cedb9a2e156422ef079102066d0
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-21 09:52:36 +0100
Commit message:

 update_21nov2018_SECOND_MASTER
 
Package: SpidermiR
Commit: 7671c71bddca61f9fc82338b7fb1ca4b08ef6482
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-21 09:30:32 +0100
Commit message:

 update_description_21_nov
 
Package: SpidermiR
Commit: 6d2f569b8477c6346ad95901b1e224ae3fb3ac49
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-20 16:48:37 +0100
Commit message:

 update_release_20novpm
 
Package: SpidermiR
Commit: 7df7f13999bb51fde70c18224c3b01c21532b826
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-20 16:47:14 +0100
Commit message:

 update master 20 november_pm
 
Package: SpidermiR
Commit: a9dfb9bfcffad67ab78252bf6cdc7245d689542d
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-20 09:19:26 +0100
Commit message:

 updateMaster_20november2019
 
Package: SpidermiR
Commit: 01cf83cee129c04961fb5a9b6fe94163d95e617e
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-19 17:02:37 +0100
Commit message:

 19novemberpm
 
Package: SpidermiR
Commit: 288300f543a2a6b1e0e59fe779213bd671f5cea7
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-19 09:40:31 +0100
Commit message:

 release
 
Package: SpidermiR
Commit: 7dd2e6d9860f1a6cf829c5e694a43eb925a572bb
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-18 17:23:17 +0100
Commit message:

 update release
 
Package: SpidermiR
Commit: 4945c9a15aaf08ad102a7d5a496007c08ae395e4
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2019-11-18 17:17:57 +0100
Commit message:

 update_developers_18november2019
 
Package: mixOmics
Commit: 59c7a85e2db2555508af7196dbd01bccdb2b1ef3
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 12:45:44 +1100
Commit message:

 perf.diablo supports progressBar on repeats
 
Package: mixOmics
Commit: c06efe58bc845ab53d33c47e05790b9242010720
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 12:45:20 +1100
Commit message:

 progressBar default to FALSE for all
 
Package: mixOmics
Commit: 3e1ff394ab1d16e5c3c96891763fef3e14478459
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 11:54:21 +1100
Commit message:

 update NEWS
 
Package: mixOmics
Commit: 529d16466744dc3e3f81c4d3a70bb670464256c0
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 11:29:07 +1100
Commit message:

 rename internal tester
 
Package: mixOmics
Commit: 432df24f24788f58892425cf290170b1db4a122b
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 11:28:13 +1100
Commit message:

 improve tune.spls tests
 
Package: mixOmics
Commit: efef231e9947801bfae02c27915918bad7e30ec6
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 11:21:38 +1100
Commit message:

 add tune.splsda tests
 
Package: mixOmics
Commit: b661f0296d621fb9f041d53bd41ee204b7d5a16c
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 11:14:57 +1100
Commit message:

 improve parallel tune.splsda
 
Package: mixOmics
Commit: ffcec88add27ce5b019890ca4801abe71227b86f
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 11:14:26 +1100
Commit message:

 reduce test cpus

as r CMD check requires max 2
 
Package: mixOmics
Commit: 75e8ac2a085b0c4071fe285c51a87168d2564e38
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 11:02:43 +1100
Commit message:

 check warning fix
 
Package: mixOmics
Commit: 8c764b045276990ef9446c5fc171ed9ab8b5bb79
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-20 13:39:03 +1100
Commit message:

 fix typo
 
Package: mixOmics
Commit: af5489eaddffc5be38166b3f6c1818ab47f32d6b
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-20 13:23:08 +1100
Commit message:

 perf DA to use FORK cluster for Unix-like
 
Package: mixOmics
Commit: 34796120520f3cd4e075aefdaedfd8620c02e4dd
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 10:46:13 +1100
Commit message:

 add tune.diablo tests
 
Package: mixOmics
Commit: cf8650d96ed57347b3fbd21a91285b26531f340f
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-20 12:37:31 +1100
Commit message:

 improve parallel setup for perf DA
 
Package: mixOmics
Commit: 365cbad603fe61b7f00b011e84d5d5b98ecaad94
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-20 12:32:51 +1100
Commit message:

 fix typo
 
Package: mixOmics
Commit: e8a8aa93ae4f4a8305d48579e447e0adf9d8678c
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 10:39:08 +1100
Commit message:

 add tune.spls tests
 
Package: mixOmics
Commit: 05462686d710243dbccce75f51e0b855b08743d6
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 10:35:33 +1100
Commit message:

 enhance parallel setup for tune.spls

* !missing(cpus) -> cpus > 1
* use FORK for non-Windows
* use on.exit so even after errors connections are closed
 
Package: mixOmics
Commit: b550da7718fcab5d27b19c728683527f02704da8
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-19 18:50:39 +1100
Commit message:

 perf.diablo supports auc

A simple average auc is calculated for all blocks
 
Package: mixOmics
Commit: 4b7eaea8ce7abf92afb70fe3af706185dab04d6e
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 10:14:23 +1100
Commit message:

 tidy up perf.diablo parallel setup
 
Package: mixOmics
Commit: 8c0aa962e36ede502b41d4ccd2bbd14942e44001
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-19 17:35:25 +1100
Commit message:

 ignore .Renviron
 
Package: mixOmics
Commit: 4deb65f5d0778dd91cc880350ebc3801ae25ce6f
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-19 17:34:26 +1100
Commit message:

 conditional print for auroc
 
Package: mixOmics
Commit: cd48fc8e6be319bcaba2a5af5395f42f8f9b3f27
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-21 09:59:47 +1100
Commit message:

 perf.diablo now parallel on nrepeat
 
Package: mixOmics
Commit: e803907f12b1e83e7603167dd87b26bec1e44558
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-19 14:37:05 +1100
Commit message:

 add cluster definition
 
Package: mixOmics
Commit: 74c978e412176f651328f023d72739777a840c8d
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-19 14:24:24 +1100
Commit message:

 perf.diablo if(!missing(cpus)) -> if(parallel)
 
Package: mixOmics
Commit: 1ae472b7e03dc618965bded651856c85230c76b6
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-18 16:12:29 +1100
Commit message:

 fix t.test.process bug when error rates are equal

When next component does not improve the error rate and the error rates are constant, return insignificant p-value
 
Package: mixOmics
Commit: 07cf18f446756dc2ebb8cc77e2cb5d7fb2781b25
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-18 14:15:54 +1100
Commit message:

 helper function to ignore $call in unit tests
 
Package: mixOmics
Commit: d1d2702c5e20d01c86656bc1d9bb87d8789a5ba0
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-20 13:49:52 +1100
Commit message:

 move stratified.subsampling
 
Package: mixOmics
Commit: e8df94ab89f8219c87e38e3d4fb69391752fd313
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-15 14:29:45 +1100
Commit message:

 export cluster once - use .onUnix()

.onUnix() checks if the OS is Unix-like to create FORK clusters
 
Package: mixOmics
Commit: f173e258cbb64deed49d2053b88df5a9d9bb7d0a
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-09-20 13:49:54 +1000
Commit message:

 drop unused variable
 
Package: mixOmics
Commit: a9dd532026a10e2b79c7bf2dcc01a9725f34d771
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-14 17:06:25 +1100
Commit message:

 add some tests
 
Package: mixOmics
Commit: ea6edadfc9eb79accc97bfd69628b9df96d2c167
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-14 17:05:26 +1100
Commit message:

 custom significance threshold for tuning of DA models
 
Package: mixOmics
Commit: 6a4f546a7b6831c9e4d7b4b8a763632283ab45aa
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-14 15:43:33 +1100
Commit message:

 more readable t.test.process with improved condition handling

## comparing to the old code:

t.test.process_old = function(mat.error.rate, alpha = 0.01)
{
    # mat.error.rate has nrep rows and ncomp columns
    # we test successively whether adding a component improves the results

    max = ncol(mat.error.rate) #number max of components included
    pval = NULL
    opt = 1 #initialise the first optimal number of components
    for(opt in 1:max)
    {
        j=opt+1
        temp = try(t.test(mat.error.rate[,opt],mat.error.rate[,j],alternative="greater")$p.value, silent=TRUE) #t.test of "is adding X comp improves the overall results"
        if(is(temp, "try-error") || is.na(temp)) # temp can be NaN when error.keepX is constant
        {
            pval = 1
        } else {
            pval = temp
        }
        #print(opt)
        #print(j)
        #print(pval)

        while(pval> (alpha) & j<max)
        {
            j=j+1
            temp = try(t.test(mat.error.rate[,opt],mat.error.rate[,j],alternative="greater")$p.value, silent=TRUE) #t.test of "is adding X comp improves the overall results"
            if(is(temp, "try-error") || is.na(temp)) # temp can be NaN when error.keepX is constant
            {
                pval = 1
            } else {
                pval = temp
            }
            #print(opt)
            #print(j)
            #print(pval)
        }

        if( (pval> (alpha))) #if all pvalues were greater than alpha, then we do not increase opt and get out of the loop
            break
    }
    ncomp_opt = opt

    return(ncomp_opt)
}

expect_equal(t.test.process(data.frame(comp1=100:104, comp2=20:24, comp3=10:14)), t.test.process_old(data.frame(comp1=100:104, comp2=20:24, comp3=10:14)))

expect_equal(t.test.process(data.frame(comp1=100:114, comp2=20:24, comp3=50:54)), t.test.process_old(data.frame(comp1=100:114, comp2=20:24, comp3=50:54)))

expect_equal(t.test.process(data.frame(comp1=10:14, comp2=20:24, comp3=50:54)), t.test.process_old(data.frame(comp1=10:14, comp2=20:24, comp3=50:54)))
 
Package: mixOmics
Commit: a44c35c8981b091077aa3fa562cd47dfc9eaea55
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-14 15:41:35 +1100
Commit message:

 add unexpected condition handler
 
Package: mixOmics
Commit: ff96aa5ca27ba85c4b85d6b817c94606caa6d5fa
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-14 15:27:31 +1100
Commit message:

 ./gitignore
 
Package: mixOmics
Commit: 3a70a2a4bd30b9c6a3d5b71811685a1a946c7e3e
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-12 14:25:22 +1100
Commit message:

 bump up devel version after bug fix
 
Package: mixOmics
Commit: a86ba1fd4f58267053ee5a204b5c0c7044e3d04d
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-11 12:47:31 +1100
Commit message:

 .check_cpus to return cpus explicitly
 
Package: mixOmics
Commit: 3c7f2ee8e0f7ec2f85e841380b6e9a5d5bf2acac
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-08 15:30:18 +1100
Commit message:

 shorter cim plot err msg
 
Package: mixOmics
Commit: 392ada854cee971ed3ee0d0b79e24df97720f9ce
Author: Al J Abadi <al.jal.abadi@gmail.com>
Date: 2019-11-08 15:23:29 +1100
Commit message:

 update NEWS
 
Package: DMRcate
Commit: 3b6ed4b55597a4dba0856912b1111aa7dd48b80f
Author: Tim Peters <t.peters@garvan.org.au>
Date: 2019-11-21 11:33:13 +1100
Commit message:

 DESC_devel
 
Package: DMRcate
Commit: 992bec0d2df8f393eb756c054d31d82390bd452a
Author: Tim Peters <t.peters@garvan.org.au>
Date: 2019-11-21 11:30:52 +1100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: DMRcate
Commit: 351ac7c6a45335bb8c86733304d252298f1b9da7
Author: Tim Peters <t.peters@garvan.org.au>
Date: 2019-11-21 11:26:00 +1100
Commit message:

 DMRcate_2.0.1
 
Package: ensembldb
Commit: 3cb567ff7568de78aab01b8e3464be019087d238
Author: jorainer <johannes.rainer@gmail.com>
Date: 2019-11-20 21:47:11 +0100
Commit message:

 Fix mapIds issue
 
Package: FlowSorted.Blood.EPIC
Commit: d2e7bbfbe77bad9de5d60868d52ebb71af3ae2cd
Author: Lucas Salas <lucas.a.salas.diaz@dartmouth.edu>
Date: 2019-11-20 15:03:30 -0500
Commit message:

 Correcting addtional datasets and vignettes
 
Package: TCGAutils
Commit: da7b5525f001644605edf644ea972f86486af8d1
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-11-20 12:54:09 -0500
Commit message:

 check for empty delimiters in IDs
 
Package: ViSEAGO
Commit: 89bc0be5623714e88841f4f2e526d44323772c76
Author: abrionne <aurelien.brionne@inra.fr>
Date: 2019-11-20 14:15:40 +0100
Commit message:

 GOterms_heatmap patch for single condition gene_frequency
 
Package: SplicingGraphs
Commit: 8aa1a421ed8a3a25bbb960db404b5681e8c24166
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-11-19 21:45:12 -0800
Commit message:

 Add updateObject() method for SplicingGraphs objects
 
Package: IRanges
Commit: 3f607cbea7c345995e28e37d554d955c019506dc
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-11-19 21:34:59 -0800
Commit message:

 Small improvement to updateObject() method for CompressedList objects
 
Package: ggtree
Commit: 860448f433c721180e776c41bad3961d03d7129c
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-20 11:58:34 +0800
Commit message:

 add reference
 
Package: CellBench
Commit: 6ce103f4be1c30bef855f020aabbcf3ac2565a9f
Author: Shians <registertonysu@gmail.com>
Date: 2019-11-20 10:58:27 +1100
Commit message:

 Version bump
 
Package: CellBench
Commit: 4a366da2802e914727eb0ce4cea7ec427081b4fb
Author: Shians <registertonysu@gmail.com>
Date: 2019-11-20 10:57:33 +1100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/CellBench
 
Package: CellBench
Commit: 0751ae3f0f2f541cfbd16dc4d0924146f31709bb
Author: Shians <registertonysu@gmail.com>
Date: 2019-11-20 10:56:19 +1100
Commit message:

 Relocated case study
 
Package: CellBench
Commit: ff8e891d012be17faf6b5ea8b6b5ba2d6dac74cd
Author: Shians <registertonysu@gmail.com>
Date: 2019-11-20 10:56:00 +1100
Commit message:

 Removed extra line
 
Package: flowTrans
Commit: c8dba37c24cb650a13e0d18f296fabe8d125f695
Author: gfinak <greg.finak@gmail.com>
Date: 2019-11-19 12:32:26 -0800
Commit message:

 Fix .Call since Rcpp exports has changed format, prefix _
 
Package: debrowser
Commit: 7d7b15340d8c8f4167976e7201880744e085cb61
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-11-19 14:53:10 -0500
Commit message:

 Search genes overlay fix
 
Package: CRISPRseek
Commit: 6f5e190b4523c86b7c3ea9ff95aba2158610fae5
Author: Julie Zhu <julie.zhu@umassmed.edu>
Date: 2019-11-19 13:27:04 -0500
Commit message:

 update documenation
 
Package: CRISPRseek
Commit: b7e9d0d1257df8b0b15ce822ffa64dc303345fd8
Author: Julie Zhu <julie.zhu@umassmed.edu>
Date: 2019-11-19 13:26:05 -0500
Commit message:

 added CRISPRscan efficacy prediction algorithm
 
Package: Pigengene
Commit: 41e4d36fe9a526d9df6d3c1fbf6061b9c03ed8f0
Author: Habil Zare <habil_zare@yahoo.com>
Date: 2019-11-19 10:08:46 -0600
Commit message:

 netwok bug fixed -> network
 
Package: easyRNASeq
Commit: 0f35769fcf19b6703622d0e664a9f4eb8ab5e3d4
Author: nicolasDelhomme <nicolas.delhomme@slu.se>
Date: 2019-11-19 16:03:12 +0100
Commit message:

 Extended the gitignore
 
Package: easyRNASeq
Commit: 7de44419975d0827ff263ecec0b55202d8afe46b
Author: nicolasDelhomme <nicolas.delhomme@slu.se>
Date: 2019-11-19 15:54:47 +0100
Commit message:

 Fixed a namespace issue
Extended the cleanup step of the vignette
 
Package: Biobase
Commit: 073511c45a6ed3060fd30a051dcc6c8abb07cd44
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-11-19 09:07:25 -0500
Commit message:

 version bump
 
Package: Biobase
Commit: 07ec9d02b6c4c1bc29097fd4b14910ddb8a63863
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-11-19 09:04:52 -0500
Commit message:

 remove long-defunct data stubs
 
Package: Biobase
Commit: a23bd22429903bbceeb984799f48e469358df393
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-11-19 09:01:05 -0500
Commit message:

 second part of update to copyEnv

- forgot not to try to map C symbol
- forgot to return new environment in copyEnv
- :(
 
Package: Biobase
Commit: 7cf646c3757d265c713d4e7f6f809efc19628da3
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-11-19 08:48:23 -0500
Commit message:

 remove dead `listToEnv` C code
 
Package: Biobase
Commit: 6c073fa923fc6d5c9d6db68ad318ace7299b1004
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-11-19 08:44:58 -0500
Commit message:

 implement copyEnv() in R

- avoids non-API INCREMENT_NAMED
- doesn't seem like this is used to copy very large environments?
 
Package: Biobase
Commit: 280f33f464a2879c0da5635360e62d1a17d53aeb
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-11-19 08:41:27 -0500
Commit message:

 listLen() is just lengths()
 
Package: scran
Commit: 869adc2d68ca9bac4bb250722d26103039910408
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-18 23:53:44 -0800
Commit message:

 Merge branch 'postrelease'
 
Package: scran
Commit: f34645a95aa4a7cd2c189d1dbabb05a57990f3f6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-18 23:53:37 -0800
Commit message:

 Drop unused levels when restricting or excluding.
 
Package: ggtree
Commit: 2d6b44a976d1f764970418725c81ab02bbc62e71
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-18 20:16:56 +0800
Commit message:

 bug fixed
 
Package: ggtree
Commit: e562021843bd136a9380e183f89e141104100711
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-02 21:21:31 +0800
Commit message:

 update readme
 
Package: ggtree
Commit: fbbd0f085d5075094b003cbdae96e1208f39678c
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-02 16:54:12 +0800
Commit message:

 rm .()
 
Package: ggtree
Commit: e6e8f4be72a96e4af8f83f2492a5064fe0032c25
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-01 17:06:55 +0800
Commit message:

 extend `xlim2` and `ylim2` to support discrete scale.
 
Package: ggtree
Commit: 79e93b9f51a6a0008e210c7c859337e8cfe4befe
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-01 13:57:59 +0800
Commit message:

 xlim2 and ylim2
 
Package: ggtree
Commit: a6ea6d25eac851ca33f11e515d26af90bb8eaba4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-01 12:31:40 +0800
Commit message:

 rm duplicated code
 
Package: ggtree
Commit: 1540db0304af470b1893640c52549c2cf9b90f12
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-01 12:24:00 +0800
Commit message:

 roxygen2md
 
Package: ggtree
Commit: 06f952f0817201d12a5ea342007c30e054430179
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-10-31 17:28:27 +0800
Commit message:

 align_x and align_y
 
Package: ggtree
Commit: 6e77743a9b1b8105accb8d2ceed27220e0d5e8bd
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-10-31 15:16:49 +0800
Commit message:

 ylim_ggtree
 
Package: ggtree
Commit: b57ec7d6c6b75da82067ff309f996dcff8c598de
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-10-30 15:41:23 +0800
Commit message:

 gitee backup
 
Package: ggtree
Commit: c2cfbee3ef926b17716c35d5d9da77a5a70edb92
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-10-30 10:08:50 +0800
Commit message:

 update makefile
 
Package: ggtree
Commit: db6d5e27e4345dd14a735a467e1924c28aa6c00a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-10-30 10:03:01 +0800
Commit message:

 fixed warning
 
Package: ensembldb
Commit: bc76de41cb49b80263406280cacdbeeca26ad7c6
Author: jorainer <johannes.rainer@gmail.com>
Date: 2019-11-19 07:41:29 +0100
Commit message:

 Fix issue in `mapIds` returning empty character if unable to map

- Fix issue in `mapIds` that returned an empty character if the provided IDs
  could not be mapped (issue #104).
- Add documentation for the new gc_content column in tx table (issue #103).
 
Package: ensembldb
Commit: bdeab1ff6ccfba9fce42909e0923beab6e654bba
Author: jorainer <johannes.rainer@gmail.com>
Date: 2019-11-18 14:06:20 +0100
Commit message:

 Add Rmd file to validate GC content

- Add Rmd file that compares the GC content determined during database creation
  with the one calculated in R using the transcript sequences.
 
Package: ensembldb
Commit: d0af53a70b58feee20e7fc2662a80bb59610ae7d
Author: jorainer <johannes.rainer@gmail.com>
Date: 2019-11-15 18:23:45 +0100
Commit message:

 Add column gc_count to the transcript table (issue #103)
 
Package: PureCN
Commit: ed7d10c7ca578bc7d1aabef86893c23ddddf79dc
Author: Markus Riester <markus.riester@novartis.com>
Date: 2019-11-18 18:08:29 -0500
Commit message:

 Updated tests for new example data.
 
Package: PureCN
Commit: 4737b259ee843c7081b433ad61bd1632ac2efdf6
Author: Markus Riester <markus.riester@novartis.com>
Date: 2019-11-18 17:05:23 -0500
Commit message:

 Fixed failed test by updating example data.
 
Package: PureCN
Commit: 964746996ad666a2850a96781238ec7855507a36
Author: Markus Riester <markus.riester@novartis.com>
Date: 2019-11-18 16:13:28 -0500
Commit message:

 callAlterations: handle breakpoints better (fixes #112).
 
Package: PureCN
Commit: 43982fda03cfe92ccffc4947ea5a0ce6c362a134
Author: lima1 <mriester@gmx.de>
Date: 2019-10-29 17:29:12 -0400
Commit message:

 Updated README for new stable version.
 
Package: methylGSA
Commit: 32762a4aff31c07464a88a51e97750815948f9dc
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2019-11-18 19:49:13 -0500
Commit message:

 updated
 
Package: methylGSA
Commit: b73d0d7bf425b9afbe7c6334390d20b9be644a18
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2019-11-18 19:47:27 -0500
Commit message:

 updated
 
Package: methylGSA
Commit: ae9d5c30c0769c30be09ae576791805112ddfac4
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2019-11-18 19:44:55 -0500
Commit message:

 updated
 
Package: RCy3
Commit: 8b00f4159ca2af1db4fdc0a91e80b4cce6ac1ed6
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2019-11-18 16:09:56 -0800
Commit message:

 fixed conflict
 
Package: RCy3
Commit: bf493e818a25db9887eca1aebd6bdc3598b64a1c
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2019-11-18 16:08:32 -0800
Commit message:

 version bump
 
Package: RCy3
Commit: c7a04e011c8a979497314717142d1343fbcd1f06
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2019-11-18 16:01:22 -0800
Commit message:

 doc fixes: roxygen update, man pages, unitTests
 
Package: RCy3
Commit: 20d0aef9b4bd32378637bf9b9883998c1e896e09
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2019-11-18 15:59:04 -0800
Commit message:

 bug fix: #82 missing param, #83 seq_along
 
Package: topdownr
Commit: cefe8376d9c3e7414ef56cae36731297e8359e09
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-11-18 21:09:30 +0100
Commit message:

 fix: .rbind for list with mixed data.frame/DataFrame
 
Package: topdownr
Commit: b24fbbcb56186b2ea7cf54b2a185ae14d252c15b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-11-18 20:18:34 +0100
Commit message:

 chore: rerun roxygen
 
Package: topdownr
Commit: 2a64f5cd77b62d8cf101ea935cc603ccb6b1bc8c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2019-11-18 20:16:53 +0100
Commit message:

 chore: remove deprecated defaultMs{1,2}Settings
 
Package: MTseeker
Commit: e2d8f1e23c9ee669dd86f36859ea98730f0d486b
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-18 14:35:06 -0500
Commit message:

 more documentation fixes
 
Package: batchelor
Commit: 8b21ea0228ce66b91ca266b807f966409c14656e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-18 11:33:31 -0800
Commit message:

 Bumped version and date, reoxygenated.
 
Package: batchelor
Commit: 173359a558957c4c7286e8c28ebb3408c2271cdb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-18 11:33:06 -0800
Commit message:

 Clarify docs around prop.k.
 
Package: MTseeker
Commit: 31e2d539a10aeaabc78ba223a724f0df53425d02
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-18 14:30:08 -0500
Commit message:

 more doc fixes
 
Package: MTseeker
Commit: a15273d017903946c15fbd80b5d7e5568c49466f
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-18 14:24:07 -0500
Commit message:

 more documentation fixes
 
Package: GEOquery
Commit: 76488d47c1b8233e5a91080aef376604b06cb22d
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-11-18 14:23:07 -0500
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/GEOquery
 
Package: GEOquery
Commit: c3b9f2d23933cacc1a30b92b1bc3cc3dcb2ea884
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-11-18 14:20:01 -0500
Commit message:

 NEWS
 
Package: GEOquery
Commit: 1ba7977221841866080fbebd6f2aa6ec483a6a5e
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-11-18 14:18:20 -0500
Commit message:

 Merge branch 'master' of github.com:seandavi/GEOquery into RELEASE_3_8
 
Package: GEOquery
Commit: 88741521a0e63c34a94b4314f730ee747bdcf049
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-11-18 12:40:06 -0500
Commit message:

 Merge pull request #89 from vlakam/master

Do not freeze on empty files 
Package: GEOquery
Commit: 568ae94fb95a3d7b0a09de8c37658e7a3da75bd9
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-11-18 12:18:21 -0500
Commit message:

 Merge pull request #96 from russHyde/scalar_bool_comparisons

fix a test that failed with strict boolean check-lengths 
Package: GEOquery
Commit: c46acf19d10f1a7ea60ffeafd9ac27364e56f622
Author: Russell Hyde <russ.hyde.data@gmail.com>
Date: 2019-11-18 16:38:29 +0000
Commit message:

 fix a test that failed with strict boolean check-lengths

The CI for GEOquery was failing (Commit: 9776a8b) with an error message
indicating that a length-12 boolean vector was being compared with `&&`.
R CMD check for R-3.6 & 3.7 are stricter than wrt Boolean comparisons.
An `&&` operator was replaced with the vectorised form `&`.
 
Package: GEOquery
Commit: 0187a5ba473eac4d93a64d5baaa92a37bf3995de
Author: petrovich <mazahakaforever@ya.ru>
Date: 2019-05-21 12:11:29 +0300
Commit message:

 Do not freeze on empty files
 
Package: GEOquery
Commit: 135c17f8fe535acda14f95a37d1be1ff2bd80f97
Author: Sean Davis <seandavi@gmail.com>
Date: 2018-12-22 13:09:16 -0500
Commit message:

 bump required readr version to 1.3.1

fixes #78
 
Package: GEOquery
Commit: 0097a5d2d25f7ef6b6a77fd7a58361060c0e8940
Author: Sean Davis <seandavi@gmail.com>
Date: 2018-12-13 06:47:42 -0500
Commit message:

 require readr >= 1.3.0 in DESCRIPTION
 
Package: GEOquery
Commit: 7e2489b1934722ef06046de5c192b2fdcb2bc8f7
Author: Sean Davis <seandavi@gmail.com>
Date: 2018-12-11 20:43:10 -0500
Commit message:

 version bump
 
Package: GEOquery
Commit: 4cb1366bbf3712613602aa9e266ec84f81cc7d76
Author: Sean Davis <seandavi@gmail.com>
Date: 2018-12-11 20:39:40 -0500
Commit message:

 with updated readr (1.3.0) fixes parsing errors

* Fixes #74
* Fixes #75
 
Package: GEOquery
Commit: ef058a5acc1642396306b8d18d5480fa4d6fd0f8
Author: Sean Davis <seandavi@gmail.com>
Date: 2018-11-29 20:36:48 -0500
Commit message:

 Version bump
 
Package: MTseeker
Commit: 6370a35a4974eb0894479d0f47cf64cbfc38028c
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-18 14:14:36 -0500
Commit message:

 vignette fixes
 
Package: MTseekerData
Commit: 225633641bb5ad94ae6030526a4332d73b508aa7
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 23:01:00 -0500
Commit message:

 add a VCF for importVCF
 
Package: MTseekerData
Commit: da09aebadaa6f04602fae0782069ac36f9738db6
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-15 09:43:28 -0500
Commit message:

 fixes for updated MTseeker
 
Package: MTseekerData
Commit: 419ad65e207e7441c6b68d428ab9ac554ad7752d
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-15 09:35:23 -0500
Commit message:

 fixes for pileup migration
 
Package: MTseeker
Commit: 54ef844d174fb87b5f6525f1f752dac265019402
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-18 13:57:05 -0500
Commit message:

 more documentation, more fixes, more correctness
 
Package: MTseeker
Commit: f23151471a4d7b04c912192197c5198abd080e90
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-18 01:39:20 -0500
Commit message:

 more documentation fixes
 
Package: MTseeker
Commit: 6910738c3a72812032f354867ef4b7b1b895aae5
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 18:53:27 -0500
Commit message:

 yet more fixes and coercion changes
 
Package: MTseeker
Commit: eeffeda57b4e1e6d23d401ff979bd2134ed5aaaf
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 18:07:38 -0500
Commit message:

 more tidying, debugging a stack overflow
 
Package: MTseeker
Commit: 67dbca576d95ed57a81a10192d38b8e057cbe129
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 18:01:38 -0500
Commit message:

 more tidying for BiocCheck and cleanup
 
Package: MTseeker
Commit: fac72d640f85120aafeb3537da1527546fee6128
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 17:50:45 -0500
Commit message:

 found another stack overflow, fixing
 
Package: MTseeker
Commit: cb601d5c58ff6b2e55bb41137f344f7ccca7b53a
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 17:32:33 -0500
Commit message:

 more fixes for documentation
 
Package: MTseeker
Commit: 1cea9f34e2a97be5874e24df4143f1649fccf935
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 17:12:26 -0500
Commit message:

 add R version req per R CMD build
 
Package: MTseeker
Commit: 6efe2c70780be7a87c79433e41ee451a9ea8db3b
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 15:42:47 -0500
Commit message:

 fix to examples in documentation
 
Package: MTseeker
Commit: ab705706b2a30bc31e0488f8fe02a1bc57376d4a
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 15:11:04 -0500
Commit message:

 Merge branch 'master' of github.com:trichelab/MTseeker
 
Package: MTseeker
Commit: 6f08e7bab0557706e6a508fe67f5bec879604438
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-17 12:34:41 -0500
Commit message:

 more fixes! API is beginning to modernize
 
Package: MTseeker
Commit: cb5b4a19501b5426920238f391bb81fc85ae5585
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-15 09:30:42 -0500
Commit message:

 Merge branch 'master' of github.com:trichelab/MTseeker
 
Package: MTseeker
Commit: 2a4db82d5cce5b237ed9ea51d443278e88cbaa9b
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-15 09:30:29 -0500
Commit message:

 bugfix
 
Package: flowCore
Commit: fc66db856cbe472a1eeef24811fdff454b28d8b3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-18 10:37:23 -0800
Commit message:

 merge
 
Package: flowCore
Commit: e4357af629b5ffe2ffa2ab3cdf47d59f1a5a2b80
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-18 10:34:11 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: flowCore
Commit: f799f8742ba6cc7491072bafbde5b7324f26579b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-18 10:33:27 -0800
Commit message:

 import cytolib
 
Package: flowCore
Commit: cf9e32787cc0f4bd603b05a12126abed0e39aee3
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:34:44 -0400
Commit message:

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 
Package: flowCore
Commit: 5f5244d5ad667959a56b868be1170337b47439fd
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:07:45 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 
Package: scDD
Commit: 031bd8af8385224036e935bc9839aee969d96988
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2019-11-18 09:21:43 -0800
Commit message:

 Update the way SingleCellExperiment is passed to computeSumFactors
 
Package: InterMineR
Commit: e05e70a1f24f6ac73b292c09fd8fed6ee2a2d6fa
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-11-18 12:00:04 -0500
Commit message:

 Next version bump to check things are ok
 
Package: InterMineR
Commit: 96baa34e8dd4aa681f1da3ba238a17c94a42906b
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-11-18 11:56:04 -0500
Commit message:

 Remove merge conflict markers and bump version
 
Package: simpleSingleCell
Commit: 4a1828f87628a371fedaa409f6bda4d6e46c6952
Author: Aaron Lun <lun.aaron@gene.com>
Date: 2019-11-18 08:46:47 -0800
Commit message:

 Bumped version and date.
 
Package: simpleSingleCell
Commit: 34357c707bd4f2e3ed6ecc0a8a70700d9eed5af1
Author: Aaron Lun <lun.aaron@gene.com>
Date: 2019-11-18 08:46:37 -0800
Commit message:

 Fix indexing of introduction.
 
Package: ViSEAGO
Commit: 8343e8581f10af478c5af494d283bcc735e59d49
Author: abrionne <aurelien.brionne@inra.fr>
Date: 2019-11-18 16:50:21 +0100
Commit message:

 see News
 
Package: ViSEAGO
Commit: f4710f5721e883e0306c25ef3a498d1c7455e6cb
Author: abrionne <aurelien.brionne@inra.fr>
Date: 2019-11-18 16:48:37 +0100
Commit message:

 description
 
Package: ViSEAGO
Commit: 5353117b6115c8d0cce3d9daaa767873e1290aaa
Author: abrionne <aurelien.brionne@inra.fr>
Date: 2019-11-18 16:47:24 +0100
Commit message:

 viSEAGO-1.0.1 see NEWS
 
Package: ViSEAGO
Commit: ebaa016df5e292baf0601fa9f7c9c28b61ba392f
Author: abrionne <aurelien.brionne@inra.fr>
Date: 2019-11-18 16:37:56 +0100
Commit message:

 ViSEAGO 1.1 see NEWS for more informations
 
Package: RMassBank
Commit: c8b00e9c3acfc909f12e6e377f6b940ca8334a3c
Author: meowcat
Date: 2019-11-18 15:59:57 +0100
Commit message:

 Bump version number
 
</div>
Package: RMassBank
Commit: 3147d9e06ae9ff955804108e5b0c194966497f6a
Author: meowcat
Date: 2019-11-18 15:58:40 +0100
Commit message:

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

# Conflicts:
#	DESCRIPTION
 
</div>
Package: RMassBank
Commit: d51d56afb401e35dfff5491afb4025ed82ed7e4d
Author: meowcat <Michael.Stravs@eawag.ch>
Date: 2019-11-18 15:49:55 +0100
Commit message:

 Merge pull request #223 from jorainer/master

Fix mzR import after mzR::header reporting NA for missing data 
Package: RMassBank
Commit: 7d45afa54e06df6122feed0a88ae680fbd663b11
Author: jorainer <johannes.rainer@gmail.com>
Date: 2019-11-15 14:28:10 +0100
Commit message:

 Fix mzR import after mzR::header reporting NA for missing data

- Fix the mzR import functionality to match the changes in recent mzR::header
  reporting `NA` instead of `0` for not set/available spectra variables.
 
Package: RMassBank
Commit: c579455cff45d1971c029a9af9189a9e65429e16
Author: meowcat
Date: 2019-06-25 14:21:49 +0200
Commit message:

 Fixed the edited compiled_ok step for multiple spectra
 
</div>
Package: RMassBank
Commit: ed8cf6f3cc40ed5cbf9d3a5ff95ac2b3862e5222
Author: meowcat
Date: 2019-06-25 14:21:13 +0200
Commit message:

 Merge branch 'master' into treutler-merge

# Conflicts:
#	R/leMsMs.r
 
</div>
Package: RMassBank
Commit: b95b9399d033403cc69234c57d1d24e29422d778
Author: meowcat
Date: 2019-04-10 18:36:01 +0200
Commit message:

 Fixes to Treutler workflow, vignette now builds almost completely
 
</div>
Package: RMassBank
Commit: 1fab56e75ed55b86c4dd9c5e803fa9274cbbd9c7
Author: meowcat
Date: 2019-04-05 15:35:05 +0200
Commit message:

 better way to handle childIdx "transmission", fixed code for rcdk 3.4.9.2
 
</div>
Package: RMassBank
Commit: e2989309782a5fed2d226d2c78a4dd462777ea38
Author: meowcat
Date: 2019-04-05 14:40:38 +0200
Commit message:

 description fixed
 
</div>
Package: RMassBank
Commit: 6165fe8ff09473ad39e4ea831ad3626c656059ad
Author: meowcat
Date: 2019-04-05 14:40:17 +0200
Commit message:

 Merge remote-tracking branch 'github/branch_treutler' into treutler-merge
Features:
* improved error handling
* central storage of adduct information
* mbWorkflow: custom comments, MASS_SPECTROMETRY and CHROMATOGRPHY fields.
 
</div>
Package: RMassBank
Commit: 260b0d5cc8848dbe7a228061309249b063560fe9
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2019-04-05 07:07:11 +0200
Commit message:

 Added the possibility to add comments with any sub tag
 
Package: RMassBank
Commit: 60b00a19c28d1abe28e92907128de93d750620cf
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2019-04-05 07:06:30 +0200
Commit message:

 Added adducts
 
Package: RMassBank
Commit: f93312d0ace28865dc72923833073ce6305f1ffd
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-11-20 13:49:15 +0100
Commit message:

 Fixed bug and implemented restarts of web queries for more error tolerance
 
Package: RMassBank
Commit: b918f80382cd937cb29d6ae3481f221bf5b0ccd6
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-11-20 08:12:48 +0100
Commit message:

 Added adducts
 
Package: RMassBank
Commit: 5aa961500d0e8f0d4c7b3a1cb2c0692290eff546
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-11-20 08:12:26 +0100
Commit message:

 http://cts.fiehnlab.ucdavis.edu/service/compound/ -> https://cts.fiehnlab.ucdavis.edu/service/compound/
 
Package: RMassBank
Commit: 80cdf2d1f922d681315695057018e3a9ec7c04bd
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-10-02 10:02:40 +0200
Commit message:

 Changed order of AC: IONIZATION and AC: ION_MODE as the record specification demands it
 
Package: RMassBank
Commit: 04032d118093daaae0ebb6a5a4eb07c20af4c9a3
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-10-02 09:27:29 +0200
Commit message:

 Corrected the position of SP in records
 
Package: RMassBank
Commit: 2ee66712a03b0db6d7013d05bb7c3a8cf1a5ddb5
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-10-02 09:26:50 +0200
Commit message:

 Added further adducts
 
Package: RMassBank
Commit: f679035ec3e30594b586fb4c61265f0ca716cdbb
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-10-02 09:26:15 +0200
Commit message:

 Added Li to DBE calculation
 
Package: RMassBank
Commit: 907bf3face1eaf08b77b8d8582c2102b57442d62
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-18 08:25:12 +0200
Commit message:

 Refined the calculation of monoisotopic masses additions using enviPat
 
Package: RMassBank
Commit: 47239b1f923816d0aae3773282fa5cc2e4684ffe
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-14 15:10:43 +0200
Commit message:

 Fixed the parsing of msp files with decimal delimiter comma instead of point
 
Package: RMassBank
Commit: dae5b04efa9ba75efae5d9ee472c931960becdb3
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-14 15:10:22 +0200
Commit message:

 Fixed bug in the record compilation in case of empty spectra
 
Package: RMassBank
Commit: e4893aba8bc89d47bd872265640857774ec826cc
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-14 15:03:29 +0200
Commit message:

 Added additional adducts
 
Package: RMassBank
Commit: e1e7fbcff7b9c3ae3dcdb370709127ad0a7e6cbd
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-06 09:42:07 +0200
Commit message:

 Fixed bug in the stored adduct information
 
Package: RMassBank
Commit: 007eae54a456c202bc1ee384384a27275bb945df
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-06 09:11:35 +0200
Commit message:

 Stored adduct information in data.frame instead of if-clauses
 
Package: RMassBank
Commit: ba570aa6eca40fb384f0e1abebf253695af4c645
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-06 08:53:44 +0200
Commit message:

 Correction for the accessibility of isotope information
 
Package: RMassBank
Commit: e3c37d9a55022ff2c4d153ceefc5a96de68397e4
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-04 14:53:29 +0200
Commit message:

 Added K to the elements of the dbe calculation
 
Package: RMassBank
Commit: 23f364fbd50e2c7670a031b36462e94d40fe22cc
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-04 14:52:52 +0200
Commit message:

 Added a check whether the elements in the molecular formulas are covered in the dbe calculation to convert strange error to explicit error
 
Package: RMassBank
Commit: e76cf96d2d4de3cdf120d760f0a582bcf2416a24
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-04 08:54:30 +0200
Commit message:

 Fixed bug for the export of invalid records
 
Package: RMassBank
Commit: a1b845040eae82339b6ec950d6ae605bbf853194
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-03 15:59:42 +0200
Commit message:

 Passed the molecular formula to the the unified adduct recognition
 
Package: RMassBank
Commit: 373a370e097864aaff4c4eee93d9777818fc2026
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-03 15:45:17 +0200
Commit message:

 Distributed the unified adduct recognition check to all remaining relevant places
 
Package: RMassBank
Commit: 14739aae09871fc3f81837c5155b6ac11fb179a8
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-03 13:41:12 +0200
Commit message:

 Added enviPat to the dependencies and fixed bug in the unified adduct recognition check
 
Package: RMassBank
Commit: ec91645efdc367c8441c70429ecf08b78a3b6cb1
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-03 13:16:07 +0200
Commit message:

 Distributed the unified adduct recognition check to all relevant places
 
Package: RMassBank
Commit: 3a27615e7d6b2f12e46da339148be5bcf8b463f8
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-09-03 12:42:17 +0200
Commit message:

 Fixed bug in the unified adduct recognition check
 
Package: RMassBank
Commit: e3d7cd59a2479f9bf3a69a36570f5272567be0d0
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-31 13:01:17 +0200
Commit message:

 Updated the adduct recognition check in a unified way
 
Package: RMassBank
Commit: 43f49f0fdce2515d3a05079d02e8b71db18d72ca
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-31 12:49:36 +0200
Commit message:

 Added 11 additional adducts: [M+K]+, [M+ACN+H]+, [M+ACN+Na]+, [M+2Na-H]+, [2M+H]+, [2M+K]+, [2M+Na]+, [2M+NH4]+, [2M+ACN+H]+, [M+ACN+2H]2+, [M+2H]2+
 
Package: RMassBank
Commit: e92f82be087e4b9b420948a272dd39806373b055
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-31 10:52:08 +0200
Commit message:

 Fixed bug: Corrected charge for adduct pNH4
 
Package: RMassBank
Commit: 66cf177f589eadf6c316f4d0760b1b6027cbe69e
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-31 10:45:44 +0200
Commit message:

 Fixed bug for modes other than pH by passing the mode parameter to findMz
 
Package: RMassBank
Commit: ee6122a2e6d0bf5bd3cf69ca613430bd1a4b486c
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-29 14:51:30 +0200
Commit message:

 Excluded empty spectra from the spectrum selection
 
Package: RMassBank
Commit: 15d799ea1317bffacb183fe7b6c49462d4e726a5
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-28 12:53:03 +0200
Commit message:

 Refined verbose output
 
Package: RMassBank
Commit: a1913cb773b0998bfd86e1927b31de8006057d58
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-28 12:48:08 +0200
Commit message:

 Refined verbose output
 
Package: RMassBank
Commit: 8c9270d656f8cc6ed63659e98dd8b18340ff7212
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-28 12:47:51 +0200
Commit message:

 Fixed that compounds can be found in a msp file if the retention time is not given in the msp file
 
Package: RMassBank
Commit: 5b374ad612e09dd7048161eb51f9e77933d447cb
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-28 12:07:41 +0200
Commit message:

 Refined verbose output
 
Package: RMassBank
Commit: 16eb71d407caae7cb3d479db8d1bc02007753d01
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-28 12:03:51 +0200
Commit message:

 Bug fixes
 
Package: RMassBank
Commit: c562f8c60bbb8ab600e7bacfdf65a2311dec5c59
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-17 09:01:50 +0200
Commit message:

 Fixed parsing of msp data in case of empty fields
 
Package: RMassBank
Commit: 635d86d703c7c4dffdb316a7cc854ff660a62f83
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-15 08:34:14 +0200
Commit message:

 Fixed bug when multiplicityFilter is not set
 
Package: RMassBank
Commit: 7fdfc02851d488379e009dfbbb6ee1258059757c
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-14 14:41:24 +0200
Commit message:

 Minor change
 
Package: RMassBank
Commit: f31d57018e2a9baec1d7b65a21fce6705530c440
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-14 13:27:45 +0200
Commit message:

 Added the optional export of invalid spectra to records; added the export of the preceursor-intensity into records; added the export of generic AC and AC information into records
 
Package: RMassBank
Commit: 2d97fa5dd2fa5e4ba07689154efd301911f94065
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-08-14 13:24:01 +0200
Commit message:

 Minor change
 
Package: RMassBank
Commit: a930e59704093ae89da31dac8ba3a68294262edc
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-07-30 14:07:50 +0200
Commit message:

 Fixed RT handling and the carry-over of Precursor intensities
 
Package: RMassBank
Commit: 1d25b28a170fa30b3422a1dc8d2b6945e0d7c8c4
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-07-30 14:06:52 +0200
Commit message:

 Added SP to MB workflow
 
Package: RMassBank
Commit: 6cf6d07091fa3c6d923827c7cf6bbd30a51a6cf2
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-07-27 15:54:56 +0200
Commit message:

 Added the option to do a strict selection of MS/MS spectra from the raw data
 
Package: RMassBank
Commit: 72707c6c6acf700e28b14c76c681de8ca27c103d
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-07-27 12:37:24 +0200
Commit message:

 Minor changes
 
Package: RMassBank
Commit: 97087e6392f9aaa7d499eb0e16619c319b4d4568
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-07-27 12:34:57 +0200
Commit message:

 added export of invalid records, decomposed the export of records and molfiles
 
Package: RMassBank
Commit: 93ba17c64b149a87a47360fd81760e8a7a6cc549
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-07-27 12:34:20 +0200
Commit message:

 added fix to keep the properties of child-spectra valid and a minor fix to aggregate spectra without error
 
Package: RMassBank
Commit: 55215a0fb3b6721e55991f97b7b6c1b38e43be7e
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-07-27 12:33:46 +0200
Commit message:

 minor changes
 
Package: RMassBank
Commit: 803084946519dc3948f2b1f498d42ada13b01542
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-07-09 12:58:31 +0200
Commit message:

 Merge branch 'master' of https://github.com/MassBank/RMassBank
 
Package: RMassBank
Commit: e1d52c947b00a5140b60ebefb6db3c1799f1b37f
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-01-10 15:18:15 +0100
Commit message:

 Merge branch 'master' of https://github.com/MassBank/RMassBank
 
Package: RMassBank
Commit: f9ef3ef92f59adece8a3be7c517bede36b9fcb9f
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-01-10 14:49:23 +0100
Commit message:

 fixed line endings #2
 
Package: RMassBank
Commit: 7f36ba82d5315ef541167e8753913b117d2b1933
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-01-10 14:38:11 +0100
Commit message:

 fixed line endings
 
Package: RMassBank
Commit: dab3e18f2b88049b5c893276a09cd5c126adaf95
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-01-10 14:01:55 +0100
Commit message:

 minor change
 
Package: RMassBank
Commit: 785c29a0bfbc04e2bc358fdb005719ddb3aa5a40
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2018-01-10 10:29:13 +0100
Commit message:

 minor changes
 
Package: RMassBank
Commit: 52ed7116472e502babb435fc2d3059c90e79206d
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2017-11-30 14:57:43 +0100
Commit message:

 Added optional parameter RMassBank.env$verbose.output which prints information about absent/filtered peaks during the msmsWorkflow
 
Package: RMassBank
Commit: 219e19e7f7e41838ced7db7c3a9170c2ae221227
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2017-11-30 14:56:52 +0100
Commit message:

 Added the msp-functions to NAMESPACE
 
Package: RMassBank
Commit: 08d02be8f0876dbc264761cf338f0a35c78db634
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2017-11-29 13:29:27 +0100
Commit message:

 fixed the pubchem-url for curl queries: http --> https
 
Package: RMassBank
Commit: 7eaad6e2e25c761f98bfb5bc9cd5befade38cdff
Author: Treutler <hendrik.treutler@gmail.com>
Date: 2017-11-29 12:58:46 +0100
Commit message:

 Added option 'msp' to parameter 'readMethod' in function 'msmsRead' and implemented the corresponding functionality in file 'leMsmsRaw.R'.
 
Package: triform
Commit: 127bc98e1d069a5e9118da8673ed3ea1f2526e97
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-11-18 09:05:04 -0500
Commit message:

 User requested deprecation
 
Package: motifRG
Commit: 742d41cd7ed1fc967cb0675c653fb79336d8454c
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-11-18 09:04:18 -0500
Commit message:

 User requested deprecation
 
Package: QUALIFIER
Commit: 02fc0ff00da2b40388da82285dc1e35f1d1b6901
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-11-18 09:03:28 -0500
Commit message:

 User Requested Deprecation
 
Package: CTDquerier
Commit: b8e8760a1fdeb9ad936c67ca42a736e42ad2cfee
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-11-18 09:02:37 -0500
Commit message:

 Deprecation

  - user unresponsive
 
Package: SELEX
Commit: 20dbc4b48d768876b1986bc1f26c7c67df2d2843
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-11-18 09:01:39 -0500
Commit message:

 Deprecate Package

  - Warned for three release cycles to fix writing to home directory
 
Package: CFAssay
Commit: 13f92910420e1c88bfad68bd2900fdb4777f4bb7
Author: Herbert Braselmann <hbr090210@gmail.com>
Date: 2019-11-18 11:25:21 +0100
Commit message:

 S3 methods in NAMESPACE file registered
 
Package: BioQC
Commit: cdc6a9b2c235bd50b0c06ef719b27bf6e50c6299
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-18 11:36:39 +0100
Commit message:

 Merge branch 'master' of github.com:Accio/BioQC
 
Package: BioQC
Commit: 2e127d82ec4a70db7200add8f9b65990bc03e5fb
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-11 09:31:32 +0100
Commit message:

 Mergenstall branch 'master' of github.com:Accio/BioQC
 
Package: BioQC
Commit: b123f49bedc51c823f815905766e67d93c10b2c4
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-07-09 09:46:20 +0200
Commit message:

 export subsetting methods for GmtList
 
Package: BioQC
Commit: 3c9e240a17d2491c09ab9feb8dd90afbccef0e3b
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-07-09 09:46:00 +0200
Commit message:

 export subsetting methods of GmtList
 
Package: BioQC
Commit: d96f44da617ba70b0472c1d23de129a59452b4ff
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-18 11:35:46 +0100
Commit message:

 new version, with additional shortcut of testing matrix/eSet with SignedGenesets
 
Package: BioQC
Commit: 4e74d548c4eefbbd945df3cb692ffc971af2ba5f
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-18 11:35:24 +0100
Commit message:

 add new shortcuts to test matrix/eSet directly with SignedGenesets
 
Package: BioQC
Commit: 5e991208d027b66dfa3a7255bd4f49dceb8fa107
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-11-18 11:35:04 +0100
Commit message:

 add new examples of testing matrix/eSet with SignedGenesets
 
Package: cola
Commit: e4f3fc19018752e047bbdf74ba55b60f77046895
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2019-11-17 21:48:17 +0100
Commit message:

 update
 
Package: cola
Commit: 8657f2cde26f70351f694c8997ef5e074f83dd1f
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2019-11-17 21:47:05 +0100
Commit message:

 temporary remove hierarchical_partition()
 
Package: cola
Commit: f0783f0aaff78b196e0df6f7fee8ac844528d01e
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2019-11-17 09:24:20 +0100
Commit message:

 update
 
Package: scran
Commit: 1d5f3a592a6d8ea86af22b7299d575f5568f8968
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 23:10:19 -0800
Commit message:

 Reoxygenated, bumped version and date.
 
Package: scran
Commit: 93650d5a38835b34da38a4f921ec610b72fd1c3e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 23:09:13 -0800
Commit message:

 Added convenient metadata to subclustering output.
 
Package: scran
Commit: ff4bf873ecabbe1236d85ff6cae250ba3009a2d4
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 00:28:40 -0800
Commit message:

 Commented on internal uses of denoisePCA with modelGeneVar.
 
Package: scran
Commit: 842d0891381deb92cefd9dced8a0eccb3ec0111b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 00:21:39 -0800
Commit message:

 Further nips and tucks to denoisePCA caveats.
 
Package: scater
Commit: 9919917822f0419a244b524a5b9e49d38aca3466
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 21:33:47 -0800
Commit message:

 Minor docfix.
 
Package: scater
Commit: c5f47241e3fee0119a07c62d2fdb706593cf91b7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 21:10:06 -0800
Commit message:

 Reoxygenated, bumped version and date, updated NEWS.
 
Package: scater
Commit: 60728d65292db99c5fa98121775d044fec06d5e8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 21:08:11 -0800
Commit message:

 Merge branch 'postrelease'
 
Package: scater
Commit: e1258b0a4b758eddd0c2d3e43a24797eb86b6fc3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 21:07:41 -0800
Commit message:

 Removed extraneous altexp= argument for computeLibraryFactors.
 
Package: scater
Commit: 63d28f2fbd488b3ffeb3512992e647967f0c83bf
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 19:43:22 -0800
Commit message:

 Added the medianSizeFactors function.
 
Package: scater
Commit: 5194bf045d916a6cddacd9e5b73a325538ae4bdb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-17 18:59:46 -0800
Commit message:

 Added geometric= option for librarySizeFactors, expanded docs.
 
Package: sesame
Commit: 4fc1a635f86b74897e1b74ec6e185c48c0634182
Author: Wanding Zhou <zhouw3@email.chop.edu>
Date: 2019-11-18 00:00:36 -0500
Commit message:

 minor NOTE fix
 
Package: sesame
Commit: 6f66d2d1c12f87f1e430859df1c86de847d9c2f4
Author: Wanding Zhou <zhouw3@email.chop.edu>
Date: 2019-11-17 23:33:49 -0500
Commit message:

 bug fix to infer type I channel
 
Package: sesame
Commit: d9b3d6e7cced76bbcc5bb33c64f460b6ed51dd40
Author: Wanding Zhou <zhouw3@email.chop.edu>
Date: 2019-11-17 23:10:31 -0500
Commit message:

 fix to ethnicity inference
 
Package: sesame
Commit: 465f7b592a9c30d6b81eedf43e35e944be2a4cfd
Author: Wanding Zhou <zhouw3@email.chop.edu>
Date: 2019-11-17 22:55:41 -0500
Commit message:

 allow multiple pvalue; IR2 and IG2 allow corrected typeI channel
 
Package: enrichTF
Commit: 33fa1d3586f3b8d3db5556c696575cfe97669d65
Author: wzthu <wzweizheng@qq.com>
Date: 2019-11-18 17:09:03 +0800
Commit message:

 version bumpuy
 
Package: enrichTF
Commit: 6a312899b9b4d3ffb13ab0058afeae63a11cd7e2
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-11-18 09:00:18 +0800
Commit message:

 fix bug
 
Package: enrichTF
Commit: 16894ce39b571b97a05c0f077a5c94fc3d797765
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-11-18 08:36:56 +0800
Commit message:

 fix bug
 
Package: enrichTF
Commit: 0a2f5c1dd52e550349e8ef938133954af03bbbd8
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-11-17 17:51:18 +0800
Commit message:

 Merge branch 'master' of github.com:wzthu/enrichTF
 
Package: enrichTF
Commit: c7a6b1490faf8dfb0d3dce86b9a48b720371a837
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-11-17 17:50:45 +0800
Commit message:

 fix bug that mclapply do not support windows
 
Package: ALDEx2
Commit: 8657ab1f149ba33047e60fa97763497642d0a284
Author: ggloor <ggloor@uwo.ca>
Date: 2019-11-17 15:42:04 -0500
Commit message:

 bug fix: aldex.corr
 
Package: ALDEx2
Commit: 249ac48be66056c1bb9f029269d499561380104d
Author: ggloor <ggloor@uwo.ca>
Date: 2019-11-17 15:34:02 -0500
Commit message:

 bug fix: aldex.corr

aldex.corr now uses the correct header names.
 
Package: cytolib
Commit: 1fc282f58b1550c114ebf1300ab382ae9e4e4598
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-17 11:24:31 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: cytolib
Commit: ed5e372cdfe586c34d45ef55e708f2fd69e168c0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-17 11:24:16 -0800
Commit message:

 bump
 
Package: cytolib
Commit: 9ee76e0e076fd73727852f3d1b76571a7af9d9cc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-15 11:51:43 -0800
Commit message:

 implement our own time parser to avoid third-party lib. close #19
 
Package: cytolib
Commit: dfec3c24802876a696d1ce214e6950efca8a331c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-14 15:40:42 -0800
Commit message:

 replace mkstemps/mkdtemp calls with boost uuid to make it portable to win
 
Package: cytolib
Commit: a2b54f8a13b8edd5faf2d6adfa4bbcd25ef5ac78
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-14 15:12:38 -0800
Commit message:

 add tools #18
 
Package: cytolib
Commit: 2b4fe53d92016b697d7214c3e15425e898475024
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-14 15:07:11 -0800
Commit message:

 add missing header for boost::filesystem. #17
 
Package: cytolib
Commit: 7e7be7aff7060835cf8c64443cb52e4e488dec7c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-14 15:00:45 -0800
Commit message:

 replace autoconf based configure by more portable R package 'configure' #18
 
Package: cytolib
Commit: 2c57014801edb8da12aec02e650caec6663a8d8d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-14 11:02:34 -0800
Commit message:

 convert path to string due to failure of auto converting on win
 
Package: cytolib
Commit: de21e38fb5276eeae4b896a3885b04a043d3d07f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-13 15:40:36 -0800
Commit message:

 rm refs to experimental/filesystem
 
Package: cytolib
Commit: d36402656a4dc86e216c9162c1c0953f7d5bb75c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-13 15:09:31 -0800
Commit message:

 bundle boost fs lib #17
 
Package: cytolib
Commit: a379d75038cd0bdb456dbe2c578840c008cd9175
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-13 12:01:21 -0800
Commit message:

 port the code from std::filesystem to boost::filesystem. #17
 
Package: cytolib
Commit: 9d69a649025e26362af77f8fe11c79e817e3ef86
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 15:35:29 -0800
Commit message:

 up makefiles for win
 
Package: iSEE
Commit: f38ae3c4fb8dd4ba28b76be541cffbf70104891a
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-11-17 15:34:55 +0000
Commit message:

 Merge pull request #326 from csoneson/kra-bump2

version bump and NEWS update 
Package: iSEE
Commit: a30fff38bae2510d0e87c436c14da5e1ee3f20ea
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-11-17 15:17:07 +0000
Commit message:

 version bump and NEWS update
 
Package: iSEE
Commit: 171091b034220c3003be1163736dc63aedaacf28
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-11-14 21:59:29 +0100
Commit message:

 Merge pull request #324 from csoneson/kra-bump

Merge Bioc versions bumps 
Package: iSEE
Commit: dab48b5ae01ecc1124a7add6d280a9335db68237
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-11-11 17:24:59 +0100
Commit message:

 Replace deprecated scater argument
 
Package: iSEE
Commit: 1d9d7b26e7d64d6180a96521f36b7f5f6f5203c8
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-11-06 22:09:00 +0100
Commit message:

 Fix error related to using && with length-8 variable
 
Package: iSEE
Commit: 63af88571a4cf26905f0135bb9d99fe0a540e8f8
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-11-06 17:46:57 +0100
Commit message:

 Replace deprecated functions
 
Package: iSEE
Commit: e0908bdefd214d45f1c3a660d5aa74c9f8bf3b27
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-11-06 17:46:29 +0100
Commit message:

 Fix code rbinding data.frame and DataFrame.
 
Package: scran
Commit: 0288f59ad0733e9166fea0b2f31f831bdbc8b1ce
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-16 22:52:59 -0800
Commit message:

 Cleaned up denoisePCA documentation.
 
Package: scran
Commit: c756843e474dae818bc9cb1891d906934f85566d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-16 21:30:31 -0800
Commit message:

 Bumped version, reoxygenated.
 
Package: scran
Commit: ae337282a676691adccd6285338d8cddb3d866ef
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-16 21:30:13 -0800
Commit message:

 Fix to summarization for other probability in coassignProb.
 
Package: HDCytoData
Commit: 3768f25428f4d2e0cfed12f9d7b12b58f623ebca
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 17:44:25 -0500
Commit message:

 version
 
Package: HDCytoData
Commit: 1bf635e65b0d2d7355dca6edd0f321a94350023b
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 17:43:19 -0500
Commit message:

 update NEWS
 
Package: HDCytoData
Commit: d6872d974fba17a9897e4a2bf106aa2e21705806
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 17:41:28 -0500
Commit message:

 update help files: non protein marker columns
 
Package: HDCytoData
Commit: c60538df763c5dfe534939c75e072d5e385d566b
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 17:33:04 -0500
Commit message:

 update vignettes
 
Package: HDCytoData
Commit: 70bae91f52f2238d659873fb7bea1eaa1473ca26
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 17:22:57 -0500
Commit message:

 fix documentation
 
Package: HDCytoData
Commit: 5e0c747e19c69f69da86bb3575c4d90d9e167c00
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 17:22:25 -0500
Commit message:

 update readme
 
Package: HDCytoData
Commit: 3321fc17eacd7dced1c0119c8e6c17246d4d1890
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 17:16:49 -0500
Commit message:

 update documentation (file sizes etc)
 
Package: scater
Commit: 61ee143f355686e2be8952557ec834121fc72f73
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-15 23:41:35 -0800
Commit message:

 Bumped version and date, reoxygenated.
 
Package: scater
Commit: cb1e4a22e7e2944eecd4b0dc6bda9af020fc346f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-15 23:30:43 -0800
Commit message:

 Merge branch 'postrelease'
 
Package: scater
Commit: ee21a6228d7569ea777cc5655bf0348ba73647d6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-15 23:20:48 -0800
Commit message:

 Added basic tests for multi-modal UMAP.
 
Package: scater
Commit: 61db2af22a82fb1581c99618306d20c1d3550c47
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-15 23:11:16 -0800
Commit message:

 Added basic wrapper around multi-modal UMAP.
 
Package: HDCytoData
Commit: e479b64bf34106ea6fe4ee1f0b7837975d97a183
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 13:32:53 -0500
Commit message:

 version
 
Package: HDCytoData
Commit: 0803e69d130034bb44c1d3acbbcd14e1a63a91d6
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 13:32:33 -0500
Commit message:

 rename 'Contribution guidelines' vignette
 
Package: trio
Commit: 7d8e916e9b22013b6260601d22e38441fc6793b4
Author: holgerschw <holger.schw@gmx.de>
Date: 2019-11-16 19:25:10 +0100
Commit message:

 Little change
 
Package: trio
Commit: 2d68f6eb4736a551581d6b084ec123e3dfd1de5e
Author: holgerschw <holger.schw@gmx.de>
Date: 2019-11-16 19:18:38 +0100
Commit message:

 Updated function

Required update because of change in LogicReg package
 
Package: trio
Commit: 90782904446153788faebb077554eac752eb1d23
Author: holgerschw <holger.schw@gmx.de>
Date: 2019-11-16 19:07:00 +0100
Commit message:

 Necessary update

Necessary update because of changes in LogicReg
 
Package: HDCytoData
Commit: ced7450bee6d8f46f7a0cff669b5d8c4713ebeb0
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 01:00:04 -0500
Commit message:

 version
 
Package: HDCytoData
Commit: a172e96d63afe169d03be67c937f4fe6cc3bc9e0
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 00:50:45 -0500
Commit message:

 fix dependencies
 
Package: HDCytoData
Commit: caba3605d47a4cfc4d16f45c13db1e93064c371d
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 00:35:33 -0500
Commit message:

 update NEWS
 
Package: HDCytoData
Commit: 60a3c13dc8bb7c515230e24730db48f5798e1981
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-11-16 00:34:36 -0500
Commit message:

 add rest of 'Examples and use cases' vignette
 

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