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GIT Logs

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

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Package: sevenbridges
Commit: 068ce845cbf3dad7aee2331970f133f17b4c92d9
Author: Nan Xiao <road2stat@gmail.com>
Date: 2018-07-15 18:43:23 -0400
Commit message:

 v1.11.2 release
 
Package: Rcpi
Commit: b25d3ee250b24ec2151f42ae09ce2659c190dd09
Author: Nan Xiao <road2stat@gmail.com>
Date: 2018-07-15 18:41:10 -0400
Commit message:

 v1.17.2 release
 
Package: phyloseq
Commit: cd7da46693026895686ae30014c40735f9e88c28
Author: Paul J. McMurdie <joey711@gmail.com>
Date: 2018-07-15 12:56:34 -0700
Commit message:

 1.25.2 ggplot2-3.0 bugfixes
 
Package: phyloseq
Commit: d9d000ccdd02c825cc502e6fcd18d3aee23bc837
Author: Paul J. McMurdie <joey711@gmail.com>
Date: 2018-07-15 12:40:32 -0700
Commit message:

 1.25.2 ggplot2-3.0 bugfix in test-plot.R

unit tests fix
 
Package: phyloseq
Commit: eccb6c118b047e2eb8b0b82243b25880fd4300e7
Author: Paul J. McMurdie <joey711@gmail.com>
Date: 2018-07-15 10:16:21 -0700
Commit message:

 1.25.1 ggplot2-3.0 bugfix analysis vignette
 
Package: phyloseq
Commit: 5c532790722d839ed2a6e991d67fa6c96f8c9745
Author: Paul J. McMurdie <joey711@gmail.com>
Date: 2018-04-19 11:51:24 -0700
Commit message:

 uptick vegan version required 
Package: phyloseq
Commit: 077f904823a6bcd94d0b7607f621d9097230c4a4
Author: Paul J. McMurdie <joey711@gmail.com>
Date: 2018-04-01 10:52:45 -0700
Commit message:

 Merge pull request #896 from nate-d-olson/patch-1

documentation typo 
Package: phyloseq
Commit: 219c68164d34e48642d2a1e20ffa047906455233
Author: Nate Olson <nolson@nist.gov>
Date: 2018-03-09 12:34:40 -0500
Commit message:

 documentation typo 
Package: scmeth
Commit: 9866dcb49cf786b5df45746b087195480288ee93
Author: Divyagash <sdivyagash@yahoo.com>
Date: 2018-07-15 14:49:26 -0400
Commit message:

 fixed downsampling error
 
Package: compcodeR
Commit: b8248df06321184ecdff45a2524e4c6ae4c7d4b5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-07-14 23:55:51 +0200
Commit message:

 Change to BiocManager
 
Package: iCOBRA
Commit: a4ae629af898c99794eb35db6e01fd602d7a8d7d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-07-14 23:47:25 +0200
Commit message:

 Use BiocManager
 
Package: RCy3
Commit: 8c12954be10fe4fbdd15a058d7fd7356d459dd8e
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-07-14 12:22:59 -0700
Commit message:

 version bump
 
Package: RCy3
Commit: d113b7e34e4ec40b0adc2cac13bac66f2521a042
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-07-14 12:20:30 -0700
Commit message:

 doc fix: feedback on vignettes
 
Package: RCy3
Commit: b793cf65c83f210e7e0da18f123df930370a3466
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-07-14 11:10:35 -0700
Commit message:

 version bump
 
Package: RCy3
Commit: 144c44ffe94381a9e0407325fdd14f443bf2411c
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-07-14 11:09:42 -0700
Commit message:

 Added deleteDuplicateEdges and deleteSelfLoops for  2.1 (dev) and future 2.2 release; fixes #35
 
Package: RCy3
Commit: 9192d956ef2ac001e2fb2b7e1e2c51b59d955cf6
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-07-14 10:15:47 -0700
Commit message:

 added function: #34 selectNodesConnectedBySelectedEdges
 
Package: RCy3
Commit: a61238b1f7f1bfdb0e4d257bd8b1801f8016ce7e
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-07-14 10:00:36 -0700
Commit message:

 bug fix: #36 selectEdgesConnectingSelectedNodes
 
Package: TCGAbiolinksGUI
Commit: a264b1632b52bb8b52b06c4df4d008264ce4c77c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-07-11 16:06:03 -0300
Commit message:

 fixing oncoprint buttons
 
Package: TCGAbiolinksGUI
Commit: 450e4207673f090536e40fe5b85a4bf5d36b6eb3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-07-11 15:51:28 -0300
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI
 
Package: TCGAbiolinksGUI
Commit: 2d7be2c377941584cba03c8680b8d211f7d91236
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-07-11 15:50:34 -0300
Commit message:

 Start to fix after shinyFiles update
 
Package: MAST
Commit: 521ef9827be0c17e3c3220a4ca92e0cb35f4af0b
Author: Andrew McDavid <amcdavid@fhcrc.org>
Date: 2018-07-14 08:51:11 -0500
Commit message:

 update instructions for installation
 
Package: chromstaR
Commit: 0bd289b0cd401f5aa1c59e88160da90cc80b4fad
Author: ataudt <aaron.taudt@gmail.com>
Date: 2018-07-14 15:39:28 +0200
Commit message:

 bugfixes in version 1.7.2
 
Package: BridgeDbR
Commit: db287d23efd972754c94dbb1afcfbabae6aa6098
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date: 2018-07-14 13:25:19 +0200
Commit message:

 Bumped version and added news about BiocManager
 
Package: BridgeDbR
Commit: fbf644531808c1ef0098945b34fc407be95bfc85
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date: 2018-07-14 13:20:44 +0200
Commit message:

 Updated to use BiocManager (from CRAN) 
Package: DominoEffect
Commit: 6af4a1d10c1cfbdc844fb05eda8911aeeb312ac1
Author: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Date: 2018-07-14 12:00:55 +0200
Commit message:

 1.1.1 move from BiocLite to BiocManager
 
Package: SWATH2stats
Commit: 3548f47691b956a55ffd0ae80bbd98120c783dbc
Author: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Date: 2018-07-14 11:54:09 +0200
Commit message:

 v.1.11.6 bug fix in convert_protein_ids for copy non_converted
 
Package: SWATH2stats
Commit: ceeb3dcf729eeb77a005d057291fa69bafe05fbe
Author: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Date: 2018-07-14 11:50:59 +0200
Commit message:

 v.1.11.5 Change from Bioclite to BiocManager
 
Package: MethylMix
Commit: 7b42c5d6fed07949ff436a48b1b20dff6be684aa
Author: lucaspatel <lucaspatel@gmail.com>
Date: 2018-07-14 00:55:14 -0700
Commit message:

 ggplot fixes, added references
 
Package: DESeq2
Commit: 573fd03cf16495856137e5431cb96830774415b1
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-07-14 08:38:09 +0200
Commit message:

 remove bioclite
 
Package: Rcpi
Commit: 6824b102779aefe50184c93a72937e96585561a5
Author: Nan Xiao <road2stat@gmail.com>
Date: 2018-07-13 21:08:02 -0400
Commit message:

 v1.17.1 release
 
Package: sevenbridges
Commit: d95eb49c1ff64f6b98b997802029c5f4037e92db
Author: Nan Xiao <road2stat@gmail.com>
Date: 2018-07-13 20:47:20 -0400
Commit message:

 v1.11.1 release
 
Package: TxRegInfra
Commit: 92725c11835572850929dd755ab7e3de008689cf
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-07-14 00:11:35 +0200
Commit message:

 deal with version mismatch in mongo CLI response
 
Package: doppelgangR
Commit: 5896aedbf15b6a65e632b7d6bcf0a6ec07a57fb8
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-13 17:25:56 -0400
Commit message:

 replace BiocInstaller with BiocManager
 
Package: MultiAssayExperiment
Commit: ce42a3e1508b32b8ddd783d8f0ad788d364e28e7
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-02 17:58:24 -0400
Commit message:

 refer to BiocManager for installation
 
Package: igvR
Commit: f14e9bad6c3ea6934d6a158959b42b430a96fa58
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2018-07-13 14:02:16 -0700
Commit message:

 column classes now checked in DataFrameQuantitativeTrack ctor
 
Package: curatedMetagenomicData
Commit: d2c38c7578a9d39f39e8097b5f3a10aaaa277fd0
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2018-07-13 21:45:17 +0200
Commit message:

 fix mergeData test
 
Package: curatedMetagenomicData
Commit: 571c410dec4f4be20162b545a617ac3a79f60e6a
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2018-07-13 19:54:37 +0200
Commit message:

 fix studyID bug in mergeData
 
Package: curatedMetagenomicData
Commit: 1c4ba581e29a69b90a4d2b02a3204b0f14e2d46f
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2018-07-13 09:51:18 +0200
Commit message:

 cherry pick correct documentation for x.is.glob
 
Package: curatedMetagenomicData
Commit: 2aa0218cd78af2397e3d95683b6f67ecc5d22ffc
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2018-07-05 16:23:11 +0200
Commit message:

 bug fix joining DataFrame and tbl_df 
Package: dmrseq
Commit: 6c89e9ab3a5bf08ee6fbd482051ef50be7e0b3df
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-07-13 15:19:53 -0400
Commit message:

 version bump
 
Package: dmrseq
Commit: 61301f42529e3f07cfcd717d0df99c401190720c
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-07-13 14:40:13 -0400
Commit message:

 test patch for svd lapack error
 
Package: pkgDepTools
Commit: 610025b40f9537de9014690973a7fe96b917a6fc
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2018-07-13 11:46:13 -0700
Commit message:

 replace BiocInstaller with BiocManager
 
Package: RaggedExperiment
Commit: 502206d953e540d7df600b0831de615e08207904
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-13 13:42:16 -0400
Commit message:

 Fix examples in assay-fx and vignette, add BiocStyle to suggests
 
Package: chroGPS
Commit: 3638b0cc3a8872a83f2de259c8a19b8b515ecf5a
Author: oreina <oreina@biocf06.irb.pcb.ub.es>
Date: 2018-07-13 15:50:34 +0200
Commit message:

 Updated vignette
 
Package: miRcomp
Commit: 36677af8e61b35a0467f69ac9d6f6aac2391f991
Author: mccallm <mccallm@gmail.com>
Date: 2018-07-13 08:50:05 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'

Add revised Shiny app code.
 
Package: miRcomp
Commit: 789792b770404da8b0546cceeebea78281ce8e61
Author: Lauren Kemperman <lkemperm@u.rochester.edu>
Date: 2018-02-25 18:19:55 -0500
Commit message:

 Increasing start for qc threshold sliders from 0 - 0.02
 
Package: miRcomp
Commit: 782447e28b887ceb5c822d78fb3c8bfca0b23108
Author: Lauren Kemperman <lkemperm@u.rochester.edu>
Date: 2018-02-25 15:32:33 -0500
Commit message:

 Updates to app.r

- download data
- tab panels
- updated captions
 
Package: OrganismDbi
Commit: c4cfc6403ef062746da007eb77f227eeb2c972cb
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2018-07-13 05:54:09 -0700
Commit message:

 replace BiocInstaller with BiocManager
 
Package: cydar
Commit: 28afb547169a4145b803ee9fa62394a0f140836e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-13 09:57:13 +0100
Commit message:

 Rebuilt NAMESPACE.
 
Package: cydar
Commit: c1b792910afd9081a9ae2bdb5d3c7aee89ce3808
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-13 09:56:46 +0100
Commit message:

 Updated documentation to describe and use new cell-level getters.
 
Package: cydar
Commit: bdf2c5ce0fe9f033996fbcaa9de8441b112878be
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-13 09:52:40 +0100
Commit message:

 Relaxed cell input checker, as center cell isn't used anywhere.
 
Package: cydar
Commit: d05f9baf5c011e76afa2119381bf2a70552fe3ef
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-13 09:51:58 +0100
Commit message:

 Added tests for new CyData cell-level info getters.
 
Package: cydar
Commit: ceb449ce0a1fb15e616451f504466797d8bc9956
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-13 09:37:29 +0100
Commit message:

 Added getters for cell-level information in CyData objects.
 
Package: cydar
Commit: c25a36eed9974a956dfd6741488a6d95f117c405
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-12 17:28:55 +0100
Commit message:

 Rebuilt NAMESPACE, added missing imports to DESC.
 
Package: cydar
Commit: 6e4198370dacda06a8245cc870637437ec3b7132
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-12 17:28:36 +0100
Commit message:

 Replace sapply with vapply, 1:... with seq_len.
 
Package: cydar
Commit: 5b464fd141f3580e488a7bc14b3ebec61bae44e8
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-12 17:19:48 +0100
Commit message:

 Bumped version number, date.
 
Package: cydar
Commit: 4b1d6e9ddcadb4f8d8b7f786bd87386700ca26ea
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-12 17:11:23 +0100
Commit message:

 Updated tests for new markernames().
 
Package: cydar
Commit: b33a3ee6171283016f2b453c8930fdf56828655d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-12 17:07:14 +0100
Commit message:

 Switched to using markernames() for finding unused markers.
 
Package: cydar
Commit: 1ff4128973731e3e201ba0bc1588db3f833890df
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-12 17:06:50 +0100
Commit message:

 Removed unnecessary argument.
 
Package: cydar
Commit: d88e673c6b4b30a47d0632186d1b302f159b7609
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-12 17:04:13 +0100
Commit message:

 Fixes to documentation links, arguments, code.
 
Package: cydar
Commit: f18d5d328a4135a0d94c8faa94f44cacb959c8db
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-11 18:46:38 +0100
Commit message:

 Updates to vignette.
 
Package: cydar
Commit: 78adfe8634476503b9493a3e4cd262f91f5f6973
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-11 18:41:11 +0100
Commit message:

 Importing and NAMESPACE-related fixes.
 
Package: cydar
Commit: d0b24e530695cb6584a9bd549e670057fec8f2ba
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-11 18:28:00 +0100
Commit message:

 Further update to example in pickBestMarkers docs.
 
Package: cydar
Commit: d83b5315cdd2f3bf16f2573b1b488e83b065dac7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-11 18:27:36 +0100
Commit message:

 Added Roxygen tags to pickBestMarkers, updated docs.
 
Package: cydar
Commit: 98a52f39a4d825918edad19e91ab0a552162d2f7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-10 11:47:19 +0100
Commit message:

 Display center location for unused markers in interpretSphere.
 
Package: cydar
Commit: ddba202fcf56619cab365e9c411ff5118ed57516
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-10 11:34:46 +0100
Commit message:

 Updated CyData class and methods documentation.
 
Package: cydar
Commit: 07aabc56571ce62ae86ebe1d2b14f1c2f634079c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-10 11:31:48 +0100
Commit message:

 Support unused markers in intensityRanges.
 
Package: cydar
Commit: f915e8e9baa70d512ee8d21c35e576bfb9d9bc76
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-10 11:02:28 +0100
Commit message:

 Streamlined interpretSpheres code, handle unused markers properly.
 
Package: cydar
Commit: e6178a2eb5257829e7de7258128ec0f15427f482
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-10 10:52:13 +0100
Commit message:

 Refactored storage of marker names.
Stored totals in prepareCellData() upon CyData construction.
Upgraded validity method, added getter for unused intensities.
 
Package: cydar
Commit: dd0a6722f08564a7abdd2efc6ff76746d3013f7a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-09 10:20:38 +0100
Commit message:

 Support CyData input in labelSpheres, added tests.
 
Package: cydar
Commit: c3fab74d478c0edc6e53d07bb972975fcc582945
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-09 10:05:42 +0100
Commit message:

 Added roxygen tags to gating functions.
 
Package: cydar
Commit: 98da0c40b0a3244a8ad7c636dbe29c130073d236
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-09 10:05:28 +0100
Commit message:

 Updated expandRadius docs.
 
Package: cydar
Commit: 7996c4fcda1158d9fec14537853ec242befc8cc9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-09 10:02:03 +0100
Commit message:

 Added simple tests for expandRadius.
 
Package: cydar
Commit: 79243bbaccf654b4ec60e2c1bc9714b12455aa00
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-09 09:40:44 +0100
Commit message:

 Removed documentation for defunct functions.
 
Package: cydar
Commit: fec76c35daf4a62de0392d75cd66960293dc4480
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-09 09:40:20 +0100
Commit message:

 Removed unnecessary diffIntDistr function.
 
Package: cydar
Commit: 238007facfcadf445b4993057de8bc1014ab5b04
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-08 12:14:47 +0100
Commit message:

 Removed references to naive in docs, minor docfixes.
 
Package: cydar
Commit: 34288377c592dccc07879cf405750ddcfae92151
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-08 12:09:31 +0100
Commit message:

 Updated docs for spatialFDR, added citation.
 
Package: cydar
Commit: f89105c4c08c4b457776f3c135bd8d1a3c91fa82
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-08 12:06:09 +0100
Commit message:

 Bugfix to spatialFDR preclustering, support CyData inputs.
Moved spatialFDR tests within test_that blocks.
 
Package: cydar
Commit: 0fdd873e5cd00dd33200f826ba52a1363ee8b6c2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-08 12:05:25 +0100
Commit message:

 Reverted cleanup to fix bug when downsample=1.
 
Package: cydar
Commit: 0f8d3602e6537b9a7b3af1f01a330d4fe024f0ab
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-07 12:06:18 +0100
Commit message:

 Cleaned up downsampling utility function.
 
Package: cydar
Commit: c36bb429c919cae99137bd6ac696727a94e0bfb9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-07 12:04:38 +0100
Commit message:

 Removed unnecessary recountCells tests.
 
Package: cydar
Commit: 394763691bdba66ea0437f72ef09eebf84a642c9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-07 12:03:49 +0100
Commit message:

 Moved plotCell* functions into test_that closures.
 
Package: cydar
Commit: 90db29fdefb0a5f82c53de7b3b6f69935d182f1c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-07 12:03:03 +0100
Commit message:

 Fixed colour interpolation to use square roots.
Added missing viridis import, explanatory comments.
 
Package: cydar
Commit: 17f402b9708741313f37f99ab12e788450efbbe9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-07 11:45:34 +0100
Commit message:

 Removed unnecessary packing tests.
 
Package: cydar
Commit: a2c524106e722edb9ceb4d03f6f53751254d9f5b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-07 11:44:43 +0100
Commit message:

 Fixed normalization-related imports.
 
Package: cydar
Commit: 773ca21c9b39de7372467f790519a2e688563edb
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-06 11:32:43 +0100
Commit message:

 Updated C++ registration code.
 
Package: cydar
Commit: 672c2ebc34a48b97b1523df6b04e48684747fa1b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-06 11:32:28 +0100
Commit message:

 Updated docs, tests for findFirstSphere.
 
Package: cydar
Commit: 7792798d4b4ad6b871d04f825a7e431d6c2e0cad
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-06 11:14:31 +0100
Commit message:

 Reverted findFirstSphere back to old behaviour.
 
Package: cydar
Commit: fb19d32ac20540102c785e3b6d471cdc6944dc50
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-06 10:31:32 +0100
Commit message:

 Updates to docs, tests for medIntensities.
 
Package: cydar
Commit: e71faf547d761688c02ebc28140b602270d34298
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-06 10:30:42 +0100
Commit message:

 Allow only unused markers in medIntensities, bugfixes to C++ code.
 
Package: cydar
Commit: afc6727067afef2d774bb52331aa8977beb66e3c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-05 16:47:31 +0100
Commit message:

 Bugfix to neighborDistances, updated docs, cleaned up tests.
 
Package: cydar
Commit: 8f1ffb0731249ff1cb2992eac4602ef081f9d553
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 13:19:17 +0100
Commit message:

 Rebuilt NAMESPACE.
 
Package: cydar
Commit: f5f1dd2b53cf8a4a17044398942b1d253588fc93
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 13:18:55 +0100
Commit message:

 Updated tests for CyData class.
 
Package: cydar
Commit: 816bbb446e42355c85bf14de649ffc4840c491d7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 13:18:28 +0100
Commit message:

 Add error message when fields are not yet set.
Bug fix to column warnings, added export tags.
 
Package: cydar
Commit: db8be9c5a62d9a2f2e840b6d6003b0ad3c530f4d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 11:49:48 +0100
Commit message:

 Consolidated CyData class and method docs.
 
Package: cydar
Commit: 03c088e0b512a27ab161e6428d6cfb1bd2be38fd
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 11:29:50 +0100
Commit message:

 Cleaned up prepareCellData docs.
 
Package: cydar
Commit: 2695b2fb016d240ef5a0052e9d6e3c0770a2511f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 11:29:07 +0100
Commit message:

 Restored storage of unused markers in prepareCellData.
Expanded tests for markers= argument.
 
Package: cydar
Commit: 5d115677ea19b47d724072ac81eda770a131cb46
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 10:52:20 +0100
Commit message:

 Updated tests for prepareCellData.
 
Package: cydar
Commit: 8c537c8d08f1c5a1acd5fbfce9e04fd1c76785df
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 10:52:08 +0100
Commit message:

 Bugfix to prepareCellData for empty/unnamed inputs.
 
Package: cydar
Commit: 0f55152f284cc18d5d80c816d0aec3f613c3838e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 10:16:09 +0100
Commit message:

 Updated docs, tests for new location of countCells output fields.
 
Package: cydar
Commit: 3c7c5d1f2d315b748bcf12146483d650f105e3e6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-04 10:11:19 +0100
Commit message:

 Moved rowData fields into rowData DataFrame.
Renamed internal getter for the metadata.
 
Package: cydar
Commit: f7d70f2654887d9f803079dd8fd5c636da35156c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-03 19:42:40 +0100
Commit message:

 Updated countCells man page, removed naive= argument.
 
Package: cydar
Commit: b5e5603725be9597d6d9b5ea1dcfbc45ab357622
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-03 19:38:54 +0100
Commit message:

 Upgraded tests for countCells.
 
Package: cydar
Commit: 760e38ed3d28faced51612f89bcb4ff9e0f06923
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-03 19:32:24 +0100
Commit message:

 Restored support for filtering in countCells.
 
Package: cydar
Commit: c2a0d80db136b8d6f0270c52beb3f305309bbae6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-03 19:10:17 +0100
Commit message:

 Bug fix to cell counting C++ code.
 
Package: cydar
Commit: 78229b6ab28f7fe587d523536e6afc7754012d1f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-03 19:09:31 +0100
Commit message:

 Restored ordering of countCells output.
Corrected downsampled for subset interpretation when raw.index=TRUE.
 
Package: cydar
Commit: 4640b6b50d08d1789162553ad93ee3c509901b37
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:48:28 +0100
Commit message:

 Fixed bugs in downsampler, cell ID storage.
 
Package: cydar
Commit: 94c5b4c3cf2db3eaa16926555c0dd9cbec3ad8db
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:47:36 +0100
Commit message:

 Fixes to validity methods.
 
Package: cydar
Commit: aab8aea444afe65c5dd004022c51fc0e81f1e86f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:31:05 +0100
Commit message:

 Fixed Roxygen tags.
 
Package: cydar
Commit: ee1d89ac74451017f6cb3840e004db5431855394
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:29:39 +0100
Commit message:

 Updated DESCRIPTION and NAMESPACE.
 
Package: cydar
Commit: 3d52ed95e220d04187c9aaa0744ffda412d83915
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:29:22 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/cydar into overhaul
 
Package: cydar
Commit: 3e5be64e1c3f8381ed64390113e9ac7b8f2d8077
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:24:57 +0100
Commit message:

 Updated Cydata validity method, getters.
 
Package: cydar
Commit: cc80fb6af20669a1be1cf9aaabe033753d0138c7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:23:26 +0100
Commit message:

 Fixed usage of check_cell_data across various functions.
 
Package: cydar
Commit: 1a16c7ec15d588d1c6dfa7e7da4ca2e91d4738fa
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:19:56 +0100
Commit message:

 Store center cell from countCells(), cell ID from prepareCellData.
 
Package: cydar
Commit: 9ee7243fa998a5af73506e0bea8da4bde48d662a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:17:52 +0100
Commit message:

 Added function to check for cell counts/assignments.
Centralized downsampling function.
 
Package: cydar
Commit: 03a3386af6f390e3aca727cf6ce3ffd4b94a1a0b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:14:43 +0100
Commit message:

 Added more validity methods, assuming prepareCellData output.
 
Package: cydar
Commit: ffee7f6c51582e353c6e86abc52ab6cdec1e015f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:13:43 +0100
Commit message:

 Updated spatialFDR to use kmknn functions.
 
Package: cydar
Commit: 1cc656e0d93fd26e28e85befa381a63351215109
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:05:27 +0100
Commit message:

 Added Roxygen tags to poolCells.
 
Package: cydar
Commit: 13de1453266853a69c94814fa385e715820d496d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 15:01:59 +0100
Commit message:

 Added Roxygen tags to cell plotting functions.
 
Package: cydar
Commit: 111c7960d5690d0fac72a8af1a45468cbde5c572
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:59:51 +0100
Commit message:

 Added roxygen tags to normalizeBatch functions.
 
Package: cydar
Commit: 3346918b3a682119a736785323ececcac51808dd
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:57:32 +0100
Commit message:

 Updated neighborDistances to use findKNN.
 
Package: cydar
Commit: b77f54486d1ac93a4c890a577a829acdd83d7cf0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:26:15 +0100
Commit message:

 Added Roxygen tags to multiIntHist.
 
Package: cydar
Commit: 862033de5c56273fea128cd1bb5f08d08d0ce99e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:25:05 +0100
Commit message:

 Updated medIntensities.
 
Package: cydar
Commit: a174b53c7daa932090179f172ebe1254711ea989
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:22:04 +0100
Commit message:

 Switched labelSpheres to use queryKNN.
 
Package: cydar
Commit: 1274a094d8f589acbd05fa61c65296e951b1abc9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:18:58 +0100
Commit message:

 Cleaned up intensityRanges.
 
Package: cydar
Commit: 3a521b7a8c826c2f4b8e68e2230030e4ecfd4458
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:17:35 +0100
Commit message:

 Corrected downsampling in countCells, store center cell.
 
Package: cydar
Commit: cfd1785ddb93e77625bedf34512ef3f3a33a560b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:12:52 +0100
Commit message:

 Preliminary clean-up of expandRadius.
 
Package: cydar
Commit: 9cfb5990b4055d87cf15fe08b669fbb2888b0634
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:07:49 +0100
Commit message:

 Preliminary clean-up of findFirstSphere.
 
Package: cydar
Commit: 44117ec5a39495bca64fb08bd1934e721932f64f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 14:00:14 +0100
Commit message:

 Updated registration of the remaining C++ code.
 
Package: cydar
Commit: 9030807ff75a14470f9175ca3a8741885256d5d7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 13:59:51 +0100
Commit message:

 Removed dependence on 'objects.h' in remaining C++ code.
 
Package: cydar
Commit: 8e0bbccd413c27e79e92e07ffbb2f5e7eba98f03
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 13:55:42 +0100
Commit message:

 Purged C++ code rendered redundant by kmknn.
 
Package: cydar
Commit: 8e7a306bddb36816322e2c16cc2df0011598a716
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 13:32:13 +0100
Commit message:

 Removed corresponding C++ code.
 
Package: cydar
Commit: 2f1e6dc64f06d36dd8be96cc1f177cd61ae5686a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-02 13:27:33 +0100
Commit message:

 Discarded ill-considered functions.
 
Package: cydar
Commit: 9435c77b1de0d5c68dea334bcc2363f267f2f303
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-01 19:21:19 +0100
Commit message:

 Restored show method for CyData objects.
 
Package: cydar
Commit: 0955634de127c8fec779f2357fd9ccf5e2b670e7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-01 19:18:09 +0100
Commit message:

 Added new namespace file for Roxygen.
 
Package: cydar
Commit: 878b777f0acaaaf09953cf0e25a9e6af1c86382d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-01 19:17:39 +0100
Commit message:

 Updated countCells to use findNeighbors and new CyData structure.
 
Package: cydar
Commit: 465118f0a56723725d8e4c5ccfa107724139f566
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-01 19:05:52 +0100
Commit message:

 Bugfixes to allow package installation, fix getters.
 
Package: cydar
Commit: d9d1b49f51c4a50075cffab58c68db854102f9d8
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-01 18:22:23 +0100
Commit message:

 Migrated prepareCellData to use kmknn::precluster.
 
Package: cydar
Commit: 997d5ec0f48a2ac84128bc9ba92ec09b92067eb6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-01 18:21:52 +0100
Commit message:

 Complete overhaul of CyData class to cut unnecessary slots.
 
Package: tximportData
Commit: df8e3386e9a4210b59b8987f1d0eefbe09197913
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-07-13 09:54:48 +0200
Commit message:

 update version number
 
Package: tximportData
Commit: c9e4c538a132d3ad2c7138ab05bcf726ba7403ca
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-07-13 09:53:43 +0200
Commit message:

 update vignette
 
Package: tximportData
Commit: 72dc26222cdeb4dd350b48c3c4d7e19067dbd443
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-07-13 09:46:51 +0200
Commit message:

 add drosophila salmon files
 
Package: GenomicRanges
Commit: 5de2da652e18ea46292217ccbe573c9afe030a49
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-07-12 23:30:16 -0700
Commit message:

 Add coercion from GenomicRanges to IRangesList

Also add coercion from GenomicRanges to CompressedIRangesList.
These 2 new coercions are equivalent to coercion from GenomicRanges to
IntegerRangesList, that is, if 'gr' is a GenomicRanges object, the 3
following coercions are equivalent and return a CompressedIRangesList
object:
        as(gr, "IntegerRangesList")
        as(gr, "IRangesList")
        as(gr, "CompressedIRangesList")
 
Package: ggcyto
Commit: d3915ce659d9bb48f75341344753f2b9ed0e28c5
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-07-12 23:29:05 -0700
Commit message:

 Merge branch 'trunk' into devel
 
Package: ggcyto
Commit: 38bacbbff9da93706883effa850a1b885a62777c
Author: wjiang2 <wenxin.jiang@gmail.com>
Date: 2018-07-13 13:26:58 +0800
Commit message:

 bump
 
Package: ggcyto
Commit: f61e3208c794e4bf2287d7cec60abfd5072d4302
Author: wjiang2 <wenxin.jiang@gmail.com>
Date: 2018-07-13 13:18:18 +0800
Commit message:

 run validate_cases(collect_cases()) to regenerate test figs from ggplot2 3.0
 
Package: ggcyto
Commit: b322eb35187810d8e197c5c41f58d0dd9c523431
Author: wjiang2 <wenxin.jiang@gmail.com>
Date: 2018-07-13 10:42:18 +0800
Commit message:

 fix #38
 
Package: ggbio
Commit: dcc79e7d9e041e40359fb188b86bf639e44f1b4d
Author: Michael Lawrence <michafla@gene.com>
Date: 2018-07-12 19:46:35 -0700
Commit message:

 version bump
 
Package: ggbio
Commit: fcfb35455336a210077cb5eada4173279e941645
Author: Michael Lawrence <michafla@gene.com>
Date: 2018-07-12 19:46:12 -0700
Commit message:

 fix geom_rect examples for ggplot2 3.0
 
Package: SDAMS
Commit: 6570adedd9973210625690eb1231f7e08e8db4c4
Author: Yuntong Li <li@li.local>
Date: 2018-07-12 15:57:57 -0400
Commit message:

 version bumping
 
Package: dmrseq
Commit: 9599f4e9514c593d4f474e6395de7171554c7d06
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-07-12 15:22:24 -0400
Commit message:

 Patch for issue #6 submitted by @LKremer https://github.com/Bioconductor/DelayedArray/issues/23
 
Package: flowClust
Commit: d7e401fed86446c8ab1abc583f9c81c2c339552c
Author: gfinak <greg.finak@gmail.com>
Date: 2018-07-12 11:15:09 -0700
Commit message:

 fix docs for roxygen 6 and remove dependence on MCMCpack
 
Package: flowClust
Commit: 09928687a7e8a22a42a019da29f64495ad3e5d3a
Author: gfinak <greg.finak@gmail.com>
Date: 2018-07-11 17:15:32 -0700
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/flowClust
 
Package: flowClust
Commit: 5f93986279b465557bc4cd3bd649334d24c655d8
Author: gfinak <greg.finak@gmail.com>
Date: 2018-04-06 08:46:42 -0700
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: flowClust
Commit: eb21d5a14092f5907d3cfec990db8c7b6b463960
Author: Greg Finak <greg.finak@gmail.com>
Date: 2017-02-08 09:26:36 -0800
Commit message:

 Bump version
 
Package: flowClust
Commit: f4200b03897310efca4dbdd4a37c7ea8c17dd29e
Author: Greg Finak <greg.finak@gmail.com>
Date: 2017-02-08 09:21:34 -0800
Commit message:

 Add a BIC method to extract the BIC criterion.
 
Package: flowClust
Commit: 209f85ec72422642773109a2b286c61ceee088fb
Author: Greg Finak <greg.finak@gmail.com>
Date: 2017-02-02 12:05:37 -0800
Commit message:

 Use algorithm  = MacQueen for kmeans
 
Package: flowClust
Commit: f861647e24e85d06add2414146942deaf088bd0a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2017-01-06 13:59:22 -0800
Commit message:

 bump
 
Package: flowClust
Commit: 76b2c48999a777c484ac1304118e3ed423d65f66
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2017-01-06 13:43:37 -0800
Commit message:

 fix a typo
 
Package: flowClust
Commit: ebe8d6ccf2d1a3d40c5c9626afd05b2501e82bec
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-11-16 13:39:53 -0800
Commit message:

 bump
 
Package: flowClust
Commit: fbd3c514e92942841076daf9828b4fdc23df20f5
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-11-16 13:36:21 -0800
Commit message:

 fix the unit test to handle the platform-dependent issue (probably has to do gsl library) that resulted in Inf value on windows
 
Package: flowClust
Commit: 7ce1475ce14712cbb118e23523be164da5912ce0
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2016-10-17 19:10:43 +0000
Commit message:

 bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@122712 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 1012291998a8d626fd654c9bda3cef742ff8b70b
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2016-10-17 18:45:06 +0000
Commit message:

 bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@122710 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 371c01d64d751f5d78add70ff625da766ca6eac6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-13 15:18:09 -0700
Commit message:

 fix check error
 
Package: flowClust
Commit: 816aa7ea389e3753641a12f1cca307dae76de760
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-13 14:59:45 -0700
Commit message:

 load flowCore explicitly in vignette since everything are in imports now.
 
Package: flowClust
Commit: ba71030b786bd64734595bc1ac6f0fa087ca0669
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-13 14:43:55 -0700
Commit message:

 export BiocGenerics::density
 
Package: flowClust
Commit: e9b50b0409c37ddbf61b290fd33e070beda1e855
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-13 12:30:43 -0700
Commit message:

 convert legacy Rd docs to roxygen
 
Package: flowClust
Commit: dbc1a10ce0cea6a155c82c81f29ecba98b54cf27
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-12 15:46:33 -0700
Commit message:

 separate some logic from hist.flowClust so that it can be reused by other kind of plot engine. (e.g ggplot)
 
Package: flowClust
Commit: 352cffc32bb904dd4bddbdfb3d1e9d230a9d4548
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-12 14:13:36 -0700
Commit message:

 turn hist method into S3 for easy debugging
 
Package: flowClust
Commit: 3209f5509f465bd83a1e8d403ab2f52306c7345f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-10 16:26:31 -0700
Commit message:

 bump
 
Package: flowClust
Commit: 47c738edaedb41c73b8f4fd5e7d123aa2f1133b7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-10 16:26:02 -0700
Commit message:

 add unit test on gated data.
 
Package: flowClust
Commit: c8311df76be164c8578e674227a8c067a0c8325b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-10 16:17:17 -0700
Commit message:

 skip subsetting when min.count/max.count are set to -1. #16
 
Package: flowClust
Commit: 1ac5ed881e5303ba880ab46f47333624cb9cb841
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-10 15:20:19 -0700
Commit message:

 Revert " #16"
It seems to remove the data points that are equal to the min/max value, which may not be desired the outcome.
But skipping this default logic automatically will generate the results that are not consistent with the old code.
I'd rather preserve this behavior for now before we figure out what's the best.

This reverts commit 00062828b4c736e993198c648fc99fd7f45b2545.
 
Package: flowClust
Commit: 00062828b4c736e993198c648fc99fd7f45b2545
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-10 13:41:58 -0700
Commit message:

  #16
 
Package: flowClust
Commit: f593a03439a4ad41ed4538f4259e427ec60de1a3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-07 17:34:23 -0700
Commit message:

 bump
 
Package: flowClust
Commit: 4cf020a035589c00eb6d9a4bd2f24fc6184ad3d6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-07 17:04:09 -0700
Commit message:

 use options(mc.cores) to determine whether run in pararell
 
Package: flowClust
Commit: 1b56d35e84ad7779a16c5dfed77e1975b9ca48ad
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-07 16:58:15 -0700
Commit message:

 move parallel package to Depends since BioCGenerics requires it
 
Package: flowClust
Commit: 45ed6e1bf3a31e8e4c03da927f659307a7fdeb5b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-07 16:40:16 -0700
Commit message:

 fix unit test
 
Package: flowClust
Commit: 2966b3e87a87e7f071dc0513cc887d75e79b880a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-07 15:50:47 -0700
Commit message:

 add nstart arguments to petentially speed up multidimensional clustering.
 
Package: flowClust
Commit: 9fdb76f6f4b76798aba4df742348992984aef2c4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-07 15:17:44 -0700
Commit message:

 unify th argument initial values amoong tmixfiler, flowClust and .flowClustK. #15
 
Package: flowClust
Commit: e3434b3b69e0b2055bd6064173026581226e3d03
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-07 14:37:04 -0700
Commit message:

 add unit test for 1d flowClust
 
Package: flowClust
Commit: 0c70521f4b3cb3d7d183ffa55590e4c0e45d7d21
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-06 14:27:59 -0700
Commit message:

 bump
 
Package: flowClust
Commit: 79cf8c85f8a8495bf5d97c5fcd5759763f67b904
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-06 14:20:26 -0700
Commit message:

 remove the dummy code of 'detectCores' that does not affect mclapply which solely relies on options("mc.cores") to control parallel cores.
 
Package: flowClust
Commit: 458f14d906db09d1bbf55b5cc900af3bda9ba3c0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-10-06 13:32:34 -0700
Commit message:

 Revert "Add default 1 core for flowClust"

This reverts commit cb9a4fb2c1372b74b9b39e114cd9f98e25a1a4f3.
 
Package: flowClust
Commit: cb9a4fb2c1372b74b9b39e114cd9f98e25a1a4f3
Author: Greg Finak <greg.finak@gmail.com>
Date: 2016-10-06 13:15:12 -0700
Commit message:

 Add default 1 core for flowClust
 
Package: flowClust
Commit: dfc531d1ca6c4f78b2aa0be2db00f21e7740047b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-06-23 16:12:32 -0700
Commit message:

 bump
 
Package: flowClust
Commit: 6b3dd9018dabac2b84d350a84abcad70c0f327f1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-06-23 16:12:14 -0700
Commit message:

 update Rd files to fix bioc warnings
 
Package: flowClust
Commit: 454c7caca190f003e54edf0c56bca3261ef27514
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2016-05-03 21:30:44 +0000
Commit message:

 bump version after creating 3.3 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@117081 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: e4770c18043713168c9f71eb91dcd8bff50ce876
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2016-05-03 21:20:18 +0000
Commit message:

 Bump versions prior to creation of 3.3 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@117079 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 854bcb3a22268f4d98636b44a43bc274c12e8ca0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2016-04-06 16:35:45 -0700
Commit message:

 merge the difference from devel branch back to trunk
 
Package: flowClust
Commit: a5d2cee99419b24896b798155a08b98eb8720844
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-05-28 03:26:41 +0000
Commit message:

 cherry-pick from devel branch regarding to the changeFixes #11. Bug in box cox transformation when lambda=1 in density plot.
 
Package: flowClust
Commit: 204a55ed9e55408b2bce3961fb37831c121625da
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-10-13 19:59:53 +0000
Commit message:

 Bumped version number of all packages after creation of 3.2 branch.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@109592 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 89a0de47a140a84ffc0e1eabd9dc0d2040b3c736
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2015-01-29 09:59:16 -0800
Commit message:

 bump version
 
Package: flowClust
Commit: 30b5a634bb2c265546a8f5174edb8a1a209d2979
Author: Greg Finak <greg.finak@gmail.com>
Date: 2015-01-28 16:59:59 -0800
Commit message:

 Fix logic in test of randomStart for warning.

Bug in test of randomStart to warn about use of prior with non-zero randomStart
 
Package: flowClust
Commit: 7cd43f6239ba0aa43914cb9227aa9934044fd210
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2015-01-13 16:01:08 -0800
Commit message:

 add GNU make to system requirements to get rid of bioc check warning
 
Package: flowClust
Commit: 4c660f678287ecc428fadf1161b14f66a09551e8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-05-14 11:45:35 -0700
Commit message:

 load parallel library before running in parallel
 
Package: flowClust
Commit: 438c7e649ab4c83024852be4e2d98d9ef7f492a7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-04-06 14:05:24 -0700
Commit message:

 close #10
 
Package: flowClust
Commit: 07276bb889cfa99e692a5afc423785ee1ac5f968
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-04-04 11:33:06 -0700
Commit message:

 bump version to catch up bioc version
 
Package: flowClust
Commit: 5a336c97fcb9658e9c22ec678ca7237d4ae06511
Author: Greg Finak <greg.finak@gmail.com>
Date: 2014-04-04 09:40:54 -0700
Commit message:

 replaced author and maintainer

accidentally deleted during a merge. 
Package: flowClust
Commit: 5830c117718a459759e8765106a85dbb71ebf946
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2014-04-04 08:42:48 -0700
Commit message:

 Fixed plotting of confidence ellipse to be faster using only 100 points and more accurate when the ellipse is very eccentric
 
Package: flowClust
Commit: 730b0af5e9dd23461867d0c12ff18658c454a173
Author: s.arora <s.arora@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-04 22:12:21 +0000
Commit message:

 modify to new biocViews to DESCRIPTION file



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@87035 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 2f6b319a3cf3a0cecc84e086e2934e40e92d1473
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-02-24 22:06:47 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: a89331e254ca594941666ce851514f161bc8295b
    Commit message:
    reslove check warning by removing the duplicated imports of plot generic
    Committed by mikejiang 
    Commit date: 2014-02-24T14:03:54-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@86755 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    
Package: flowClust
Commit: a68041334c4c2cf4c7ef6a843f7b1483ce33d13b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-02-24 14:05:00 -0800
Commit message:

 Merge commit '3184507443a317ca7950035ea13dcb57413908b6'
 
Package: flowClust
Commit: 13130146ca5a71c63d7e037cf225532746ab6f1b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-02-24 14:04:35 -0800
Commit message:

 Merge branch 'master' of github.com:RGLab/flowClust
 
Package: flowClust
Commit: a89331e254ca594941666ce851514f161bc8295b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-02-24 14:03:54 -0800
Commit message:

 reslove check warning by removing the duplicated imports of plot generic
 
Package: flowClust
Commit: a5682f9561a80fa50d39f495ac1be6beca7a0353
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-02-24 13:37:32 -0800
Commit message:

 remove multicore from suggest list in DESC file #9
 
Package: flowClust
Commit: 89d75614851470b3c99c5c0011b63f31eda23fdc
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-02-19 22:44:57 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commit(s).

Commit information:

    Commit id: 84a133e6ef3d6ad10f49d309044ca3f3ca878e5d
    Commit message:
    rev DESC
    Committed by mikejiang 
    Commit date: 2014-02-19T14:39:20-08:00

    Commit id: 0ee4f5ec7d4b844035f317ccfeb8752d1ff54533
    Commit message:
    Merge branch 'master' of github.com:RGLab/flowClust
    Committed by mikejiang 
    Commit date: 2014-02-19T14:44:28-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@86601 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    
Package: flowClust
Commit: 0ee4f5ec7d4b844035f317ccfeb8752d1ff54533
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-02-19 14:44:28 -0800
Commit message:

 Merge branch 'master' of github.com:RGLab/flowClust
 
Package: flowClust
Commit: 8d4fbc62def06d4c4eb792c7e7bff6300b4b0f80
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-02-19 22:43:36 +0000
Commit message:

 conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@86600 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 84a133e6ef3d6ad10f49d309044ca3f3ca878e5d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-02-19 14:38:41 -0800
Commit message:

 rev DESC
 
Package: flowClust
Commit: 3184507443a317ca7950035ea13dcb57413908b6
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-02-05 19:15:10 +0000
Commit message:

 merge from bioc-devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@86111 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 41c4ca8d42a6d7fe86b78435c797c9f647e58362
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-02-05 19:12:39 +0000
Commit message:

 merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@86110 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 431cb100b5385a961c10fb3ad99f007ef4194ef6
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2014-01-30 14:49:38 -0800
Commit message:

 error checking the length of K before testing the validity of the prior
 
Package: flowClust
Commit: b644ad8511623948e95697d2100a6bc4d2dc1623
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-24 18:51:57 +0000
Commit message:

 remove multicore from DESC

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@85787 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 351e11f891b98c3da532d8d0833c89d15264d01e
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-21 21:40:44 +0000
Commit message:

 deprecate the usage of multicore

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@85685 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 0b8d5ae0c3f5fcd715edb4f86c0596f4ec6c7630
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-21 13:36:21 -0800
Commit message:

 Merge commit 'c2d4b02464bc0785b3c1a7156ef64e333308a150' into trunk
 
Package: flowClust
Commit: fb3d67d87341a8e53fe9d597f45fcac93c86827a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-21 13:36:02 -0800
Commit message:

 close #9
 
Package: flowClust
Commit: c00f552c15d5cce71506aff5397c7d95e15af93c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-21 13:09:25 -0800
Commit message:

 close #8
 
Package: flowClust
Commit: daec7206ff1add5dd1e73ea6364c6fb4e900884f
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-21 19:56:26 +0000
Commit message:

 merge from biocdevel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@85679 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: c2d4b02464bc0785b3c1a7156ef64e333308a150
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-21 19:53:37 +0000
Commit message:

 rm multicore reference in vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@85678 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 306b66b1f00b2afd0b6f5adb1806f89b9e73b5fc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-21 11:53:17 -0800
Commit message:

 Merge commit '1c8498c6983c901151d5d0a9456775a9763ecf9d' into trunk
 
Package: flowClust
Commit: a83706c9e93c200cb4646e0ddf0b97fd32618af1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-21 11:52:57 -0800
Commit message:

 rm multicore reference in vignette
 
Package: flowClust
Commit: 9ffb7eafe71b4abd84737fc5a1c584470582ad58
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-21 18:12:10 +0000
Commit message:

 update DESCRIPTION FILE

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@85667 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 1c8498c6983c901151d5d0a9456775a9763ecf9d
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-21 18:06:48 +0000
Commit message:

 merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@85666 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 681b4e04a64db17e1e00ab7eecd45dfa228d07ce
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-21 18:06:45 +0000
Commit message:

 merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@85665 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 5db42fd7ed15e34d378decadee124f5400943743
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-21 10:05:27 -0800
Commit message:

 Merge commit '09a283054603231808931c3e2db1eb4bf3fa5a46' into trunk
 
Package: flowClust
Commit: 143f19a522d00d0dafcaf0644630d190fddb41d4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-21 10:05:04 -0800
Commit message:

 update DESC
 
Package: flowClust
Commit: 7a873d8f204dff8619ea101030f371467fdcbe34
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-13 03:17:02 +0000
Commit message:

 bump version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@85467 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 52437363d9a8b1751e157ce05bba31295af4039f
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-12 01:13:26 +0000
Commit message:

 update DESC

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@85449 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 691e0732c56c6a884956f47e26a6dc1c0b9747f0
Author: m.jiang <m.jiang@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-01-10 23:21:59 +0000
Commit message:

 merge from bioc -devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@85430 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 08da5b7e2a0d0304b0d7629ae4b406f7df9e3ba8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-08 15:24:45 -0800
Commit message:

 add me to maintainer list
 
Package: flowClust
Commit: 09a283054603231808931c3e2db1eb4bf3fa5a46
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-08 14:00:34 -0800
Commit message:

 merge from git
 
Package: flowClust
Commit: b716a0a0a8f302b239240583f479e288861b2b80
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-08 14:00:16 -0800
Commit message:

 Merge commit 'fbf4edceebbef669e20622a5a7dacd61dc23978d' into trunk
 
Package: flowClust
Commit: fbdee1fa9f719bfb4e0bdc6c2605d00df13e57d4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-08 13:59:49 -0800
Commit message:

 manually merge changes from svn
 
Package: flowClust
Commit: f434a6b91af808273b71766436e49ad0bd2f57d5
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-08 13:55:00 -0800
Commit message:

 bump version
 
Package: flowClust
Commit: 754a57c682a2e24056801dc66464cdbb333f1cb8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2014-01-08 13:53:11 -0800
Commit message:

 add missing gsl header files to bundled gsl library. close #5
 
Package: flowClust
Commit: fbf4edceebbef669e20622a5a7dacd61dc23978d
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-11-01 20:03:24 +0000
Commit message:

 rename inst/doc to vignettes and bump version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@82482 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: e2ef2d6970c4efc143c8f9f1f870c416fac6d18b
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-10-14 21:47:19 +0000
Commit message:

 bump version after release branch has been created

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@81644 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 62030c589f462af4a2874fb72da7744027314fe1
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-10-14 21:43:43 +0000
Commit message:

 Creating branch for BioC 2.13 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowClust@81643 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 01d03aaed8358469ebd3ef9d5a8f314a73aef8da
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-10-14 21:29:21 +0000
Commit message:

 bump versions prior to creating BioC 2.13 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@81642 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 8e10b536f18a419f6b1d3750b04e1d588d9b3a15
Author: John Ramey <johnramey@gmail.com>
Date: 2013-05-31 14:42:51 -0700
Commit message:

 Initialization of cluster labels now always uses prior if provided.
 
Package: flowClust
Commit: 810f8fb971b9c7364b45a533d51cc67f17987725
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2013-05-30 09:54:25 -0700
Commit message:

 bump version
 
Package: flowClust
Commit: b5c1089e8f57ada94ed30cdeab6822aa95e1abcc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2013-05-07 17:19:54 -0700
Commit message:

 Merge branch 'trunk' of github.com:RGLab/flowClust into trunk
 
Package: flowClust
Commit: 223116789451ba0ec704de4e9010897b3ebd5075
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-04-03 22:06:11 +0000
Commit message:

 Bump y in version x.y.z to odd number in devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 3419ab08506cba3ff73a3d9403685f0466bf722e
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-04-03 21:32:27 +0000
Commit message:

 bump y of x.y.z version number for BioC 2.12 release

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@75263 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: c8d45a7d8dc13f43c3fe0aac46d01ba1c9fb51df
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-21 10:26:51 -0800
Commit message:

 Merge svn to trunk. Fix to build on windows by removing multicore dep
 
Package: flowClust
Commit: e8da1045d4d781ca85c9a4485b0054114f241468
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-21 18:24:23 +0000
Commit message:

 bump version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73670 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 00f09726deae61248adb98969798781d070bc4d3
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-21 18:23:34 +0000
Commit message:

 Remove multicore dependency so that this builds on widows

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73669 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 57fa41f0e34b495894d3a5d4427383ba6800bda1
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-20 02:42:26 +0000
Commit message:

 Merge from github trunk. Changes to use bundled gsl lib

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73627 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 3ae017a21f64d93e32c95786e6ebba281b23ac64
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-19 18:41:00 -0800
Commit message:

 Merge svn commit 'b681c912e55f35a3e1754d370c737deca9f98fc4' into trunk
 
Package: flowClust
Commit: 890e79b184ae3eee1276273d534c2594832c8d8e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2013-02-19 17:13:43 -0800
Commit message:

 Merge commit '07d3ae79fadd32a9b68ee778a2f9b39d7aaf3cb0' into trunk
 
Package: flowClust
Commit: 51b5fb908398f835239c975f00c2cf2d68e96241
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2013-02-19 17:01:20 -0800
Commit message:

 update Makevars.win to adapt to the current gsl library settings in bioc windows server. Issue  #5
 
Package: flowClust
Commit: 4801c00d97fd3b04cbcd77b9fec0a3d7483355c2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2013-02-19 11:19:36 -0800
Commit message:

 bundled trimmed version of gsl library. close #5
 
Package: flowClust
Commit: eb9bfed85503e293caed2a82ae28b46ff38e50e0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2013-02-15 17:07:31 -0800
Commit message:

 change configure and Makevars.in to use bundled gsl library. Issue #5
 
Package: flowClust
Commit: 76dee3595f061c8059e76ac30c1f794a6d521de6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2013-02-15 17:06:12 -0800
Commit message:

 change configure and Makevars.in to use bundled gsl library
 
Package: flowClust
Commit: 07d3ae79fadd32a9b68ee778a2f9b39d7aaf3cb0
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-13 18:32:51 +0000
Commit message:

 Fix Makevars.win so package will build on windows.
Remove multicore from suggests and library(multicore) from vignette
because it is apparently not needed and multicore is not available
on windows.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73468 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: b681c912e55f35a3e1754d370c737deca9f98fc4
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-13 18:32:51 +0000
Commit message:

 Fix Makevars.win so package will build on windows.
Remove multicore from suggests and library(multicore) from vignette
because it is apparently not needed and multicore is not available
on windows.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73468 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 2ace25b2ec1d5c4f37b2158e4d42f3831a62ccf5
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-12 20:14:28 +0000
Commit message:

 bump version and fix DESCRITPION file

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73427 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 2db8686cfc0bb74b3c821ba8072ffe6dc6ad3739
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-12 18:13:56 +0000
Commit message:

 fix typo....

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73419 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 47bbf8677414a8fe2e96abca2bda77767c7c0be2
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-11 09:05:37 -0800
Commit message:

 Merge branch 'master' of github.com:RGLab/flowClust
 
Package: flowClust
Commit: 2c574a91623317ce5ee5bd17ca67f539392f41f4
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-11 17:05:13 +0000
Commit message:

 Added two docs

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73354 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 70a7c78ec97c3b3551de3ae5bf526911209b5a36
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-11 09:00:30 -0800
Commit message:

 Added documentation Rd files for two functions
 
Package: flowClust
Commit: 28b0f4206bb4e806430e29ddb93d8dc05e7a7c74
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-11 08:31:49 -0800
Commit message:

 Merge branch 'master' of github.com:RGLab/flowClust
 
Package: flowClust
Commit: 818ee7c3782d9d27fcce53005be46d789a2be1aa
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-11 16:30:48 +0000
Commit message:

 bump version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73353 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: bbc84398a5b390f8c9c2856ac6d25a985fa11cb0
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-11 16:30:21 +0000
Commit message:

 Remove dependency on synchronicity

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73352 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 4ccc50af269a66e5045ad251b2f4895139ba61ab
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-11 08:30:02 -0800
Commit message:

 Remove dependency on synchronicity
 
Package: flowClust
Commit: 1feb4e7894af33af74022895dc55213d8bbc85a3
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-11 08:29:17 -0800
Commit message:

 Remove dependency on synchronicity
 
Package: flowClust
Commit: fd3fc7b8be3e60a37ca51086eebaf58aa0c3086e
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-08 00:58:52 +0000
Commit message:

 Quick update to vignette to show an example of using priors with flowClust.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73273 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: c7226585ea963325f09425b834cf3e98ebd9f231
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-08 00:58:46 +0000
Commit message:

 Added functionality to flowClust2Prior for addCluster, to add an additional vague prior for extra components to the model.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73272 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 84120a06f7c70713ca1943f8cd6942e8614375c9
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-08 00:58:38 +0000
Commit message:

 Fixed check warnings related to documentation. Removed dependencies on flowWorkspace

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73271 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: a5c12ecec7b077f51b32a71a2c22dc2b6cf299c9
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-02-08 00:58:25 +0000
Commit message:

 Update to flowClust 2.99, ready to move to 3. Merged into current devel svn

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@73270 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 9eb1a330d64fd33cb7629fef1cd2d34c633f4e74
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-07 16:57:52 -0800
Commit message:

 Quick update to vignette to show an example of using priors with flowClust.
 
Package: flowClust
Commit: 588b085e61d60e698ea93e79539f3f2cd4385de6
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-07 16:31:09 -0800
Commit message:

 Added functionality to flowClust2Prior for addCluster, to add an additional vague prior for extra components to the model.
 
Package: flowClust
Commit: 30b75f9d1939688bd7cf75b14e6505611d7f1fd5
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-07 14:51:17 -0800
Commit message:

 Fixed check warnings related to documentation. Removed dependencies on flowWorkspace
 
Package: flowClust
Commit: 0dde88fa9e4a8532205564e6427bcc6baaf4bd34
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-07 11:40:19 -0800
Commit message:

 Update to flowClust 2.99, ready to move to 3. Merged into current devel svn
 
Package: flowClust
Commit: 84c1016d95edc6d4f984bdf966fdf8f0f31e30e9
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2013-02-06 21:07:00 -0800
Commit message:

 Remove dependency on multicore and snowfall. Added more robust peakMatch.R functionality used in OpenCyto
 
Package: flowClust
Commit: 0ec8646f714bce06a7fc689c32d6e38da369a5b2
Author: John Ramey <johnramey@gmail.com>
Date: 2013-01-16 16:26:51 -0800
Commit message:

 Fixed an issue in 'dmvt' when 'x = 0'. Bumped version. Closes #3
 
Package: flowClust
Commit: 639d66cea29dda18ca220243761f0474e531f9ad
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2012-10-23 09:00:35 -0700
Commit message:

 Fix to plotting when usePrior=yes, lambda=1, and trans=1. Warning when lambda!=1, trans=1,usePrior=yes
 
Package: flowClust
Commit: 25bded20887a0c43e0030e96840f9a57b8e9a7f7
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2012-10-19 13:00:47 -0700
Commit message:

 Fixed a bug with gaussian flowClust and priors
 
Package: flowClust
Commit: 12a09dbceb6a426b48059dd26f73929b91be024e
Author: John Ramey <johnramey@gmail.com>
Date: 2012-10-17 12:27:33 -0700
Commit message:

 For the Bayesian version of flowClust, if the number of features is 1, we now use the prior densities to initialize the cluster labels instead of K-means.
 
Package: flowClust
Commit: 04cfe6b7784dae078976673b01360eeba96d4205
Author: John Ramey <johnramey@gmail.com>
Date: 2012-10-17 11:30:57 -0700
Commit message:

 Updated dmvtmix to allow the degrees of freedom to be given for each mixture component. If only one value is given, it is used for each mixture component.
 
Package: flowClust
Commit: 37a69a3d0c2344cd7c7951b50056c49f1e1ba9f9
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-10-01 22:43:56 +0000
Commit message:

 bump package versions after creating 2.11 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 0d59a7bca6d13fdaae288d3fbcae3afcfbc1632f
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-10-01 22:16:24 +0000
Commit message:

 Bump all packages before creating 2.11 branch.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 43fe6f336fb7d81c20e82e0490d2561209ffecef
Author: John Ramey <johnramey@gmail.com>
Date: 2012-09-28 15:41:29 -0700
Commit message:

 Fixed shifted offset by 1 for Box-Cox transformation when trans = 0 in getEstimates(), hist(), and dmvt().
 
Package: flowClust
Commit: 1a76038b38240d3f285fb6609f148cf0191009b6
Author: John Ramey <johnramey@gmail.com>
Date: 2012-09-27 17:42:28 -0700
Commit message:

 Enabled the tmixFilter class to utilize the prior parameters for the Bayesian version of flowClust.
 
Package: flowClust
Commit: 401ad228bb34145631bcb4438d17ae3cbb6e53bb
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2012-09-14 13:19:55 -0700
Commit message:

 Added README.md text
 
Package: flowClust
Commit: e3e258d2ab0f467496310247a282af14d6802e4f
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2012-09-14 13:12:01 -0700
Commit message:

 added .gitignore
 
Package: flowClust
Commit: c8d69a217964291b10ba5fdffe423655b7389238
Author: Greg Finak <gfinak@fhcrc.org>
Date: 2012-09-14 13:11:13 -0700
Commit message:

 Bayesian FlowClust - initial commit
 
Package: flowClust
Commit: b7abf1bdd67a42ad68217d044855e3e42ceacfb0
Author: Greg Finak <greg.finak@gmail.com>
Date: 2012-09-14 12:59:03 -0700
Commit message:

 Initial commit
 
Package: flowClust
Commit: 6dac3e9a59eba9da473461df8b33d74aabeec8c3
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-30 22:15:56 +0000
Commit message:

 bumped version numbers after creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@64680 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 1e8a09b06dab447d63b6029f15231a5dc95de662
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-30 22:05:02 +0000
Commit message:

 first version bump prior to creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 314f779659b1caaa89aafb87210f81fb2e8f69e0
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-19 21:04:31 +0000
Commit message:

 Fixed warnings in doc with Ulist and Uvector. No idea how to get rid of these warnings in general. This seems to be an issue with rrcov

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@64116 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 6a9704aace6c6e51abdb6124ac8665e395071a64
Author: g.finak <g.finak@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-09 18:41:05 +0000
Commit message:

 Fixed errors for density generic. Now method imported from BiocGenerics. Version bump to propagate.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@63692 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: e821a59a45187ea42105a7c7b646b79b0c881623
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-05 05:53:27 +0000
Commit message:

 Import plot and summary from stats4 instead of BiocGenerics.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@63459 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: ba708ba78a2f63d6102e45aeaba46a3f2d6487ab
Author: mtmorgan@fhcrc.org <mtmorgan@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-02-25 06:50:42 +0000
Commit message:

 plot, summary, split S4 generics

- plot, summary imported from BiocGenerics
- split promoted from S3
- additional code tidy -- avoid partial argument matching; use lower
  case in Sweave tags


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@63151 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: f0e0638eb4189ae726c838e45d4a8d3b2e2a836e
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-11-16 17:05:56 +0000
Commit message:

 these packages should be bumped after all; they use gsl, not netcdf

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@60389 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 17f01b0d84a398b45bbdca4987730fb062b50a87
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-11-16 05:01:51 +0000
Commit message:

 reverting to r60372 because packages in devel don't need to be bumped because of a netcdf change affecting release only

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@60380 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 9a01d940ca8c6442191525034336a4201596bf42
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-11-16 01:49:57 +0000
Commit message:

 bumped versions to trigger propagation of packages built against libgsl.a (static instead of dynamic)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@60374 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 0d172b2c06c73cefaf29cd258d4ba2767b2b6bb5
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-10-31 23:12:28 +0000
Commit message:

 version bump for start of 2.10 development cycle

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@59924 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: c60431996e89e28025dcdc29e110c9a1e72f3cd3
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-10-31 22:59:03 +0000
Commit message:

 bumped package version numbers prior to creating 2.9 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@59920 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 876a99145921dfd8b91c60ca27acd1c697a87bd8
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-06-13 22:40:41 +0000
Commit message:

 Use $(LIB_GSL)$(R_ARCH)/lib instead of $(GSL_LIB)
and $(LIB_GSL)$(R_ARCH)/include instead of $(GSL_INC) in Makevars.win
to accomodate Windows bi-arch builds.
No version bump.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@56153 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 72480d92f25b92491700962e1d11fad991072fe1
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-04-13 22:36:43 +0000
Commit message:

 Bumped version numbers again for new BioC 2.9 devel cycle.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@54802 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: c0816d7eb2b0886d7880538dd33043b131b9c8bf
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-04-13 22:27:35 +0000
Commit message:

 Bumped version numbers for BioC 2.8 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@54800 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 9fa0e36eb55c86378b03fb3b4bb4beaa0f0c3a7d
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-10-18 05:57:44 +0000
Commit message:

 Bumped version numbers again for new BioC 2.8 devel cycle.
ERRATA: Previous bump was for BioC 2.7 release (of course), not 2.6!


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@50295 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 9e72c9cf594326a8d57e1aefa3fbd47e8746ad99
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-10-18 05:34:23 +0000
Commit message:

 Bumped version numbers for BioC 2.6 release


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@50293 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: e32af585075dfaf41a7fef749e64f9ba87f05886
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-09-20 00:52:43 +0000
Commit message:

 fixed a small bug to give correct plots when trans=0 and lambda!=1

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@49483 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 9b34318e27df10b6c526e3e0d2a2a4d4b1879cbf
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-07-19 13:24:52 +0000
Commit message:

 # Move multicore to Enhances field so that it can be built on windows

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@48200 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: f9e51d771df39cc370e9293acf7373de4f487753
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-07-07 20:25:19 +0000
Commit message:

 # Fixed the version number

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@47972 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 5ad7c789e7a6f2b1bc86e49c4bfed537651555f0
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-07-07 17:56:19 +0000
Commit message:

 Added support for parallel computation via the multicore and snowfall packages. I also improved the way flowClust checks for singularity problems. The code is not interrupted anymore, instead we return NaN for the log likelihood. I have also added NEWS and CITATION files.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@47970 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 777070330ff0388ff592afa771028ea85437a07b
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-05-26 19:01:40 +0000
Commit message:

 Now supported on 64-bit Windows. Thanks to Arnaud Droit from Raphaël Gottardo's
lab for providing GSL binaries for this platform.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@47151 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: b3de6f1f158733207fab2bee7dafe985a1f7589c
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-05-21 17:37:46 +0000
Commit message:

 # I have added the possibility to interrupt via Crtl-C. This can be useful for long computations.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@47067 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 442fd82fd1cb1e0a009644233c1129f998a5832f
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-23 01:25:14 +0000
Commit message:

 fixed a small bug after dropping dependency on mclust

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@46437 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 753048ddf8805af457ae106609160c04fc2255f4
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-22 18:45:15 +0000
Commit message:

 Bumped version numbers for BioC 2.7 trunk

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@46405 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 181ed66e90f57a08dc293757e826a3fbef8c0c9f
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-22 18:21:23 +0000
Commit message:

 Bumped version numbers for BioC 2.6 release

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@46401 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: f49e55a21b80dc4a9220eb4b0b4d783abeaff498
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-22 14:29:20 +0000
Commit message:

 Replaced package= to PACKAGE= in .C calls.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@46377 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: bee8c45ef8ab61c94a5cc7baec0972dd9772ff35
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-22 08:18:58 +0000
Commit message:

 drop the dependency on mclust

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@46369 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 234827d18add8ef84ec5edc7176989dc33efa6bc
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-22 08:18:29 +0000
Commit message:

 drop the dependency on mclust

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@46368 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 0f53afa547369e823b1762563bd160fe36597c8f
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-20 18:47:41 +0000
Commit message:

 replaced 'gewurz' by 'win64' in UnsupportedPlatforms field

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@46267 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: ffd0fc44de3cf6afc37ec1f2ce220522e89f4570
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-19 01:05:18 +0000
Commit message:

 Tagging the package as NOT SUPPORTED on 64-bit Windows for now. (Couldn't find
or build the GSL for this platform. Does anybody know how to do that?)


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@46175 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 642f18f12ecf60f26937fdc5d11f6a220abca342
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-10-27 23:45:24 +0000
Commit message:

 Package version bump for BioC 2.6 devel.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@42686 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 93534c3f19cf6f773ec69a06e974878c2c33fe01
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-10-27 23:33:29 +0000
Commit message:

 Package version bump for BioC 2.5 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@42684 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 343a496a7b09318c79fdeb6f0e184edb1eb63ce6
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-10-15 19:45:02 +0000
Commit message:

 update vignette and README

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@42415 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 57503fd48eae7085b03f5ff7d3039bc52fa2c7dc
Author: c.wong <c.wong@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-10-15 18:28:16 +0000
Commit message:

 bumped version number after adding FlowCytometry into the biocViews
field in DESCRIPTION.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@42411 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 433f575e6b9334677579cd63cdd761fcbe040ec1
Author: fhahne <fhahne@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-10-12 12:11:28 +0000
Commit message:

 cleaning up some documentation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@42312 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 47afe82726f6b659583a7d2c615d4f130fc2d1df
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-10-10 20:46:06 +0000
Commit message:

 if randomStart>1, allow EM solution to be sought from the 2nd best initial start in case convergence fails from the best initial start, and so on.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@42301 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 5d0f1775be9f7b49c75e1757f80fc6d0b56ce8f0
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-09-15 15:22:36 +0000
Commit message:

 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@41696 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: d76c5b0d45c896cc4fca58974bc80c2b8d98134a
Author: fhahne <fhahne@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-07-02 22:56:10 +0000
Commit message:

 fixing a minor issue with the conversion to multipleFilterResults and also a documentation glitch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@40493 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: a3f6e20672a1e28c53f43703c145a2723e9c9cc5
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-05-20 22:38:00 +0000
Commit message:

 small fix to hist() method for subsetting when the object is one-dimensional

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@39589 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: f5e547caca918a77d9cfe3296b87050ecb92e5a2
Author: fhahne <fhahne@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-05-05 18:41:21 +0000
Commit message:

 adding a summarizeFilter method in order to collect the information from the filterResult

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@39310 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: ff2c6223b77304669fda9fd2f2425f4cd3eee91d
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-20 23:44:07 +0000
Commit message:

 Bumped pkg versions for BioC 2.5 devel line.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@39015 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 537635241469ab71925541ad371f90db4aaf6fd9
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-20 23:24:12 +0000
Commit message:

 Bumped pkg versions for BioC 2.4 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@39013 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: f08b7fa2ff829fdc28c65c2333d9e6d91b8cc966
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-07 01:20:29 +0000
Commit message:

 bumping flowClust version to 2.0.4

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@38532 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: e3f6f638de459261233e2b7e316134d5917a244f
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-07 01:15:00 +0000
Commit message:

 minor updates to documentation files

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@38531 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: a3939959243c9960f2f8f48a4d5e9fa725431d97
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-06 15:27:14 +0000
Commit message:

 a fix to Map.Rd

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@38507 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 442cdf3ac064d6ca4e786316fdb0ab5000492e36
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-03 22:37:02 +0000
Commit message:

 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@38479 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 2b8c1f2634d7451b784e6823cb6cb8df93f3de71
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-03 22:33:34 +0000
Commit message:

 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@38478 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: dad72f76881aa7db55504ff670df0029b3f65a24
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-03 22:28:23 +0000
Commit message:

 initialization using random partitioning

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@38477 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 887948333d498a471eca5974049f21d9e8d7c821
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-03-19 22:07:09 +0000
Commit message:

 Changed biocViews entry of Statistics to Bioinformatics.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@38070 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: db1eb38ebc0d7d3d33e92f3eb7b8fbd70f92ce9b
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-02-27 19:31:25 +0000
Commit message:

 modified .ellipse() to get rid of the precision problem arisen due to the large difference in the lengths of the two axes of an ellipse

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@37641 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 7d8fc139850153d58c153556980f07b507f39b0e
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-02-12 23:35:40 +0000
Commit message:

 small fix: rectify the problem of not transforming the mu estimates in getEstimates() and the plotting methods when lambda is 1.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@37358 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: fdb8b46eac7d9d993518cf66b4e11d532d5da2f6
Author: c.wong <c.wong@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-02-04 18:43:07 +0000
Commit message:

 fixed Rd 2 parser warnings 


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@37134 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 1f2d1cc5a388773946a3eae24befffce3ba1cee5
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-02-03 23:13:48 +0000
Commit message:

 Using pkg-config in configuration to make it easier to build against the GSL library.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@37108 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 2e077f2217129b4a2ed8f9d08601af9477b23bae
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-01-12 19:11:28 +0000
Commit message:

 bulk update; version 2.0

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@36572 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: ad6defb2ed52add730ab7f2530619d8cdde1472c
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-21 22:46:31 +0000
Commit message:

 Bumping version numbers for BioC 2.4 devel.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@34814 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: f9a63f15da432a7747168564f1a2b780026cf425
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-21 22:32:58 +0000
Commit message:

 Bumping version numbers for BioC 2.3 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@34811 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 5a6adb6e02c0dc0663a12b3aa3a41d2313bd2446
Author: fhahne <fhahne@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-09 03:37:40 +0000
Commit message:

 fixed access to parameters slot which has changed in flowCore

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@34337 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: ac9f8e7ad9a22ccc38008d5af2e96b52a5d3a1b6
Author: fhahne <fhahne@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-09 03:34:26 +0000
Commit message:

 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@34335 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: df593c54caba29afc0e35d7f675325a0d4b9f6b3
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-08 20:54:53 +0000
Commit message:

 some changes to cope with recent redefinition of "parameterFilter" class in flowCore (the "parameters" slot now takes a "parameters" object (which is a list) instead of a character vector; changed tmixFilter function and %in% method accordingly)


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@34322 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 4000a5821628a67fe04e8085d62f8c85a726dc6b
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-09-25 21:16:10 +0000
Commit message:

 when K takes a vector of values, hier clustering needs to be applied only once since the classification tree is the same for all values of K

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33969 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: f5367faf84e1273d45ad8880f86be22e5f978421
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-09-23 03:45:37 +0000
Commit message:

 Major update: enable K to take a vector of values, and include the option of running short EMs for random initializations
- add classes flowClustList and tmixFilterResultList
- define all the utility and plotting methods for these two classes
- include the criterion replacement method
- add optional arguments criterion, B.init, tol.init to flowClust()
- update all man pages and the vignette
- bump version to 1.7.0
NOTE: there is a mysterious bug found when defining the tmixFilterResultList class.  The data part cannot be assessed directly by typing the object name; it has to be assessed through the .Data slot.  Tracked down to find that it may be related to the multipleFilterResult or AssayData class it extends.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33886 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 7b8aa6d27688a3d406e0cf23de3472f5a95b84a0
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-09-09 05:54:53 +0000
Commit message:

 minor changes to split and tmixFilter man pages

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33635 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: b94a01ddeb9fdb9c222614d3f3bdd502e0d7ad70
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-09-09 03:50:35 +0000
Commit message:

 added criterion function;
made changes to man pages and vignette according to Florian's suggestions about the split/Subset method (dropped the select argument, deprecated the split argument);
dropped select argument also for Subset (with signature data.frame/matrix)


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33634 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 750742fce5747d4843b2054ea898d5809e684b93
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-09-04 17:03:30 +0000
Commit message:

 fixed (back) the problem of deallocation of PrecisionTmp

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33567 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: dd200f9795094c809838d52779d18ee2534cbf55
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-09-04 02:26:38 +0000
Commit message:

 add criterion()

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33557 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 391707b7c8f9c848ada129cbcaffbcdbd03bde96
Author: fhahne <fhahne@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-09-03 23:22:10 +0000
Commit message:

 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33554 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 0abbd886b9f8e95af94c320c499c14c0ad413468
Author: fhahne <fhahne@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-09-03 23:08:51 +0000
Commit message:

 bumped version number

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33553 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 90740af3a38b6f0885e776c5979f5e462b2684ea
Author: fhahne <fhahne@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-08-30 04:00:11 +0000
Commit message:

 code beautification and fixes for flowCore integration

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33488 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 7cf6ca36b2530dd087b757925babbcf79a6a64f7
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-08-28 18:45:29 +0000
Commit message:

 some more updates:
in C code, update YTrans when estimating lambda in M-step instead of in update_z_u() -- just increase efficiency, shouldn't bring changes to outputs
update hist method
minor changes to README, vignette, etc.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33458 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 4d3979aef21a7daf3e2b628589affd6ec4770a48
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-08-21 19:26:18 +0000
Commit message:

 option for gaussian mixture model
make existing methods adapt to gaussian mixture model
fix minor bugs in density plots
update man pages to reflect recent additions/changes
update getEstimates; includes an approximate variance estimate

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@33318 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 437ea7a69f7d090db192ffb8ca990142cbdd33da
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-06-30 13:48:44 +0000
Commit message:

 update getEstimates(); includes an approximate variance estimate

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@32487 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 954adb440eb971c2f7af90ee4f9633f24c0dca5b
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-06-04 16:43:39 +0000
Commit message:

 # Fixed a small typo when deallocating the memory

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@32122 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 3bd8872b6d120e2b7fdf73f2fa17b94239c3176b
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-06-03 21:02:41 +0000
Commit message:

 # Remove an unnecessary README file and modify the DESCRIPTION FILE

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@32111 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: d07a2c8955a739e09c916359cc6b20d2920ad189
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-06-03 20:48:32 +0000
Commit message:

 # Forgot to bump up the version number

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@32110 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 72f3ddb54a197b0244d95b2853aae55b4a727e1d
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-06-03 20:42:30 +0000
Commit message:

 # I have fixed a small memory leak.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@32109 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 21cca342eab8aa0c194d0d85eafc7db80f06747f
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-05-01 23:31:49 +0000
Commit message:

 update README instructions for Windows users; move README to inst directory

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31469 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 7791a4a49e74adab316ce1c5826ab43e31382caf
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-30 09:04:18 +0000
Commit message:

 update README instructions for Windows users

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31440 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 813ad847533a22979429b3d7d339ae5e55cb0285
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-30 06:37:41 +0000
Commit message:

 minor change to Makevars.win

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31439 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 009c0b58320250041b31bad4cbf4b08303594959
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-30 00:25:58 +0000
Commit message:

 Updating the version number for the trunk post-BioC 2.2 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31432 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 99942935db4ccefe195387bfb2fc91ba0a959f88
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-29 23:50:18 +0000
Commit message:

 Updating the version number for the BioC 2.2 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31430 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: b41597ac5e8d5447d54af0ca45f3ed3ef7b94653
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-29 02:23:34 +0000
Commit message:

 Changed unprintable character to '.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31401 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 68fd652c616b357a46e786e84134c0ef3befd7fd
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-23 23:37:18 +0000
Commit message:

 # I have removed the verbose on the number of iterations. I have also updated the Makevars.win, and declared the pointers that previously gave warnings.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31288 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: f58babfe2317b3ff190c62e8681256e4a161050c
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-23 01:20:07 +0000
Commit message:

 # Another minor change

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31262 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: ce6a79fc4853a78b051b71da8da7d1285d7ecf46
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-21 21:25:23 +0000
Commit message:

 # More fixes on the autoconf

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31253 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: b7ff63e0ce370df823a1256fda955698c673f36e
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-21 00:36:18 +0000
Commit message:

 # I have made another minor change in the autoconf file.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31223 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: bab1d4968933fb4141b1907c5696e9f6313a34a9
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-18 21:44:22 +0000
Commit message:

 # I now use gslcblas by default to avoid any problems.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31180 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 8184173e68ae1d2f67bb6e02c2fff1b3204b1fda
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-18 17:56:25 +0000
Commit message:

 modified namespace - not to import the curv2filter, curv1filter and quadGate classes from flowCore for compatibility with previous versions of flowCore

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31160 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 7530ae99178f31f2189ad0e7ba8e65a28c06d691
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-18 17:29:04 +0000
Commit message:

 # I have now included a README file for instructions on how to include flowClust under Windows. I have also modified the Makevars.win.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31157 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: eb077198781715d05d34459f838a4417988480b0
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-18 09:11:28 +0000
Commit message:

 modified namespace - import only relevant classes and methods instead of the whole namespace from flowCore

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31147 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 7445b7976a137744d0927fd932e7843a7f85d8ee
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-17 22:48:27 +0000
Commit message:

 # I have changed the configure script to use (by default) the same BLAS libraries as R. 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31139 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 35558c161f79974874fbe8db6d648e72ca8ce8f7
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-16 17:53:33 +0000
Commit message:

 # I have bumped the version number to reflect the addition of the Makevars.win

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31110 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 1151e4d0677ea3e7731a256b4a1dd0ad1be6763f
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-15 12:50:10 +0000
Commit message:

 minor changes in flowClust.c (esp. up_data_z_weight) and BoxCox.C to increase computational efficiency;
compute output covariance matrix (sigma) in C

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@31091 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 331d469bc311f3c750a5a926d8428d2f9c713a15
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-10 21:11:37 +0000
Commit message:

 # I have added a Makevars.win

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@30992 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 06d3f7e95b35e41c474e682bd53769f86365a08c
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-09 23:03:27 +0000
Commit message:

 setMethods.R - put back default value in the replacement function

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@30972 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 50d33a261709bb97d5a261d5ed47259d417d8594
Author: k.lo <k.lo@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-09 05:34:40 +0000
Commit message:

 namespace - quotation marks removed
flowClust.c - comment out R_init_flowClust
setMethods.R - remove default value in the replacement function
all for testing only

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@30947 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: e117f19a679159ac08682f0c16c1f238d3bcaa88
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-08 19:40:35 +0000
Commit message:

 # I have bumped down the required version of GSL from 1.8 to 1.6.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@30927 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 404bd08c38ca1cf679bf62099863bbee862a6448
Author: raph@stat.ubc.ca <raph@stat.ubc.ca@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-07 23:26:14 +0000
Commit message:

 # Updated the configure script.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@30897 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: flowClust
Commit: 9c18006d06c58d7c3bdcc62c78e7db189ed25194
Author: m.carlson <m.carlson@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-03-28 20:10:14 +0000
Commit message:

 Adds the flowClust package to bioconductor.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust@30737 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: pathifier
Commit: cfb6bb45814228fcf80b93d8f980722adaabbdc4
Author: Assif Yitzhaky <Assif.Yitzhaky@weizmann.ac.il>
Date: 2018-07-12 19:23:52 +0300
Commit message:

 Update for new version of princurve
 
Package: dmrseq
Commit: 299627cd4c96b102bb64686fd69edbd6d3e2d370
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-07-12 11:55:00 -0400
Commit message:

 Update docs; version bump
 
Package: ClusterSignificance
Commit: 5861d584859becccbfc9dbc4d00af67ae7a43b4c
Author: jasonserviss <jason.serviss@ki.se>
Date: 2018-07-12 10:18:55 +0200
Commit message:

 version bump
 
Package: CellTrails
Commit: a46b0dbefd0b16bf5dd599381436c38c4bb44993
Author: dcellwanger <dc.ellwanger.dev@gmail.com>
Date: 2018-07-12 01:02:28 -0700
Commit message:

 Vignette update.
 
Package: CellTrails
Commit: 39531d493666b5676106291f5d64820428d272a1
Author: dcellwanger <dc.ellwanger.dev@gmail.com>
Date: 2018-07-12 00:59:15 -0700
Commit message:

 Updated vignette.
 
Package: IHWpaper
Commit: d111c7f670376c2964aaf735148bff6d7a4d5b08
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2018-07-11 18:49:09 -0700
Commit message:

 update arxiv reference
 
Package: IHWpaper
Commit: 45f948a61fe18462c0433e4d25983c13efb2a185
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2018-07-11 17:54:19 -0700
Commit message:

 remove release from travis again, bump version
 
Package: IHWpaper
Commit: 7ee860244f8c2c3774ecdc272613675ff694fedf
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2018-07-11 16:38:07 -0700
Commit message:

 turn off evaluation of composite figures from nmeth paper
 
Package: IHWpaper
Commit: 3aa528c326c7651e6d36a0983599073bd1cd2ed7
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2018-07-11 13:28:57 -0700
Commit message:

 check both against release and devel on travis
 
Package: IHWpaper
Commit: 1807c796754dbfa82b8c7bf5cfa2d7e520ba3d9f
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2018-07-11 01:56:26 -0700
Commit message:

 explicitly refer to utf8 encoding
 
Package: IHWpaper
Commit: af859d177d1742f143a69762f555cf3d37e4c255
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2018-07-10 23:53:27 -0700
Commit message:

 remove non-ascii characters from IHW-BY vignette
 
Package: IHWpaper
Commit: 8b6e835da53f6e5d47b3f22cf57be2f728219565
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2018-07-10 20:13:18 -0700
Commit message:

 add latex2exp
 
Package: IHWpaper
Commit: 4ed528a54922b879564d6a2ebd87583d0116fa7c
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2018-07-10 18:39:13 -0700
Commit message:

 add hQTL data example vignette
 
Package: RaggedExperiment
Commit: 201130edcfddbae3811cdf10e4929fae8dcabf03
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-11 17:59:57 -0400
Commit message:

 add assay schematic
 
Package: RaggedExperiment
Commit: 0f28374a50613ae63293e8f42c94866c1a59928b
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-11 14:29:44 -0400
Commit message:

 version bump
 
Package: RaggedExperiment
Commit: 9fdcfbf0779d3508af7ae0afc288f946758b60d6
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-11 14:29:31 -0400
Commit message:

 update examples according ss@110916
 
Package: RaggedExperiment
Commit: 96161709e569639b899b8d2de56d6e735006fe94
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-11 14:26:48 -0400
Commit message:

 update simplify arguments in coerce-functions
 
Package: KEGGlincs
Commit: 5ee6befb789744075bbf19f2c3716481c9f10af8
Author: Shana White <vandersm@mail.uc.edu>
Date: 2018-07-11 11:53:46 -0400
Commit message:

 Try to correct Version number again
 
Package: KEGGlincs
Commit: b9f9b7bac0a9afe5e805f9ef76db2200a8f347ff
Author: Shana White <vandersm@mail.uc.edu>
Date: 2018-07-11 11:47:05 -0400
Commit message:

 Fix merge conflict and correct Version number
 
Package: KEGGlincs
Commit: 7b7ab156b049f0fa59a066471f21d6719379119b
Author: Shana White <vandersm@mail.uc.edu>
Date: 2018-07-11 11:41:51 -0400
Commit message:

 mend merge
 
Package: KEGGlincs
Commit: a5a1c2f08b6764b5fa26d1b35d433b2dde3c68b8
Author: Shana White <vandersm@mail.uc.edu>
Date: 2018-07-11 11:07:12 -0400
Commit message:

 delete update_remotes.sh
 
Package: KEGGlincs
Commit: fc6f3d684b65dd4b5a49573acc7288e3ef8f746e
Author: Shana White <vandersm@mail.uc.edu>
Date: 2018-07-10 16:12:46 -0400
Commit message:

 add function grab_KO_data and data to run it
 
Package: KEGGlincs
Commit: 19817d2d198479d9cb69836c9cf7fc18f1b8f997
Author: Shana White <vandersm@mail.uc.edu>
Date: 2018-07-10 11:58:15 -0400
Commit message:

 Bump version number to initiate bug fix
 
Package: KEGGlincs
Commit: 6103507ba3f65a41513e0017ab0a33c9d429eeb7
Author: Shana White <vandersm@mail.uc.edu>
Date: 2018-07-05 13:18:40 -0400
Commit message:

 Add GET step for getting raw tables
 
Package: Onassis
Commit: b3f675a07537ec9939a27060f4caed9e7ac56f80
Author: egaleota <eugenia.galeota@ieo.eu>
Date: 2018-07-11 17:39:01 +0200
Commit message:

 bug fix: updated DESCRIPTION
 
Package: Onassis
Commit: 8184e377150c452c18f405ae6b6484b3b18f5f0a
Author: egaleota <eugenia.galeota@ieo.eu>
Date: 2018-07-11 16:57:39 +0200
Commit message:

 bug fix: The vignette has been changes in order to include SessionInfo information and solve some bugs when using GEOmetadb and SRAdb. The function of GEO_Handler have been changed to call dbConnect from the namespace of GEOmetadb
 
Package: compEpiTools
Commit: fd3ab8a3a629e8ac37f2612a6bcd708c624b0514
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2018-07-11 12:16:17 +0100
Commit message:

 getPromoterClass bug
 
Package: ClusterSignificance
Commit: 9826ba0fab58eccf14d7e15d9257b7686bdb65fe
Author: jasonserviss <jason.serviss@ki.se>
Date: 2018-07-11 11:51:57 +0200
Commit message:

 Merge branch 'master' of https://github.com/jasonserviss/ClusterSignificance
 
Package: ClusterSignificance
Commit: f26104cfce4415a4641fd62ed1ff927a89438901
Author: jasonserviss <jason.serviss@ki.se>
Date: 2018-07-11 11:51:53 +0200
Commit message:

 fixing vignette spelling mistake
 
Package: ClusterSignificance
Commit: c44ad2630bfde99d04bc17c03b780253e4678b9e
Author: Jason Serviss <jason.serviss@ki.se>
Date: 2018-07-11 11:36:39 +0200
Commit message:

 Merge pull request #1 from rcannood/master

Update ClusterSignificance 
Package: ClusterSignificance
Commit: 0e61ce7f349b3faac6474ecc1cc6ae0533d83e07
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-10 22:04:48 +0200
Commit message:

 add .Rbuildignore file to fix NOTES
 
Package: ClusterSignificance
Commit: b18bbf2963cd6e67aaa10b3c36c1ec04c12272f2
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-10 20:35:41 +0200
Commit message:

 temporarily add dynverse/princurve@devel for travis
 
Package: ClusterSignificance
Commit: e9ac1f5124d312e47bc267088d226df2f2e0a7f2
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-10 20:34:56 +0200
Commit message:

 ClusterSignificance will only work with princurve 2.0.5
 
Package: ClusterSignificance
Commit: dbb7a5198a7d3a10b0c1852647e3618f942ba275
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-10 20:05:03 +0200
Commit message:

 update ClusterSignificance for princurve 2.0.4
 
Package: ReadqPCR
Commit: 6b8c71b4276f7e594e86ff0ddf5a15ce17b03be3
Author: Jim <jimrperkins@gmail.com>
Date: 2018-07-11 11:15:40 +0200
Commit message:

 Try to remove windows build errors for ExpressionSet-class
 
Package: limma
Commit: bd300a86d3412132cc50d35439be750f0ead8e33
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2018-07-11 19:02:46 +1000
Commit message:

 11 July 2018: limma 3.37.3

- goana.Rd now explains more explicitly that p-values are unadjusted
  for multiple testing.

- arrayWeights.Rd now mentions minimum dimensions for expression
  object.
 
Package: apeglm
Commit: 9332eedfe8e29c7ed6313103396739b738577829
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-07-11 10:45:03 +0200
Commit message:

 typo
 
Package: chroGPS
Commit: 6c6c35150b5657d129ed98050c667f3e0ceab0fe
Author: oreina <oreina@biocf06.irb.pcb.ub.es>
Date: 2018-07-11 10:08:11 +0200
Commit message:

 Fix bug using smartbind with rankFactorsbyProfile result
 
Package: apeglm
Commit: 7473f7e4608d630556d10ad73eae78e5a48d078b
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-07-11 10:03:31 +0200
Commit message:

 add zinb link to the vignette
 
Package: tximport
Commit: 9a3e380f07ec6c5addcc02ddfef47a2ff1359dec
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-07-11 09:54:06 +0200
Commit message:

 update vignette to mention 3 prime
 
Package: GoogleGenomics
Commit: 70f51a223accbadea25f0d406f6c9675e6e113de
Author: lshep <shepherl@gmail.com>
Date: 2018-07-11 03:39:37 -0400
Commit message:

 User requested deprecation

  - https://support.bioconductor.org/p/110861/
 
Package: GoogleGenomics
Commit: 1c0bf673b8e5608d541c56c8040f9cb9ab292475
Author: lshep <shepherl@gmail.com>
Date: 2018-05-15 08:26:48 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/GoogleGenomics
 
Package: GoogleGenomics
Commit: 8f024761d4f8942e2d2c20e148c21ab8142d8a8a
Author: lshep <shepherl@gmail.com>
Date: 2017-10-30 16:32:53 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/GoogleGenomics
 
Package: GoogleGenomics
Commit: 2648eb26f25388d4e16e239029e9107577592b67
Author: lshep <shepherl@gmail.com>
Date: 2017-09-20 07:42:22 -0400
Commit message:

 Merge branch 'master' of github.com:Bioconductor/GoogleGenomics
 
Package: GoogleGenomics
Commit: ff3b8e9c7b92a92cebf5fdae9a16935332ad67ac
Author: lshep <shepherl@gmail.com>
Date: 2017-09-01 09:02:20 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: GoogleGenomics
Commit: 5c61e5dcd236bf10fd89f2a2b3d68faa99217435
Author: lshep <shepherl@gmail.com>
Date: 2017-08-29 12:10:35 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: mygene
Commit: edd254cfbb2120f557ffadcb9cbb2461d658f4c9
Author: Cyrus Afrasiabi <cyrus.afrasiabi@gmail.com>
Date: 2018-06-21 16:43:35 -0700
Commit message:

 Uncommenting zero-length check here...
 
Package: mygene
Commit: 2bca13ef1e07d4ff90703a716a0c5564d7fbe7df
Author: Chunlei Wu <anewgene@yahoo.com>
Date: 2018-06-14 16:14:35 -0700
Commit message:

 more bugfix instructions
 
Package: ClassifyR
Commit: fb9d35706b9061008e0ddb97be0c02b98b7ef6ab
Author: Dario Strbenac <dstr7320@uni.sydney.edu.au>
Date: 2018-07-11 13:00:06 +1000
Commit message:

 - Sample information bar of samplesMetricMap can now display numeric data.
 
Package: Rsubread
Commit: 8a7ca297247589da2695071bdd70dae299be0c6e
Author: Wei Shi <shi@wehi.edu.au>
Date: 2018-07-11 12:39:34 +1000
Commit message:

 Fix a typo in atgcContent.Rd file.
 
Package: dmrseq
Commit: 1441031df918e297a0a0155d13b1772f9d653007
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-07-10 19:45:56 -0400
Commit message:

 Don't smooth lines unless at least 10 cpgs
 
Package: dmrseq
Commit: f34e3de5f7a550c24aaf663788a6507deb6d9ac4
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2018-07-10 17:40:15 -0400
Commit message:

 Add option to skip plotting lines
 
Package: TCGAutils
Commit: 49478043f465ebac62eef961b5e02bef1b59622f
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-10 18:42:26 -0400
Commit message:

 rename removeOriginals to keep and set to FALSE
 
Package: TCGAutils
Commit: 6369981eff6ef920a5eff356203b7b2ae7a184ea
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-10 18:39:51 -0400
Commit message:

 rename qReduceTCGA to qreduceTCGA similar to qreduceAssay
 
Package: slingshot
Commit: 6cab2eef52ca62893ca4354ff89763915c95304f
Author: Kelly Street <kstreet@berkeley.edu>
Date: 2018-07-10 14:44:16 -0700
Commit message:

 version bump to 0.99.12
 
Package: slingshot
Commit: 11b61072e19a5a513d23d12522fcbac62bcec864
Author: Kelly Street <kstreet@berkeley.edu>
Date: 2018-07-10 14:29:28 -0700
Commit message:

 added missing comma to .shrink_to_avg(), formatting changes to getCurves().
 
Package: TCGAutils
Commit: 69579a645f5c5d8b6d0f6cd72ca23349b5bb2662
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-10 17:32:18 -0400
Commit message:

 bug fix: remove :: and pkgName from call in pkg dep error
 
Package: TCGAutils
Commit: 39b09272c5248d129dca3191e01fa95eab9e0bf5
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-10 16:37:57 -0400
Commit message:

 version bump
 
Package: TCGAutils
Commit: c493c27149f4bfddd0b38b8dc608b6bc44cdfc16
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-09 15:34:52 -0400
Commit message:

 indentations
 
Package: TCGAutils
Commit: 7d496405237f18a2e6c2734ff1651520c05e2e6c
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-06 16:41:04 -0400
Commit message:

 bug fix: use replacement function, fix example
 
Package: TCGAutils
Commit: f93937342f6b84b312b14ac090ec59870bbdd9c1
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-07-05 20:04:34 -0400
Commit message:

 incorporate changes from curatedTCGAData branch @lwaldron
 
Package: topdownr
Commit: c6193038f8bcadd3a30b7fb887e185f03bb69b30
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-07-06 14:03:21 +0200
Commit message:

 Don't use rownames while combining elementMetadata
 
Package: topdownr
Commit: 96efdf429bde9e726ffdcd5d6e3859e893d4e018
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-07-06 14:01:15 +0200
Commit message:

 Fix as(tds, "MSnSet") unit test
 
Package: topdownr
Commit: c603256b97c2736a8e46580d093a0b3cc9544c97
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-06-03 21:29:54 +0200
Commit message:

 Fix `FragmentViews` start/end/width/labels for internal fragments
 
Package: topdownr
Commit: 5b0a02f72a3a7880224a260c98577f5b6bed03b4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-06-03 20:37:20 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: topdownr
Commit: c6e8dfdd532da4aa47bd65ffb1b5ca5b9a9c6772
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-06-03 20:32:41 +0200
Commit message:

 Adapt to MSnbase 2.7.2 with internal fragments; see lgatto/MSnbase#82
 
Package: topdownr
Commit: d0f176afe6ee9fe51a6088abc4711e9d4b40fa24
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-02-24 23:03:29 +0100
Commit message:

 Bump github devel version
 
Package: SDAMS
Commit: 115abf424a55e4601919885a90090d17c0f762d3
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 13:46:30 -0400
Commit message:

 bug fix: additional arguments passed to SDA
 
Package: SDAMS
Commit: 0194e134128be8f9741a15714513bec2c4eb6077
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 13:00:34 -0400
Commit message:

 fix conflicts in version change
 
Package: SDAMS
Commit: 291a7ec5e8e5902c0175b06686d80dc7db1aadaa
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 11:01:08 -0400
Commit message:

 additional arguments passed to qvalue
 
Package: SDAMS
Commit: 7ccfe560fa76bd1b305c8805f9f6080514ae9607
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 10:58:34 -0400
Commit message:

 verison bumping
 
Package: SDAMS
Commit: a5c0c85bcd6129e6a5e3d8ea709cbb81fe4b61c1
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 10:57:57 -0400
Commit message:

 verison bumping
 
Package: SDAMS
Commit: feb1f44621d09953863d9c08517bfac11dc11764
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 10:55:49 -0400
Commit message:

 allow adjustment of covariates
 
Package: SDAMS
Commit: c3fcd402d3516bcd7fc00ed591a9e796ca6268e7
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 10:54:30 -0400
Commit message:

 minor bug fix
 
Package: SDAMS
Commit: f885bd4f98d810b396e3d2bbbb821d6234a12102
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 10:51:46 -0400
Commit message:

 bug fix ignore
 
Package: SDAMS
Commit: 55d571dff16c76291af9bde2be792a21cb9f0f6d
Author: Stat-Li <36005627+Stat-Li@users.noreply.github.com>
Date: 2018-07-10 10:37:23 -0400
Commit message:

 Delete .DS_Store 
Package: SDAMS
Commit: 2f12681b9835d5ca6b2fd971d822dceaf49f3181
Author: Yuntong Li <li@li.local>
Date: 2018-07-10 10:17:08 -0400
Commit message:

 bug fix SDA
 
Package: SDAMS
Commit: b368479657624871ff5c9b0b55d767c8645dd47e
Author: Yuntong Li <li@li.local>
Date: 2018-07-09 15:15:35 -0400
Commit message:

 bug fix
 
Package: Sconify
Commit: dd53634236f7ff7953cc049e2c42ac5fde12ebcd
Author: tjburns08 <burns.tyler@gmail.com>
Date: 2018-07-10 18:14:42 +0200
Commit message:

 Fixed conflicts in version change
 
Package: Sconify
Commit: 042aac2e109d7f3df1960f1627984db828ca977e
Author: tjburns08 <burns.tyler@gmail.com>
Date: 2018-06-27 14:03:04 +0200
Commit message:

 Description update following the BioC rules.
 
Package: Sconify
Commit: 7022cad5ce562576576b87da1a6c4ebc0e0fe255
Author: tjburns08 <burns.tyler@gmail.com>
Date: 2018-06-24 11:25:00 +0200
Commit message:

 Merge branch 'master' of https://github.com/tjburns08/Sconify
 
Package: Sconify
Commit: 7a75f1e15403008f6ba6d4d1dc0c6e2ccb01aa54
Author: tjburns08 <burns.tyler@gmail.com>
Date: 2018-06-24 11:23:36 +0200
Commit message:

 Updated MakeHist for ggplot2 to be compatible with the June 25 release of the newest version of ggplot2.
 
Package: Sconify
Commit: 942d00ed2fddd3177a43fe53ee866f2d16f1f903
Author: Tyler Burns <burns.tyler@gmail.com>
Date: 2018-04-22 20:12:04 +0200
Commit message:

 Update README.md

Clarified what Sconify's output can give you, and added a special section for people with little programming experience. 
Package: Sconify
Commit: b56721d9b034e56bc79e5e858927cfa9567dbdec
Author: Tyler Burns <burns.tyler@gmail.com>
Date: 2018-04-22 20:02:59 +0200
Commit message:

 Add files via upload

Modified the Sconify proof of concept picture, so it only shows the t-SNE maps, and not the Wanderlust ribbon diagrams. 
Package: Sconify
Commit: 96ea8447863c038ff9bd62cfa1e082da64790ebf
Author: Tyler Burns <burns.tyler@gmail.com>
Date: 2018-04-22 20:02:11 +0200
Commit message:

 Delete sconify_proof_of_concept.png

Deleted this file in order to replace it with one that is more focus (doesn't have panel B). 
Package: Sconify
Commit: cc01f4113abe12f0341008ef7ec93fc770b0df93
Author: Tyler Burns <burns.tyler@gmail.com>
Date: 2018-04-22 20:00:57 +0200
Commit message:

 Update README.md

Added a visual explanations section. 
Package: Sconify
Commit: cc7a17067542c19736aa1419384a6363196ef7a0
Author: Tyler Burns <burns.tyler@gmail.com>
Date: 2018-04-22 18:24:05 +0200
Commit message:

 Add files via upload

Added some images for the Sconify readme file. They will sit in the Vignettes section. 
Package: Sconify
Commit: d7f6d753a9571a9476392b8f4cdc659a1fcdf194
Author: Tyler Burns <burns.tyler@gmail.com>
Date: 2018-04-22 18:11:20 +0200
Commit message:

 Create README.md

Created the README file for the Sconify package directly within Github. This will be updated soon to include the BioC link. 
Package: KEGGlincs
Commit: 289fabb60e3a61015b62ed3b65e051b7145bc9cc
Author: Shana White <vandersm@mail.uc.edu>
Date: 2018-07-10 11:37:15 -0400
Commit message:

 bump version number
 
Package: BiFET
Commit: 6b1633ed6d2c3ce823b3e766d895f9684eca7658
Author: Ahrim Youn <youna@mlg-jgm164.jax.org>
Date: 2018-07-10 11:12:53 -0400
Commit message:

 change versin number
 
Package: simpleSingleCell
Commit: 6d6fe3cb9b3b45defab45cfa20a07cdcf6bf9156
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-10 11:57:40 +0100
Commit message:

 Removed recommendation for parallel analysis.
 
Package: slingshot
Commit: 32c61d5077d7ba90ba727a5c8575dd88ae5c252d
Author: Kelly Street <kstreet@berkeley.edu>
Date: 2018-07-09 21:29:28 -0700
Commit message:

 bumped version number to 0.99.11 (incorporating recent updates from Robrecht for compatibility with princurve >= 2.0.4)
 
Package: slingshot
Commit: 2cefae11085dfedbfb8a6573f0d835fd63d7a4e2
Author: Kelly Street <kstreet@berkeley.edu>
Date: 2018-07-09 14:57:07 -0700
Commit message:

 Merge pull request #19 from dynverse/develop

 ord parameter from project_to_curve was removed from princurve 2.0.4 
Package: slingshot
Commit: c710e6ed88cf2d1f8ffb4f7b00b854f864b34d5c
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-09 23:30:21 +0200
Commit message:

 change LHS division into RHS multiplication to avoid division by zero
 
Package: slingshot
Commit: 2dad6906b0aea40477badd604f0bb8aec418b013
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-09 23:29:53 +0200
Commit message:

 cast object to matrix before alling project_to_curve
 
Package: slingshot
Commit: f82501fd29a7e62eca181e85988a518543b0c28a
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-09 23:29:13 +0200
Commit message:

 put comma in the right place
 
Package: slingshot
Commit: 35ac2658a752d952d76da56648bc61699af4b64c
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-09 22:56:13 +0200
Commit message:

 ord parameter from project_to_curve was removed from princurve 2.0.4
 
Package: slingshot
Commit: 65423af65c24ccf9f4cb00d6efb8134d398770f3
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2018-07-09 22:53:32 +0200
Commit message:

 Merge remote-tracking branch 'upstream/develop' into develop
 
Package: slingshot
Commit: 1bc5160fc03d1f72a90b20ceefcc35fce106bfec
Author: Robrecht Cannoodt <brechtus@gmail.com>
Date: 2018-06-18 16:08:00 +0200
Commit message:

 Merge remote-tracking branch 'upstream/develop' into develop
 
Package: slingshot
Commit: f53eec384ade00c3f24360e49a43bf6b3c913e8f
Author: Robrecht Cannoodt <brechtus@gmail.com>
Date: 2018-06-06 14:15:20 +0200
Commit message:

 add DS_Store to gitignore
 
Package: rexposome
Commit: 4367648726f94ca3ed035174c8d32b929a89992b
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2018-07-09 23:09:49 -0400
Commit message:

 Bump version

 
Package: rexposome
Commit: 130d37cc8381705eca52579763ad225544b110ae
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2018-07-09 22:42:01 -0400
Commit message:

 Merge Release 3.6

 
Package: rexposome
Commit: 496cca063dad2507c82f27da33e5e3454d289cac
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2018-06-16 16:34:58 -0400
Commit message:

 Improves examples for correlation.
 
Package: rexposome
Commit: 79bed810ba645f0a5758b8276563fb914478481e
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2018-06-02 22:10:55 -0400
Commit message:

 Updated correlation calcuclation between continuous and categorical.
 
Package: rexposome
Commit: e49d28f454a5892e019d7190781fc3b62bf8c7de
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2018-06-02 22:02:32 -0400
Commit message:

 Added extra warnings and improved name method for ExWAS.
 
Package: rexposome
Commit: e05cf5aee8570a10ed87f831b791a196e9cce90c
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2018-05-15 07:52:48 -0400
Commit message:

 Update IQR (2) standardization

 
Package: rexposome
Commit: 7f54360bf2b10d786dd06073baef2a1e22d09ad4
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2018-05-12 11:22:07 -0400
Commit message:

 Downgrade requirement for R

 
Package: rexposome
Commit: af0841fba6c622491e9c7f2e7c327b2d29b763fd
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2018-05-12 11:09:31 -0400
Commit message:

 Updated standardize for exposome

Added "iqr2" standardization method. Updated version of the project according to biocondcutor. 
Package: rexposome
Commit: e81bc7edcf972dc27bfe087f4b310fe6884f0b03
Author: carleshf <carles.hernandez@gmail.com>
Date: 2018-01-11 14:17:11 +0100
Commit message:

 ..
 
Package: rexposome
Commit: a7816bce5d88f5d97468e6a0f8977833e6bef9b2
Author: carleshf <carles.hernandez@gmail.com>
Date: 2018-01-09 23:12:55 +0100
Commit message:

 Improved 'plotEffect' to properly show current exposure's names.
 
Package: rexposome
Commit: c8b9c978673d14a62b9c02a5a170fc902e36cccc
Author: carleshf <carles.hernandez@gmail.com>
Date: 2018-01-09 23:09:39 +0100
Commit message:

 Removed psygenet2r dependence. Updated 'plotExwas' for 'ExposomeSet' to properly show current exposure's names. Now it also indicates the exposure effect.
 
Package: rexposome
Commit: 1c7500beb0b4aad894435b172c99f8f39c05e5e2
Author: carleshf <carles.hernandez@gmail.com>
Date: 2018-01-09 22:41:08 +0100
Commit message:

 Improved 'exwas' for 'ExposomeSet'. Now returns a row per categorical comaprison.
 
Package: rexposome
Commit: e9262aa4cfe5582aefe1b3d341ccf953ca1c86bf
Author: Carles Hernandez-Ferrer <kuragari.ch@gmail.com>
Date: 2017-11-24 12:04:19 +0100
Commit message:

 Merge branch 'master' of https://github.com/isglobal-brge/rexposome
 

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