Removed intercept for new design= behaviour in findMarkers().
 

 Bumped version number, date.
 

 Preserve order of groups in pairs= for combineMarkers output.
 

 no docs on bioc
 

 update news
 

 fix conflicts
 

 update docs
 

 add new vig
 

 evaluated CP chunk
 

 vignette update
 

 2.0 update
 

 new datasets added
 

 missing data treatment added
 

 version bump
 

 Updated comments for overlapExprs.
 

 Fixed conflicts in version change
 

 change descr
 

 fixed url
 

 Further clean-ups to NEWS.
 

 Documentation cleanups, mostly for 'seealso' sections.
 

 Bumped version number, date.
 

 Updated combineMarkers docs.
 

 Renamed 'effect' to 'overlap' for Wilcoxon tests.
 

 Stripped back overlapExprs documentation and tests.
 

 Removed SnowParam tests, as these are slow.
 

 Switched to approximate Wilcoxon for scalability.
 

 Cleaned up pairwiseTTests docs.
 

 Migrated testing utilities out of pairwiseTTests.
 

 Documented pairwiseWilcox.
 

 Added dedicated pairwise Wilcoxon testing function.
 

 - Folding cross-validation schemes now use stratified random sampling to allocate samples to folds, so that every fold contains an almost identical proportion of classes to the entire data set.
 

 Updated manual entries for getMappedEntrezIDs, gometh and gsameth to explain new optional argument for passing in the array annotation.
 

 added UTF-8 encoding for roxygen2 and changed example for RunCRE_HSAStringDB
 

 reorder phenotypes to match cov.mat in null model

Since the covariance matrix may be block diagonal, we should not
reorder it. Instead, reorder the data frame to match cov.mat.
fitNullModel for AnnotatedDataFrame now calls the data.frame
method, and createDesignMatrix is a function, not a method, that
operates on a data.frame only. This makes it easier to deal with
all sample.id operations in one place. The sample.id argument no
longer specifies the order of samples, only which ones to include.
 

 corrected vignette to proper target population to be consistent with plot example
 

 use DelayedArray when returning methylation
 

 introduce new data and code for actual MSIsensor scores provided by M Bailey
 

 merge
 

 Some important piece not committed due to merging conflict
 

 Adjust help
 

 Version bump
 

 update README
 

 Update README
 

 Added BPPARAM option to findMarkers.
 

 More conservative termination in cyclone() to overcome numerical imprecision.
 

 Added option for coefficient return for internal LM fitter.
 

 Added support for parallelization in pairwiseTTests.
 

 Merge refactor branch into master

 

 Tweak and update unit tests

 

 Tweak collapseBSseq()

 

 Add TODO

 

 Rename findCytosines as findLoci and document

 

 Regenerate NAMESPACE

 

 Modify BSmooth()

- Automatic selection of appropriate BACKEND and better control over HDF5 options (when applicable)
- Tweak unit tests
 

 Remove deprecated arguments

Kasper wants these removed without deprecation/defunct cycle 

 Explicitly gunzip to tempfile()

Avoids error 'gzip: stdout: No space left on device' (https://github.com/Rdatatable/data.table/issues/717#issuecomment-226038307) 

 colGrid() and rowGrid() moved to DelayedMatrixStats as of v1.3.4

 

 Don't import stats::qnorm

Need to use the S4 generic `qrnom()` from DelayedArray. It's default method is `stats::qrnom()`, so it does the right thing. 

 extract_block() was replaced with read_block() in DelayedArray 0.7.15

 

 Update TODOs

 

 Add strand argument to findCytosines
 

 Passing R CMD check locally without errors

- There are still warnings and notes
- And still more stuff to re-factor 

 Quieten R CMD check

 

 Fix bug in BSmooth()

Accidentally deleted some still-required code in 9392512c7b4229e5a58258544d454d3edf1e58ba 

 Update TODOs

 

 Add some TODOs and NOTEs
 

 Add TODOs

 

 Update read.bismark() documentation
 

 Fix bug in `combine()` that merged adjacent loci

- Cannot use `union()` as that calls `reduce()` with `min.gapwidth = 1L`, which leads to adjacent (unstranded) loci being combined into a locus with width == 2.
- Re-ran `inst/scripts/get_BS.chr22.R` to update the included data, `BS.chr22` 

 Add `BACKEND` and `...` arguments to `BSmooth()`

- The user can now set the name of the HDF5 file via the `...` arguments
- Use a single IPC lock when writing `coef` and `se.coef` to RealizationSink. Previously, process A could write to `coef` and process B could write to `se.coef` simultaneously, but this can create a race condition if, for example, both `coef` and `se.coef` are in the same HDF5 file.
This change means that, in this example, process 'A' must wait for process 'B' to finish before being able to begin writing `coef` to the RealizationSink.
- Update `BSmooth()` documentation 

 Update 'Collate' in DESCRIPTION

 

 Use a single IPC lock when writing M and Cov to RealizationSink

Previously, process A could write to 'M' and process B could write to 'Cov' simultaneously, but this can create a race condition if, for example, both 'M' and 'Cov' are in the same HDF5 file.
This change means that, in this example, process 'A' must wait for process 'B' to finish before being able to begin writing 'M' to the RealizationSink. 

 Add TODOs

 

 Rename 'gr' argument in read.bismark() as 'loci'

 

 Add FWIRanges and FWGRanges, use in read.bismark()

 

 Split out R/read.bismark.R

Slightly formalise intermediate objects lociDT and BSseqDT.
Split these out into their own files.
Refine construction of 'gr' from Bismark files. 

 Add TODOs 

 Work in progress: refactoring bsseq

- BSseq objects can once again use ordinary matrix objects as assays.
- Reimplement `BSmooth()` more-or-less from scratch:
  - Switch from 'parallel' to 'BiocParallel' for parallelization. This brings some notable improvements:
    - Smoothed results can now be written directly to an on-disk realization backend by the worker. This dramatically reduces memory usage compared to previous versions of 'bsseq' that required all results be retained in-memory.
    - Parallelization is now supported on Windows through the use of a 'SnowParam' object as the value of `BPPARAM`.
    - Improved error handling makes it possible to gracefully resume `BSmooth()` jobs that encountered errors by re-doing only the necessary tasks.
    - Detailed and extensive job logging facilities.
  - Fix bug in `BSmooth()` with the `maxGap` parameter.
- Re-factor BSseq() constructor and add fast, internal .BSseq() constructor.
- Re-factor collapseBSseq() and combine(). Should be much more performant.
- Use beachmat to implement fast validity checking of 'M' and 'Cov' matrices.
- Resave BS.chr22 (supplied data) using integer for storage mode of assays to reduce size.
- Switch from RUnit to testthat. testthat has better integration with code coverage tools that help when refactoring. 

 Merge

 

 s
 

 d
 

 sepira
 

 Merge pull request #10 from YC3/18sept

18sept 

 Add files via upload 

 LICENSE bump 

 Update DMR.plot.R

genome Ideogram change 

 DMRcate_1.12.1_vignettefix
 

 Update DMRcate-internal.Rd 

 Main function, dmrcate(), re-organised and sped up.
 

 DMRcate_1.10.9, ty to Jenny Drnevich for bugspot
 

 Faster version with no 'apply' calls.
 

 DMRcate_1.10.7
 

 DMRcate_1.10.5
 

 DMRcate_1.10.4, ty to Xavier Pastor for patch
 

 Messages in cpg.annotate()
 

 DMRcate_1.10.2. Thank you to Yuan Tian and Eugene Wang for bugspotting
 

 1.10.1 DESCRIPTION 

 DMRcate_1.8.7
 

 DMRcate_1.8.5
 

 DMRcate_1.6.53, correct environment errors
 

 DMRcate_1.6.52, ty to Jesper Maag for finding a bug in DMR.plot()
 

 DMRcate_1.6.5, ty to Eric Smith for bug report
 

 namespace update
 

 DMRcate_1.6.2
 

 dummy removal
 

 DMRcate_1.6.1 (release)
 

 Delete extraneous files
 

 DMRcate_1.7.1 again
 

 DMRcate_1.5.61
 

 add devtools, git2r to install directions 

 Add explicit installation directions 

 initial checkin of patches to mainstream DMRcate
 

 Commit made by the Bioconductor Git-SVN bridge.

Consists of 1 commit.

Commit information:

SVN Revision number: 102591
Commit message:
Bump versions prior to creating 3.1 branch.

Committed by d.tenenbaum
Committed at: 2015-04-16T19:42:01.524374Z
 

 DMRcate_1.3.1 bump again
 

 DMRcate_1.3.1 again
 

 DMRcate_1.3.1
 

 Commit made by the Bioconductor Git-SVN bridge.

Consists of 1 commit.

Commit information:

SVN Revision number: 95439
Commit message:
Bump package versions prior to creating the 3.0 branch.

Committed by d.tenenbaum
Committed at: 2014-10-13T21:38:33.867451Z
 

 DMRcate_1.1.5
 

 DMRcate_1.1.3

<- becomes = in data.frame creation
 

 DMRcate version 1.1.1

Removed sentence in vignette relating to development version
 

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

Commit information:

    Commit id: 61e6a247ce01002959a3a373b10ea07c59254547
    Commit message:
    DMRcate_0.99.11

    - Beta fold-change incorporated into annotate()
    - maxbetafc added to returned results
    - grey lines added to DMR.plot at beta = {0, 0.5, 1}
    - Formula slightly changed in vignette
    Committed by timpeters82 
    Commit date: 2014-03-26T18:33:22+11:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87929 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    

      Package: DMRcate

      Commit: 61e6a247ce01002959a3a373b10ea07c59254547

      Author:  timpeters82 <Tim.Peters@csiro.au> 

      Date: 2014-03-26 18:33:15 +1100

      Commit message:


	  
		
 DMRcate_0.99.11

- Beta fold-change incorporated into annotate()
- maxbetafc added to returned results
- grey lines added to DMR.plot at beta = {0, 0.5, 1}
- Formula slightly changed in vignette
 
    
  
    

      Package: DMRcate

      Commit: a6194e68fdeff98a8202a1610a644b958de4a30a

      Author:  t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2014-03-24 23:38:03 +0000

      Commit message:


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

Commit information:

    Commit id: f3f03c12bde0606c57d304f566486d3c9b67c1b6
    Commit message:
    DMRcate_0.99.10

    Updated vignette to reflect DMRcate still being in R-devel
    Committed by timpeters82 
    Commit date: 2014-03-25T10:37:46+11:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87821 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    

      Package: DMRcate

      Commit: f3f03c12bde0606c57d304f566486d3c9b67c1b6

      Author:  timpeters82 <Tim.Peters@csiro.au> 

      Date: 2014-03-25 10:37:39 +1100

      Commit message:


	  
		
 DMRcate_0.99.10

Updated vignette to reflect DMRcate still being in R-devel
 
    
  
    

      Package: DMRcate

      Commit: 86f7b928b94521c45dcde855078f3c5f641bdafe

      Author:  t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2014-03-21 06:26:40 +0000

      Commit message:


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

Commit information:

    Commit id: 532bded6d65aac5f3cc0f58895582c5fba70ed6c
    Commit message:
    DMRcate_0.99.9

    Clarification over preference of M-values in vignette, plus one instance
    of formatting in man page
    Committed by timpeters82 
    Commit date: 2014-03-21T17:26:26+11:00

    Commit id: e2d6b32524217e1b7d53775d74d74e2569b1a981
    Commit message:
    Bumping DESCRIPTION

    bump to 0.99.9 in DESCRIPTION
    Committed by timpeters82 
    Commit date: 2014-03-21T17:26:26+11:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87687 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    

      Package: DMRcate

      Commit: e2d6b32524217e1b7d53775d74d74e2569b1a981

      Author:  timpeters82 <Tim.Peters@csiro.au> 

      Date: 2014-03-21 17:26:17 +1100

      Commit message:


	  
		
 Bumping DESCRIPTION

bump to 0.99.9 in DESCRIPTION
 
    
  
    

      Package: DMRcate

      Commit: 532bded6d65aac5f3cc0f58895582c5fba70ed6c

      Author:  timpeters82 <Tim.Peters@csiro.au> 

      Date: 2014-03-21 17:24:34 +1100

      Commit message:


	  
		
 DMRcate_0.99.9

Clarification over preference of M-values in vignette, plus one instance
of formatting in man page
 
    
  
    

      Package: DMRcate

      Commit: dd0281cebcaf2938430838e936182274d777184e

      Author:  t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2014-03-19 00:26:43 +0000

      Commit message:


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

Commit information:

    Commit id: 5f8f365fba5c85d38d27e2fd63aa373da6c8f789
    Commit message:
    DMRcate_0.99.8

    Minor changes in formatting surrounding \textit{p}-value
    Committed by timpeters82 
    Commit date: 2014-03-19T11:26:22+11:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87590 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    

      Package: DMRcate

      Commit: 5f8f365fba5c85d38d27e2fd63aa373da6c8f789

      Author:  timpeters82 <Tim.Peters@csiro.au> 

      Date: 2014-03-19 11:26:14 +1100

      Commit message:


	  
		
 DMRcate_0.99.8

Minor changes in formatting surrounding \textit{p}-value
 
    
  
    

      Package: DMRcate

      Commit: aa78d72febd1be650d301741f28935c37806f28f

      Author:  t.peters <t.peters@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2014-03-17 06:23:43 +0000

      Commit message:


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

Commit information:

    Commit id: 3437a6f80a2c0db27b9ebdbb6590f12aac339987
    Commit message:
    DMRcate_0.99.7

    Changed bad formatting and obsolete object names in the man pages.
    Committed by timpeters82 
    Commit date: 2014-03-17T17:23:22+11:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87496 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    

      Package: DMRcate

      Commit: 3437a6f80a2c0db27b9ebdbb6590f12aac339987

      Author:  timpeters82 <Tim.Peters@csiro.au> 

      Date: 2014-03-17 17:23:22 +1100

      Commit message:


	  
		
 DMRcate_0.99.7

Changed bad formatting and obsolete object names in the man pages.
 
    
  
    

      Package: DMRcate

      Commit: 59bc62ef514f1b5de78dd2cf03cc664b86b2e21a

      Author:  mtmorgan@fhcrc.org <mtmorgan@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2014-03-08 06:50:46 +0000

      Commit message:


	  
		
 add DMRcate to repository and manifest


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate@87230 bc3139a8-67e5-0310-9ffc-ced21a209358
 
    
  
    

      Package: powerTCR

      Commit: 7067a0a109cfec09974975275bc4e1d917662bf8

      Author:  Hillary Koch <hillary.koch01@gmail.com> 

      Date: 2018-09-17 00:12:47 -0400

      Commit message:


	  
		
 removed excess in vignettes
 
    
  
    

      Package: FGNet

      Commit: 511e6e7065f9f427d2637050864b563c7dbef04b

      Author:  Sara Aibar <sara.aibar@kuleuven.vib.be> 

      Date: 2018-09-16 23:15:06 +0200

      Commit message:


	  
		
 v 3.15: Deprecate plotKegg()
 
    
  
    

      Package: QuaternaryProd

      Commit: 095ca0623e08bfbc3baa40e652401e6d034a4d4a

      Author:  kolonel <carlfakhry@gmail.com> 

      Date: 2018-09-16 12:11:40 -0500

      Commit message:


	  
		
 added a check for progressBar
 
    
  
    

      Package: scran

      Commit: 8ad777bd151bc12baf8d4c9f8c9926bd7e166839

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 16:12:11 +0100

      Commit message:


	  
		
 Moved combining method details from ?combineVar to ?combinePValues.
 
    
  
    

      Package: scran

      Commit: 87dfd62d22c480b36593d570924a073d16949e8d

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:55:02 +0100

      Commit message:


	  
		
 Rebuilt NAMESPACE, bumped version number and date, updated NEWS.
 
    
  
    

      Package: scran

      Commit: 29845ef2cdcdad276ca011a09f3dab64b3fe1d6b

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:51:40 +0100

      Commit message:


	  
		
 Removed obsolete .combine_pvalues utility.
 
    
  
    

      Package: scran

      Commit: 02febaa91e45b66480d49e027d73855348ddf332

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:50:59 +0100

      Commit message:


	  
		
 Switched pairwiseTTests to use combinePValues for Stouffer's.
 
    
  
    

      Package: scran

      Commit: 136214c6ed41b3b32e07565de5d5449a2cb56aa7

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:48:40 +0100

      Commit message:


	  
		
 Shortcut for only one vector in combinePValues.
 
    
  
    

      Package: scran

      Commit: 5bee1049f6c50232878fabdafefe1684c4a65d14

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:36:08 +0100

      Commit message:


	  
		
 Split testVar and combineVar tests to separate files.
 
    
  
    

      Package: scran

      Commit: 53ce38474b923936db1571109f99ba09d78e306d

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:35:06 +0100

      Commit message:


	  
		
 Switched combineVar to use combinePValues internally.
 
    
  
    

      Package: scran

      Commit: d93d1902cb0bb1deb9b90dc506fe29680d4179ba

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:34:24 +0100

      Commit message:


	  
		
 Protect against p=0 and 1 in Z method for combinePValues.
 
    
  
    

      Package: scran

      Commit: 8a6552ce8aa9c11da1937ea68f63170f980221b1

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:29:27 +0100

      Commit message:


	  
		
 Support weights as a list in combinePValues.
 
    
  
    

      Package: scran

      Commit: 5d0e3ec3602beb23abdf1d15c704e4ea81de80bd

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:16:18 +0100

      Commit message:


	  
		
 Switched combineMarkers to use combinePValues.
 
    
  
    

      Package: scran

      Commit: 45ab45b00180f4d803443425c6521d9932d650f8

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:02:29 +0100

      Commit message:


	  
		
 Fixed a log bug in combinePValues.
 
    
  
    

      Package: scran

      Commit: f87bbfccb09e5f524aa8e84af6f9221aa71f7879

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 15:01:08 +0100

      Commit message:


	  
		
 Added explicit tests for combinePValues.
 
    
  
    

      Package: scran

      Commit: d107154ef21b87a6f697138bf9b4cc82dad8b3fa

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 13:07:51 +0100

      Commit message:


	  
		
 Documented combinePValues.
 
    
  
    

      Package: scran

      Commit: 05c97fc28dd3e40648d1fea1495cf5a097917fff

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 13:06:53 +0100

      Commit message:


	  
		
 Updated Simes C++ code to accept a list.
 
    
  
    

      Package: scran

      Commit: 535cbd0792381db3f2baa3f76058ee2970fc3650

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-16 12:56:13 +0100

      Commit message:


	  
		
 Rolled out specific function for p-value combining.
 
    
  
    

      Package: chimeraviz

      Commit: 8948ba91129ec08a65472a7563740b089639377b

      Author:  Stian Lågstad <stianlagstad@gmail.com> 

      Date: 2018-09-16 16:53:01 +0200

      Commit message:


	  
		
 Fix small stuff
 
    
  
    

      Package: chimeraviz

      Commit: 05c968870a62fb79a3a754e7012ca62932ab43b8

      Author:  Stian Lågstad <stianlagstad@gmail.com> 

      Date: 2018-09-16 15:53:08 +0200

      Commit message:


	  
		
 Fix typo
 
    
  
    

      Package: chimeraviz

      Commit: e4f8ae759eaf25d102ba4cf7f59f04cf560798fd

      Author:  Stian Lågstad <stianlagstad@gmail.com> 

      Date: 2018-09-16 15:32:06 +0200

      Commit message:


	  
		
 Link to citations
 
    
  
    

      Package: chimeraviz

      Commit: 039349785903e8e1d9b81f78f411c16537b6d39d

      Author:  Stian Lågstad <stianlagstad@gmail.com> 

      Date: 2018-09-16 15:31:59 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: chimeraviz

      Commit: bd3f6fd2f7bf40e9fddbfa25fc25bb9384136095

      Author:  Stian Lågstad <stianlagstad@gmail.com> 

      Date: 2018-09-16 15:25:10 +0200

      Commit message:


	  
		
 Avoid readr because of https://github.com/tidyverse/readr/issues/750
 
    
  
    

      Package: plotGrouper

      Commit: aec3c83f20914954df3c9749af125d1edd58093e

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-15 21:51:59 -0700

      Commit message:


	  
		
 Fix placement of comparison segments
 
    
  
    

      Package: plotGrouper

      Commit: ff7e3fbe14c99556ec7c95016d39047df4dcfa8c

      Author:  jdgagnon <jgagnon@vpn-10-48-4-203.ucsf.edu> 

      Date: 2018-09-15 09:47:16 -0700

      Commit message:


	  
		
 udpate README
 
    
  
    

      Package: mzR

      Commit: 59a4c51a7a90c712c7adf7e83055510e1d2b547a

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-15 23:11:27 +0200

      Commit message:


	  
		
 reference correct issue number
 
    
  
    

      Package: mzR

      Commit: f77fa9ea0d9bec67003fa37d00768e8258642eaf

      Author:  Laurent Gatto <laurent.gatto@gmail.com> 

      Date: 2018-09-15 22:48:48 +0200

      Commit message:


	  
		
 Merge pull request #182 from sneumann/fix181

Closing #181 
    
  
    

      Package: mzR

      Commit: 6e6b87d510d366f18b9ba24669bb13a0adddd7c6

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2018-09-15 22:34:04 +0200

      Commit message:


	  
		
 More elegant fix for #181
 
    
  
    

      Package: mzR

      Commit: 00f65ff95c67a28cac504c827ac4ba2227b8291f

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2018-09-15 22:11:56 +0200

      Commit message:


	  
		
 Closing #181
 
    
  
    

      Package: mzR

      Commit: e7ed4bd57e8087a7333d08a6521ed463ee1cddf8

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-13 23:15:13 +0200

      Commit message:


	  
		
 bump gh devel version
 
    
  
    

      Package: amplican

      Commit: 64c05b4dab96f4cfed5c1f129b8e78d95bb58a22

      Author:  JokingHero <kornellabun@gmail.com> 

      Date: 2018-09-15 21:48:21 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: amplican

      Commit: 349e91a28d7dae930c7e62f290d9bdd6f66c5c4f

      Author:  JokingHero <kornellabun@gmail.com> 

      Date: 2018-09-15 21:47:26 +0200

      Commit message:


	  
		
 hopefully will fix inconsistent behaviour of knitr when plotting grid objects from child
 
    
  
    

      Package: amplican

      Commit: 31b17fd6f27d942a9a2ce7e84342f8ead68fb129

      Author:  JokingHero <kornellabun@gmail.com> 

      Date: 2018-09-15 21:10:43 +0200

      Commit message:


	  
		
 fixed naming of the vignette FAQ
 
    
  
    

      Package: scran

      Commit: 8e3daadb1a60d653291286258182e20ecbb89d1d

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 18:14:39 +0100

      Commit message:


	  
		
 Merge branch 'master' of https://github.com/MarioniLab/scran
 
    
  
    

      Package: scran

      Commit: f11e2ec67da8038315d62aa0f9f7fcc80e8e7d6f

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 18:05:12 +0100

      Commit message:


	  
		
 Documented log-behaviour of findMarkers.
 
    
  
    

      Package: scran

      Commit: b1c9ca4493cd754984c6567ec48d2bf48dc69cba

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 18:04:57 +0100

      Commit message:


	  
		
 Updated doubletCluster tests for new log behaviour of findMarkers.
 
    
  
    

      Package: scran

      Commit: dcf6c9248b0052d78e917a98e3973de07528cc94

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 18:02:15 +0100

      Commit message:


	  
		
 Updated doubletCluster for log-p-values from findMarkers.
 
    
  
    

      Package: scran

      Commit: ee16c29085572383a61f747e91153dad66c273d9

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 17:49:19 +0100

      Commit message:


	  
		
 Added Details and Examples for combineMarkers documentation.
 
    
  
    

      Package: scran

      Commit: 31902fd5b97e8b667097734edcd5321558764042

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 17:43:04 +0100

      Commit message:


	  
		
 Discarded redundant findMarkers tests, small updates.
 
    
  
    

      Package: scran

      Commit: f61cfe56d65aeb2f3d86cb7f1e0f85342caa403c

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 17:42:22 +0100

      Commit message:


	  
		
 Bugfix to findMarkers for passing log-p values.
 
    
  
    

      Package: scran

      Commit: 4dc81afb145aff7e3fe8c58e91b2a0efd7bb3700

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 17:39:13 +0100

      Commit message:


	  
		
 Protect linear model t-test from discreteness.
 
    
  
    

      Package: scran

      Commit: bf1cccfbca9019b937fe3cd4ea2b6d8d84c723b5

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 17:30:20 +0100

      Commit message:


	  
		
 Added tests for all modes of pairwiseTTests.
 
    
  
    

      Package: scran

      Commit: 7a25226c47e344019809fdf349f41a74a1accb52

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 17:06:01 +0100

      Commit message:


	  
		
 Bugfix for linear model t-test standard error.
Remove intercept check, require intercept-free design as input.
 
    
  
    

      Package: scran

      Commit: 70f97531e17a16fb748b129d5dbc1118c09895bf

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 15:40:02 +0100

      Commit message:


	  
		
 Bugfix for Stouffer's method in pairwiseTTests.
 
    
  
    

      Package: scran

      Commit: 125e9ab185b80aeccba730d3ab6d87802c8bbd58

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 14:51:44 +0100

      Commit message:


	  
		
 Bugfix when lfc!=0 for pairwiseTTests.
 
    
  
    

      Package: scran

      Commit: ecee82097fe98f41094d11651c1cf61208e2a7cc

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 13:47:44 +0100

      Commit message:


	  
		
 Migrated docs from findMarkers to pairwiseTTests.
 
    
  
    

      Package: scran

      Commit: 1327f9e64e8b6755664b7cb0e7efd6d3e7e8abd7

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 12:17:01 +0100

      Commit message:


	  
		
 Migrated testing code from findMarkers to pairwiseTTests.
 
    
  
    

      Package: scran

      Commit: 4184722d05bce9c4c3ce2191482a60978cb6bc8f

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 19:25:15 +0100

      Commit message:


	  
		
 Rebuilt NAMESPACE.
 
    
  
    

      Package: scran

      Commit: d7a875b7e726dd351c358f5cd71dd2b4c9a83bda

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 19:24:54 +0100

      Commit message:


	  
		
 Bugfix for returning full stats, added tests for full.stats=TRUE.
 
    
  
    

      Package: scran

      Commit: 1a1b546e14ce1f9048109285a0d9dd200c5f6c9a

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 19:15:26 +0100

      Commit message:


	  
		
 Documented combineMarkers (except for example).
 
    
  
    

      Package: scran

      Commit: aa7b599ffab51271b76a51b0b63cdbc6024954fe

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 18:58:26 +0100

      Commit message:


	  
		
 Added tests for combineMarkers.
 
    
  
    

      Package: scran

      Commit: df56fd2ce34c6cead8102f1af4f07fe0cb1909d0

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 18:58:17 +0100

      Commit message:


	  
		
 Protect against silly inputs, streamling multiple testing correction.
 
    
  
    

      Package: scran

      Commit: 28f9b5c600a7744082113ae3af0f863c10a11ec7

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 16:01:02 +0100

      Commit message:


	  
		
 Added separate source file for marker-related utilities.
 
    
  
    

      Package: scran

      Commit: 4313ca91a05ca18326be5634933c7a151ada4807

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 15:59:00 +0100

      Commit message:


	  
		
 Split off marker list combining code into a separate function.
 
    
  
    

      Package: scran

      Commit: c119c7d2fdf3a423031c01a278f81b043825afed

      Author:  Aaron Lun <LTLA@users.noreply.github.com> 

      Date: 2018-09-13 09:13:31 +0100

      Commit message:


	  
		
 Merge pull request #19 from PeteHaitch/patch-1

Typo 
    
  
    

      Package: scran

      Commit: 3c1e7cde96b047e48f4e50d74a586f8b1fb80e9d

      Author:  Peter Hickey <peter.hickey@gmail.com> 

      Date: 2018-09-13 09:59:19 +1000

      Commit message:


	  
		
 Typo 
    
  
    

      Package: scran

      Commit: 1722bef6f00771deb9b55ea32e13c57dc0924a74

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-12 16:35:16 +0100

      Commit message:


	  
		
 Bumped version number, date.
 
    
  
    

      Package: scran

      Commit: 676c496fd4ded1c90128622be661537f53c62a19

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-12 16:34:28 +0100

      Commit message:


	  
		
 Protect against numerical imprecision in score comparisons.
 
    
  
    

      Package: simpleSingleCell

      Commit: 0a60fed6edf17d863da77d2f0ac7d74c16487706

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-15 18:13:42 +0100

      Commit message:


	  
		
 Fixed vignette order on the landing page... again.
 
    
  
    

      Package: plotGrouper

      Commit: ca153db2d277aef9cfa1c16caec36d2ed191e33e

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-15 09:27:21 -0700

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: scruff

      Commit: 859a3ccb941d3ce9b5daf4f81ac97955afef4b28

      Author:  zhewa <314100793@qq.com> 

      Date: 2018-09-15 11:23:07 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: scruff

      Commit: 7107eba2122a22faa3bf693ada6c81902d7cc2a6

      Author:  zhewa <314100793@qq.com> 

      Date: 2018-09-15 11:16:02 -0400

      Commit message:


	  
		
 include = c("filtered", all) in tenxBamqcplot
 
    
  
    

      Package: IsoformSwitchAnalyzeR

      Commit: 9e8b170c8441d197318de6d9cd6d55d2f022caff

      Author:  kvittingseerup <k.vitting.seerup@gmail.com> 

      Date: 2018-09-15 08:45:34 +0100

      Commit message:


	  
		
 Minor update to isoformSwitchTestDEXSeq
 
    
  
    

      Package: plotGrouper

      Commit: b4af0a581b4c9e5d1f1b9210399247568848dc28

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-14 16:39:43 -0700

      Commit message:


	  
		
 update README & vignette
 
    
  
    

      Package: flowWorkspace

      Commit: 84b753b68fc15dd89362d91fe45be7ec454443b2

      Author:  mikejiang <wjiang2@fhcrc.org> 

      Date: 2018-09-14 15:15:57 -0700

      Commit message:


	  
		
 Merge branch 'trunk' into devel
 
    
  
    

      Package: flowWorkspace

      Commit: ebb13af5f4e6b992704b3ff25906da1fd29f4126

      Author:  mikejiang <wjiang2@fhcrc.org> 

      Date: 2018-09-14 15:15:15 -0700

      Commit message:


	  
		
 bump
 
    
  
    

      Package: flowWorkspace

      Commit: 8d90c229049cf91596f76a1560916f32a1bd8254

      Author:  mikejiang <wjiang2@fhcrc.org> 

      Date: 2018-09-14 15:14:26 -0700

      Commit message:


	  
		
 add plot_diff_tree
 
    
  
    

      Package: amplican

      Commit: 47f1ed16efd193df85b539c2ae766cea1686845a

      Author:  JokingHero <kornellabun@gmail.com> 

      Date: 2018-09-14 21:48:38 +0200

      Commit message:


	  
		
 fix for description merge confict
 
    
  
    

      Package: amplican

      Commit: 1d300cc8356fb4aeb59efc1cf69b838aca576fe9

      Author:  JokingHero <kornellabun@gmail.com> 

      Date: 2018-09-14 21:37:24 +0200

      Commit message:


	  
		
 some bug fixes, improvemnets to HDR, example of base editor
 
    
  
    

      Package: amplican

      Commit: f1d302d3bd1b0159438e0aa86dc73d511bd72988

      Author:  JokingHero <kornellabun@gmail.com> 

      Date: 2018-08-15 15:28:17 +0200

      Commit message:


	  
		
 export min_freq to the amplicanPipeline for easier manipulation
 
    
  
    

      Package: sesame

      Commit: fdea046245eda3438391f7d3bced190e1e5f40a2

      Author:  Wanding Zhou - Bioinformatics <zhouwanding@gmail.com> 

      Date: 2018-09-14 13:48:30 -0400

      Commit message:


	  
		
 Merge pull request #5 from ttriche/master

fix build issue (cheezy kludge: use \dontrun) and add CITATION (S00PER IMPORTANT!!1) 
    
  
    

      Package: sesame

      Commit: ace8f9e337c93a877e8619d1a63a92d07087825c

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-09-14 13:05:18 -0400

      Commit message:


	  
		
 typo in CITATION format, fixed
 
    
  
    

      Package: sesame

      Commit: 8649febbde921ba963487294056bc0daafddd4dd

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-09-14 13:03:33 -0400

      Commit message:


	  
		
 quote year in citation
 
    
  
    

      Package: sesame

      Commit: f87a94b79a7e6360b9e98fb084def07d307cf96f

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-09-14 13:02:26 -0400

      Commit message:


	  
		
 added CITATION for citation("sesame")
 
    
  
    

      Package: sesame

      Commit: 218a8f0f850f61e5c837f8872026b45b898e1984

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-09-14 12:55:53 -0400

      Commit message:


	  
		
 add citation
 
    
  
    

      Package: sesame

      Commit: 0448c8f7c9a1a1de8d1911cac17bbfded256ea07

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-09-14 12:52:25 -0400

      Commit message:


	  
		
 fix build issue
 
    
  
    

      Package: HDF5Array

      Commit: a124ba38844c2911dd5bc388ea4acf190ea24048

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2018-09-14 10:24:46 -0700

      Commit message:


	  
		
 write_array_to_sink() was renamed BLOCK_write_to_sink() in DelayedArray
 
    
  
    

      Package: DelayedArray

      Commit: 998fa6af9f1f9ff78691ce00ae8cab0a3542f32a

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2018-09-14 10:21:20 -0700

      Commit message:


	  
		
 Rename (and improve) write_array_to_sink() -> BLOCK_write_to_sink()

Also add "type" method for RleRealizationSink objects.
 
    
  
    

      Package: QuaternaryProd

      Commit: ba370fb48763a385e8b9173b4a877c0ce1082ea4

      Author:  kolonel <carlfakhry@gmail.com> 

      Date: 2018-09-14 12:00:29 -0500

      Commit message:


	  
		
 update version number
 
    
  
    

      Package: QuaternaryProd

      Commit: 08cd88baa9a807d317a97323780d45098e93782b

      Author:  kolonel <carlfakhry@gmail.com> 

      Date: 2018-09-13 23:15:22 -0500

      Commit message:


	  
		
 Added the option for specifying an arbitrary network and added a progress bar when computing pvalues over the causal network
 
    
  
    

      Package: TFutils

      Commit: 6da0fd696da8485b8b332cf15aa16d39bfd600b2

      Author:  Vince Carey <stvjc@channing.harvard.edu> 

      Date: 2018-09-14 12:18:02 -0400

      Commit message:


	  
		
 minor changes
 
    
  
    

      Package: seqplots

      Commit: 66230d41f2bb83db21e3c524d2c65a11779fc240

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-09-14 17:17:45 +0100

      Commit message:


	  
		
 version bump to 1.19.3
 
    
  
    

      Package: TabulaMurisData

      Commit: 6bc3af4418d9351d1732ef0741927d5ce2a7be53

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2018-09-14 18:01:27 +0200

      Commit message:


	  
		
 Add iSEE to Suggests
 
    
  
    

      Package: seqplots

      Commit: bef58872272f297b1dd6222237b7de066e876e02

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-09-14 16:58:20 +0100

      Commit message:


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

      Package: seqplots

      Commit: cf9e0c3de82678847a3ad61429f449850dc9e5d8

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-09-14 10:45:30 +0100

      Commit message:


	  
		
 clusters are properly assigned in single thread mode, fixes #38
 
    
  
    

      Package: seqplots

      Commit: 08cd0dd6bd568b6627fbde536eb9d01eab65c1d4

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-09-13 19:02:12 +0100

      Commit message:


	  
		
 use single core calculations by default, fixes #43
 
    
  
    

      Package: seqplots

      Commit: 750edb43525370c33d00fb5ed260df06810570f9

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-05-02 11:11:07 +0100

      Commit message:


	  
		
 remove test for unused features
 
    
  
    

      Package: seqplots

      Commit: b50e5ff3f16fa2f410f5de64938add4b744fa3c5

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-05-02 11:07:42 +0100

      Commit message:


	  
		
 add parameter to determine sorting distance
 
    
  
    

      Package: seqplots

      Commit: 43546b89e597d0fb0b68cd7569f8545826d87f68

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-05-01 19:17:03 +0100

      Commit message:


	  
		
 heatmap plotting function takes options to sort by specific tracks, sort by anchored distance and cluster based on anchored distance, and annotate clusters using external vector
 
    
  
    

      Package: seqplots

      Commit: d7863b832833d754e0391491d5a745b6c3bacd2c

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-03-01 12:24:52 +0000

      Commit message:


	  
		
 removed "library' or 'require' calls for: ‘BSgenome’ ‘RSQLite’ ‘rtracklayer’
 
    
  
    

      Package: seqplots

      Commit: 99e521ba38cec7b4b45532a2fc9bfe8321436722

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-02-28 20:18:18 +0000

      Commit message:


	  
		
 export for getREF function
 
    
  
    

      Package: seqplots

      Commit: 0e5aeb2225bd7bef2a2b605e31f3f134d779f157

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-01-27 17:04:16 +0000

      Commit message:


	  
		
 getPlotSetArray: if track list is named, use the names instead of paths to annotate the output
 
    
  
    

      Package: seqplots

      Commit: 893d5432eac27b46e45c6971891d8cd64ae3c900

      Author:  przemol <pstempor@gmail.com> 

      Date: 2018-01-09 20:03:47 +0000

      Commit message:


	  
		
 add_local_file - function to add files to local SeqPlots installation
 
    
  
    

      Package: seqplots

      Commit: c8f1f33e42d1762141e769449dd157d2f2f44896

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-11-02 16:47:54 +0000

      Commit message:


	  
		
 docs update
 
    
  
    

      Package: seqplots

      Commit: 40789caf89521a561588fa6c2893aaf71fb5177a

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-27 17:28:57 +0100

      Commit message:


	  
		
 further support for chromosome check for genomes in FASTA files - TODO: add support for motif plots
 
    
  
    

      Package: seqplots

      Commit: d494a83decdf8e629df2d465910df7f1f1aa4688

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-27 15:30:34 +0100

      Commit message:


	  
		
 support for uploading narrowPeak files
 
    
  
    

      Package: seqplots

      Commit: e06362e752ccfba80861db21a7f334106c70f47b

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-27 15:26:50 +0100

      Commit message:


	  
		
 docs update
 
    
  
    

      Package: seqplots

      Commit: 2dc11b4ba81a66655cc6527320a18cf0af10208c

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-27 15:26:31 +0100

      Commit message:


	  
		
 Import function for narrowPeak format
 
    
  
    

      Package: seqplots

      Commit: f40a0cfd7acd3cc2cfeca343085581555e23c019

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-27 15:21:14 +0100

      Commit message:


	  
		
 use FASTA genomes for uploaded files
 
    
  
    

      Package: seqplots

      Commit: d297808bbfa0dc1e1aee5cf75d1a234c56f099dc

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-27 15:01:18 +0100

      Commit message:


	  
		
 Logic for adding FASTA files in GUI
 
    
  
    

      Package: seqplots

      Commit: cdeef028fdd7c1cfbfd8b2061759221e6ff7845a

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-20 14:52:54 +0100

      Commit message:


	  
		
 Merge branch 'master' of github.com:Przemol/seqplots

# Conflicts:
#	inst/seqplots/server.R
 
    
  
    

      Package: seqplots

      Commit: a70d2e15c1ee9d8d8470344ffa0c1110aee0c830

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-20 14:49:44 +0100

      Commit message:


	  
		
 adding BW files from Query String - bugfix
 
    
  
    

      Package: seqplots

      Commit: a8f355e174bb314d22d2a09bef55e3b254c98bbb

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-20 14:49:44 +0100

      Commit message:


	  
		
 adding BW files from Query String - get metadata info from query string
 
    
  
    

      Package: seqplots

      Commit: 9a160b2b680269444121123bebd0981871489cd0

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-20 14:18:04 +0100

      Commit message:


	  
		
 adding BW files from Query String - error handling
 
    
  
    

      Package: seqplots

      Commit: faa74fa3b630d3c978e0ea2b55d95dd31f5a641b

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-20 13:49:27 +0100

      Commit message:


	  
		
 adding BW files from Query String - modal dialog and session self closing
 
    
  
    

      Package: seqplots

      Commit: ad7fb036eada0094738be3dd8cd417dddb3e1e7f

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-19 17:11:50 +0100

      Commit message:


	  
		
 adding BW files from Query String
 
    
  
    

      Package: seqplots

      Commit: 5ee60e81ddefbe46dc1507ee4582dc9229c61c26

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-19 16:41:51 +0100

      Commit message:


	  
		
 fix for converting custom genomes files from wig to bigwig files - seqinfo object is created based on data in wig file
 
    
  
    

      Package: seqplots

      Commit: 0231349947378b0480ec323a1c95c7a9abdfb40b

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-19 13:28:29 +0100

      Commit message:


	  
		
 further reduction in warnings while testing
 
    
  
    

      Package: seqplots

      Commit: 86b0d8ef4c3c612a9963c3f550cc39aa67b5af3b

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-18 17:57:24 +0100

      Commit message:


	  
		
 initial support for genome in FASTA format plus various warnings suppressed
 
    
  
    

      Package: seqplots

      Commit: 61cff9733c503bf1af30e093c3eab5cfe054792b

      Author:  przemol <pstempor@gmail.com> 

      Date: 2017-09-18 16:08:41 +0100

      Commit message:


	  
		
 fixed url filed in CITATION
 
    
  
    

      Package: plotGrouper

      Commit: 33393b35902497ce34990ebda5c6b3d136c2bd45

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-14 08:13:17 -0700

      Commit message:


	  
		
 Update DESCRIPTION
 
    
  
    

      Package: plotGrouper

      Commit: 6603cc8a35a6e79f3061b7a5a338fb63daaa0eee

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-14 08:03:03 -0700

      Commit message:


	  
		
 update README
 
    
  
    

      Package: Onassis

      Commit: 5d738704823330833555c046c91504ff16a75d44

      Author:  egaleota <eugenia.galeota@ieo.eu> 

      Date: 2018-09-14 16:06:24 +0200

      Commit message:


	  
		
 Bug fix: removed some rmarkdown not showing correctly the vignette text
 
    
  
    

      Package: maEndToEnd

      Commit: 2e5cae5f8221ce0cd75cdf8237b7dfce57a847d3

      Author:  klaus <bernd.klaus@embl.de> 

      Date: 2018-09-14 11:50:32 +0200

      Commit message:


	  
		
 small change to reactome output
 
    
  
    

      Package: maEndToEnd

      Commit: 0bf62d07b1821f48296bfaa51f5a0cf0f357ce35

      Author:  klaus <bernd.klaus@embl.de> 

      Date: 2018-09-14 11:14:06 +0200

      Commit message:


	  
		
 minor firxes to the RLE section
 
    
  
    

      Package: maEndToEnd

      Commit: ab2f87f9ef667dab25ea3bc0fb21a24bf1c36beb

      Author:  klaus <bernd.klaus@embl.de> 

      Date: 2018-09-14 09:58:22 +0200

      Commit message:


	  
		
 modified the latex conversion check so that it does not throw an error when working interactively
 
    
  
    

      Package: maEndToEnd

      Commit: 589fdd67b9ec66967cff0b74577cff8b0ee6f99b

      Author:  Steffireise <steffi[at]reisenauer-online.de> 

      Date: 2018-09-03 13:10:26 +0200

      Commit message:


	  
		
 changed book name "genomics class" to "Biomedical Data Science" and "Michael Irizarry" to "Rafael Irizarry"
 
    
  
    

      Package: maEndToEnd

      Commit: 321faefd8137514b84c89ef907e48333b3f86f5b

      Author:  Steffireise <steffi[at]reisenauer-online.de> 

      Date: 2018-09-03 12:44:02 +0200

      Commit message:


	  
		
 remove section on target options "full" and "extended"
 
    
  
    

      Package: tRNAscanImport

      Commit: bc7dc2592832b05da243a1bf574b6c1b50f61ac9

      Author:  Felix Ernst <felix.ernst@ulb.ac.be> 

      Date: 2018-09-14 09:52:20 +0200

      Commit message:


	  
		
 vignette update
 
    
  
    

      Package: tRNAscanImport

      Commit: 4902d7b9e52e1bcbebd717357dcb9ec529d73bc2

      Author:  Felix Ernst <felix.ernst@ulb.ac.be> 

      Date: 2018-09-14 08:44:17 +0200

      Commit message:


	  
		
 README.md update
 
    
  
    

      Package: IsoformSwitchAnalyzeR

      Commit: 1e2bbac107d91821a772d85579cd8b6390a790b0

      Author:  kvittingseerup <k.vitting.seerup@gmail.com> 

      Date: 2018-09-14 08:51:34 +0200

      Commit message:


	  
		
 Version bump for Bioconductor
 
    
  
    

      Package: PREDA

      Commit: 4b14ed727389d171fc2b423b3eafe3c17b3411d9

      Author:  itagliaf <itagliaf@node1.cluster.ifom.eu> 

      Date: 2018-09-14 08:30:18 +0200

      Commit message:


	  
		
 bug fix: removing samr dependency as no more available
 
    
  
    

      Package: M3C

      Commit: 329b333fe8901dce807183e5d4e7abb4069c24fa

      Author:  crj32 <chris.r.john86@gmail.com> 

      Date: 2018-09-14 07:17:05 +0100

      Commit message:


	  
		
 removed html file
 
    
  
    

      Package: M3C

      Commit: 47e0919a6ee80d34e16089a3bd8e2e545812db2c

      Author:  crj32 <chris.r.john86@gmail.com> 

      Date: 2018-09-14 07:15:26 +0100

      Commit message:


	  
		
 vignette edits
 
    
  
    

      Package: M3C

      Commit: 76bdec6551cf646a3ad31c8e526261732ce987f2

      Author:  crj32 <chris.r.john86@gmail.com> 

      Date: 2018-09-14 07:06:09 +0100

      Commit message:


	  
		
 fixed vignette error
 
    
  
    

      Package: RCy3

      Commit: e477941a0edc27200d8fb29856bbb15561b02d17

      Author:  Alexander Pico <apico@gladstone.ucsf.edu> 

      Date: 2018-09-13 22:57:50 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: RCy3

      Commit: 4c68141c77eeeda3d7032799e866146d61a07dfe

      Author:  Alexander Pico <apico@gladstone.ucsf.edu> 

      Date: 2018-09-13 22:57:30 -0700

      Commit message:


	  
		
 replaced sapply with vapply; replace factors in dfs
 
    
  
    

      Package: RCy3

      Commit: cdbd07c0520d6d1ee37fc4f285b73c6891cb88fc

      Author:  Alexander Pico <apico@gladstone.ucsf.edu> 

      Date: 2018-09-13 20:43:56 -0700

      Commit message:


	  
		
 rotate deprecated and updated news; version bump
 
    
  
    

      Package: MSnbase

      Commit: bd951d064df0cb8eab004a9a83fdff361d708348

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-13 23:52:24 +0200

      Commit message:


	  
		
 no docs on Bioc
 
    
  
    

      Package: MSnbase

      Commit: 01e6144523387f225444225fb2ed97ca5653cd81

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-13 23:51:19 +0200

      Commit message:


	  
		
 merge master and update pkgdown
 
    
  
    

      Package: MSnbase

      Commit: 7a0b1804465a8b82cf303582fc0f0a2746564b8a

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-13 23:27:10 +0200

      Commit message:


	  
		
 add scan.number.s. numeric test
 
    
  
    

      Package: MSnbase

      Commit: 56635ba78ae3064799d9912ff71a7cbed6303c59

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-13 16:21:58 +0200

      Commit message:


	  
		
 don't assume charge in plotDensity (issue #359)
 
    
  
    

      Package: MSnbase

      Commit: de90cc36be6c5545f0f8d3bb2e1c163f56ddaf2e

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-04 07:25:47 +0200

      Commit message:


	  
		
 add note about parallel processing
 
    
  
    

      Package: MSnbase

      Commit: 448d33fc052893050678540a8401c5e966560993

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-08-21 12:40:17 +0200

      Commit message:


	  
		
 bump version for gh devel
 
    
  
    

      Package: mzR

      Commit: ac3bc6fffe30151733e3b116a515677ac7cf88ac

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-13 23:14:04 +0200

      Commit message:


	  
		
 update news
 
    
  
    

      Package: mzR

      Commit: 55057452e20b0c253041231d988166c3b485744d

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-13 23:12:02 +0200

      Commit message:


	  
		
 Merge branch 'master' of github.com:sneumann/mzR
 
    
  
    

      Package: mzR

      Commit: 38c8544318263a84b9876c2ec4af1bd712ead50c

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-09-13 23:11:52 +0200

      Commit message:


	  
		
 specParams returns numeric scan.number.s.
 
    
  
    

      Package: mzR

      Commit: d00e3cace0e4dd1721f6dc515e9f213c966f7789

      Author:  sneumann <sneumann@ipb-halle.de> 

      Date: 2018-09-13 14:02:39 +0200

      Commit message:


	  
		
 Merge pull request #179 from sneumann/featureRemovelibnetCDF

Feature removelibnet cdf 
    
  
    

      Package: mzR

      Commit: 523282dbcc0fb617522b445df14a9d912340b942

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2018-09-12 08:47:30 +0200

      Commit message:


	  
		
 Bump version. Merged changes close #178
 
    
  
    

      Package: mzR

      Commit: 87f92cbc09c1d6730a6c880ca139f67339df0506

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2018-09-11 17:54:45 +0200

      Commit message:


	  
		
 Remove leftover static netCDF for windows
 
    
  
    

      Package: mzR

      Commit: 187568290d8671cc181666858adf7a418ba5316d

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2018-09-11 17:27:38 +0200

      Commit message:


	  
		
 Add runinfo and instrumentinfo to test_cdf
 
    
  
    

      Package: mzR

      Commit: dfbd825f35f1c66cf69c980662a6bc3b02413f4b

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2018-09-10 10:41:50 +0200

      Commit message:


	  
		
 Removed netCDF.h, can already be used by xcmsRaw
 
    
  
    

      Package: HiCcompare

      Commit: abe677b6bd4b2aae559487190439d60f338935c9

      Author:  jstansfield0 <stansfieldjc@vcu.edu> 

      Date: 2018-09-13 16:43:36 -0400

      Commit message:


	  
		
 add warning for inter-chr interactions
 
    
  
    

      Package: HiCcompare

      Commit: cc2181e57af12795059bf89fb570d1ce0614a68f

      Author:  jstansfield0 <stansfieldjc@vcu.edu> 

      Date: 2018-09-13 16:19:19 -0400

      Commit message:


	  
		
 add cluster example to vignette
 
    
  
    

      Package: BiocOncoTK

      Commit: 84c7716d48ba9cf48dbd44d2198ef09684cd8812

      Author:  Vince Carey <stvjc@channing.harvard.edu> 

      Date: 2018-09-13 16:33:39 -0400

      Commit message:


	  
		
 add option to exclude mss from bindMSI
 
    
  
    

      Package: sesame

      Commit: e9d5fb3d1f2c00629def03398b012381021eae15

      Author:  zwdzwd <zhouwanding@gmail.com> 

      Date: 2018-09-13 16:22:06 -0400

      Commit message:


	  
		
 version bump 0.99.5
 
    
  
    

      Package: sesame

      Commit: f1e2cde9af43033b6b194ffd8775a5ea359f8815

      Author:  zwdzwd <zhouwanding@gmail.com> 

      Date: 2018-09-13 13:08:41 -0400

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/master'
 
    
  
    

      Package: sesame

      Commit: 2a23fdc6ec3dcd0783ea92adb30967695af73cc6

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-09-10 18:30:03 -0400

      Commit message:


	  
		
 minor, message omitted
 
    
  
    

      Package: sesame

      Commit: 2d26aad382b95cf04c2d9ef19bb1b51f22292412

      Author:  Wanding Zhou - Bioinformatics <zhouwanding@gmail.com> 

      Date: 2018-08-30 17:18:15 -0400

      Commit message:


	  
		
 Merge pull request #4 from ttriche/patch-1

fix sesamize 
    
  
    

      Package: sesame

      Commit: 321e9e77f4e2c445bf81bcae361db96d4ba31d7b

      Author:  Tim Triche, Jr <tim.triche@gmail.com> 

      Date: 2018-08-30 17:16:08 -0400

      Commit message:


	  
		
 fix sesamize 

this was driving me insane 
    
  
    

      Package: sesame

      Commit: bc6b3eea7690f33d120ffd76cf13f18aa65b264e

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-08-06 14:52:38 -0400

      Commit message:


	  
		
 minor, message omitted
 
    
  
    

      Package: sesame

      Commit: 07f2cb30b4ba6980652be7e9534fafb2e2ebfd58

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-08-04 09:59:41 -0400

      Commit message:


	  
		
 added parameters to opensesame
 
    
  
    

      Package: sesame

      Commit: c8d664ad6da378cc6c0fc51f17899cf8a433f0a8

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-08-02 16:53:16 -0400

      Commit message:


	  
		
 document regeneration
 
    
  
    

      Package: sesame

      Commit: 577023386ac83de61f27442ca573f45720106aa5

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-08-01 23:29:47 -0400

      Commit message:


	  
		
 update to openSesame and sesamize, incorporate Tim's code
 
    
  
    

      Package: sesame

      Commit: 4ca1319dd1d7656d786645e4664445d8b6b6bfe2

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-07-17 21:30:17 -0400

      Commit message:


	  
		
 minor, message omitted
 
    
  
    

      Package: sesame

      Commit: 9cd2a699e3264d6b8fc61707074d1bd382d2edaa

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-07-17 21:30:04 -0400

      Commit message:


	  
		
 openSeSAMe pipeline
 
    
  
    

      Package: sesame

      Commit: 35e094fa6e5ba5d2999a0393243e9058b40d6eef

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-06-12 14:56:55 -0400

      Commit message:


	  
		
 exported getNormCtls
 
    
  
    

      Package: sesame

      Commit: 84eeb09c05a7aeb6e70bcebcff52759cffe399f5

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-06-11 22:01:10 -0400

      Commit message:


	  
		
 Merge branch 'ttriche-master'
 
    
  
    

      Package: sesame

      Commit: 67fef74187d0d0f0d73b8631f054bcc249f290ed

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-06-11 22:00:52 -0400

      Commit message:


	  
		
 minor fix to stop message
 
    
  
    

      Package: sesame

      Commit: 3f6f9c24917be61d26118dcf995dd21df2c0f0a4

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-06-11 22:00:00 -0400

      Commit message:


	  
		
 fix to sapply usage, plugged in searchIDATprefixes to SigSetListFromIDATs, added \value etc.
 
    
  
    

      Package: sesame

      Commit: ed926929fc9d961d4b6a50d9041de3592d4e4e64

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-10 14:50:36 -0400

      Commit message:


	  
		
 fix formatting in `show` method for SigSetList
 
    
  
    

      Package: sesame

      Commit: 6c3e14220197dd4d22684926d55a9fa6923734dc

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-10 14:46:33 -0400

      Commit message:


	  
		
 refactor SigSetListFrom* to take a list of IDAT stubs
 
    
  
    

      Package: sesame

      Commit: 63d730088af94fe67c19937fc0f0023bd330fa49

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-09 19:12:05 -0400

      Commit message:


	  
		
 be more selective about importing methods from S4Vectors
 
    
  
    

      Package: sesame

      Commit: 30ff1bf653e508d546670ac2626a4a0b1946707b

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-09 19:08:47 -0400

      Commit message:


	  
		
 let the user know how long a load is likely to take
 
    
  
    

      Package: sesame

      Commit: 649fb476e4ceb7dc0f90dc2265f5dc960d37b54f

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-09 19:05:33 -0400

      Commit message:


	  
		
 cleanup SigSetListFromPath
 
    
  
    

      Package: sesame

      Commit: 8428dedc4bae52148c7876039998c5234b4d140f

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-09 18:32:51 -0400

      Commit message:


	  
		
 more SigSetList cleanup, and some progress messages
 
    
  
    

      Package: sesame

      Commit: 52fb020689e881e75a458584eb8949cbdac62b3e

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-09 18:28:25 -0400

      Commit message:


	  
		
 more SigSetList cleanup
 
    
  
    

      Package: sesame

      Commit: d83f7bbdad5f02455a87c3efb28d1391e87da564

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-09 18:14:01 -0400

      Commit message:


	  
		
 derrrrrrp... left some old cruft in SigSetList `show` method
 
    
  
    

      Package: sesame

      Commit: ef391c3a6e6ab7d642ca049bd1f18d6c4b23ec94

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-09 18:11:35 -0400

      Commit message:


	  
		
 debuggina and slimming down SigSetList
 
    
  
    

      Package: sesame

      Commit: ffa90cd3e1e3a7baf2efaad42369f991822c36d9

      Author:  ttriche <tim.triche@gmail.com> 

      Date: 2018-06-09 18:03:58 -0400

      Commit message:


	  
		
 add SigSetList class
 
    
  
    

      Package: sesame

      Commit: 9f66eaf79a4600baff3b21058147c2961efa1910

      Author:  Tim Triche, Jr <tim.triche@gmail.com> 

      Date: 2018-06-09 17:14:12 -0400

      Commit message:


	  
		
 Merge pull request #1 from zwdzwd/master

load gzipped IDAT 
    
  
    

      Package: sesame

      Commit: e77935e175c36cee4f9c87daa58ac12f6a4780d6

      Author:  Wanding Zhou <wanding.zhou@vai.org> 

      Date: 2018-06-09 17:08:36 -0400

      Commit message:


	  
		
 load gzipped IDAT
 
    
  
    

      Package: sesame

      Commit: 41ace372ce8fcf1fc4b326d17c1aad6831b92302

      Author:  Wanding Zhou - Bioinformatics <zhouwanding@gmail.com> 

      Date: 2018-06-09 13:27:40 -0400

      Commit message:


	  
		
 Merge pull request #2 from ttriche/patch-2

Begin cleanup of vignette 
    
  
    

      Package: sesame

      Commit: ab310bfdf7cc664f932f09c41cee2bf11cba3ca7

      Author:  Tim Triche, Jr <tim.triche@gmail.com> 

      Date: 2018-06-08 15:14:14 -0400

      Commit message:


	  
		
 Begin cleanup of vignette

Great vignette -- almost too complete!  Just some minor copy editing 
    
  
    

      Package: BiocParallel

      Commit: 13c2187c2569ebbbe8a3853cd8bc8853c18923f9

      Author:  Martin Morgan <martin.morgan@roswellpark.org> 

      Date: 2018-09-13 16:07:07 -0400

      Commit message:


	  
		
 implement bpexportglobals()

- export options() to workers
- default TRUE
 
    
  
    

      Package: DelayedArray

      Commit: 643acc55cae3ab9d04b66c80b8e86b5d34f1ce8c

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2018-09-13 10:22:55 -0700

      Commit message:


	  
		
 Add bplapply2()

bplapply2() is a simple wrapper to BiocParallel::bplapply() that
propagates base::.Options to the workers. Not exported because
DelayedArray is obviously the wrong place for this (a better place
would be in BiocParallel).
 
    
  
    

      Package: DelayedArray

      Commit: c1d49e7247ea7ea2be12d541cd33bd5533d2bedb

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2018-09-13 09:46:49 -0700

      Commit message:


	  
		
 Disable feature implemented in last 2 commits

No more in-house mechanism for automatic propagation of DelayedArray
user-controlled global options to workers (fails on some clusters).
DelayedArray options are stored again in base::.Options.
 
    
  
    

      Package: logicFS

      Commit: a98a2c782b2e08b7b06eb1dfbf71584c188923d3

      Author:  holgerschw <holger.schw@gmx.de> 

      Date: 2018-09-13 17:32:09 +0200

      Commit message:


	  
		
 Just testing
 
    
  
    

      Package: DESeq2

      Commit: 600c6c20fca6c2d54148bea17ac31c424ac69336

      Author:  mikelove <michaelisaiahlove@gmail.com> 

      Date: 2018-09-13 10:56:36 -0400

      Commit message:


	  
		
 add Wolfgangs linear model mu
 
    
  
    

      Package: methylKit

      Commit: e379aaa79779752fbdf66765f584dec563d32df4

      Author:  alexg9010 <alex.gos90@gmail.com> 

      Date: 2018-09-13 15:46:47 +0200

      Commit message:


	  
		
 update NEWS and version bump to 1.7.8
 
    
  
    

      Package: methylKit

      Commit: aea7cc7069ccceadd179f92f4362123eaedaf803

      Author:  alexg9010 <alex.gos90@gmail.com> 

      Date: 2018-09-13 15:43:34 +0200

      Commit message:


	  
		
 add tests for applyTbxByOverlap
 
    
  
    

      Package: methylKit

      Commit: d057cadac6a27438043d7e2c6b853e7bfeae432a

      Author:  alexg9010 <alex.gos90@gmail.com> 

      Date: 2018-09-13 15:42:54 +0200

      Commit message:


	  
		
 fix for applyTbxByOverlap

Fixes https://github.com/al2na/methylKit/issues/131
 
    
  
    

      Package: Pi

      Commit: 2424b7236b9117c0e2b964e83f6c698135b3af47

      Author:  Hai Fang <hfang.shanghai@gmail.com> 

      Date: 2018-09-13 10:35:20 +0100

      Commit message:


	  
		
 Update to the version 1.9.3
 
    
  
    

      Package: simpleSingleCell

      Commit: a75668988ff7b4c03e90fa9adfc6ba9daa1565a7

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 09:30:58 +0100

      Commit message:


	  
		
 Bumped version number, date.
 
    
  
    

      Package: simpleSingleCell

      Commit: dcf31ab53a0b9be6baf2abc3f75c1d68fe51f15e

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 09:30:42 +0100

      Commit message:


	  
		
 Fixes to doublet workflow, added standard ending text.
 
    
  
    

      Package: simpleSingleCell

      Commit: e1ade84db7280d98c917d169561cde10a4f498fe

      Author:  Aaron Lun <aaron.lun@cruk.cam.ac.uk> 

      Date: 2018-09-13 09:24:37 +0100

      Commit message:


	  
		
 Fixed ordering of index entries.
 
    
  
    

      Package: ChAMP

      Commit: a1e6cdc421cf74c6072dddf79d609617ecf3e422

      Author:  JoshuaTian <tianyuan1991hit@gmail.com> 

      Date: 2018-09-13 14:54:00 +0800

      Commit message:


	  
		
 Fixed bug in champ.CNA()
 
    
  
    

      Package: ChAMP

      Commit: be71ab8e85176526af2678ebb27bacda3ba4a179

      Author:  JoshuaTian <tianyuan1991hit@gmail.com> 

      Date: 2018-09-13 14:45:43 +0800

      Commit message:


	  
		
 Fixed bug in champ.CNA()
 
    
  
    

      Package: DelayedArray

      Commit: 625a795c6258c2ea91bccd38d4b2fedce12e3069

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2018-09-12 22:31:48 -0700

      Commit message:


	  
		
 Tweak to propagation of user-controlled global options to workers

Fail early and graciously if a worker fails to inherit DelayedArray
user-controlled global options (which will happen on a cluster where
the nodes don't have access to the tempdir() of the head).
 
    
  
    

      Package: plotGrouper

      Commit: 4eae95c5b7de8ef609f12a6a0fb247fc28d24735

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-12 19:49:45 -0700

      Commit message:


	  
		
 Merge pull request #69 from jdgagnon/develop

fix typo in DESCRIPTION 
    
  
    

      Package: plotGrouper

      Commit: a3ea9117f5ff934ed712ccf4cb7f1a469a56cf32

      Author:  jdgagnon <jgagnon@vpn-10-48-1-102.ucsf.edu> 

      Date: 2018-09-12 19:49:11 -0700

      Commit message:


	  
		
 fix typo in DESCRIPTION
 
    
  
    

      Package: plotGrouper

      Commit: 147ee1709c254d2a6774db1c234d0f5d243c216f

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-11 13:18:20 -0700

      Commit message:


	  
		
 Merge pull request #68 from jdgagnon/develop

Fix README 
    
  
    

      Package: plotGrouper

      Commit: 32b16fd13919232663d6e20fe71f10f21ee880ed

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-11 13:17:53 -0700

      Commit message:


	  
		
 Fix README
 
    
  
    

      Package: plotGrouper

      Commit: c03d8ca84a5bdb4509cce8539184f02238bebebb

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-11 12:46:20 -0700

      Commit message:


	  
		
 Merge pull request #67 from jdgagnon/develop

Update vignette/README & version bump 
    
  
    

      Package: plotGrouper

      Commit: cb4d0ee221d9186f69b1adb14fc0347eca480ea5

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-11 12:45:13 -0700

      Commit message:


	  
		
 Update vignette/README & version bump
 
    
  
    

      Package: plotGrouper

      Commit: f4cf5f3965ecc54b9557e7581429a97108a4da66

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-11 12:05:22 -0700

      Commit message:


	  
		
 Merge pull request #66 from jdgagnon/develop

Merge pull request #65 from jdgagnon/master 
    
  
    

      Package: plotGrouper

      Commit: 45ab87fa3d87664c67fc9d43613a1b1df17651f2

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-11 12:05:04 -0700

      Commit message:


	  
		
 Merge pull request #65 from jdgagnon/master

pull from master 
    
  
    

      Package: plotGrouper

      Commit: dd88ac87d833a29619bcfbfdfcc670af6361092c

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-11 12:03:48 -0700

      Commit message:


	  
		
 Update README
 
    
  
    

      Package: plotGrouper

      Commit: de6edf1f0c60d07a9fba29cf8a52ba0e65385d33

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-11 09:06:07 -0700

      Commit message:


	  
		
 Merge pull request #63 from jdgagnon/develop

Add build info from Bioconductor to README 
    
  
    

      Package: plotGrouper

      Commit: c9ced34d2eaf5351999cab4d409322759ddb5631

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-11 08:59:56 -0700

      Commit message:


	  
		
 Add build info from Bioconductor to README
 
    
  
    

      Package: plotGrouper

      Commit: 4e45a9c45b4965ebe8e2e7b5cbb7ff2e203e9374

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-10 21:01:28 -0700

      Commit message:


	  
		
 Merge pull request #62 from jdgagnon/develop

Develop 
    
  
    

      Package: plotGrouper

      Commit: 6d71b57099e7dba002a9289dd38a1af54e1e2771

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-10 21:00:55 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: plotGrouper

      Commit: 427bad547bb19f7e96278ce3cae2d38d5b7238be

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-10 20:59:26 -0700

      Commit message:


	  
		
 improve look of log transformations
 
    
  
    

      Package: plotGrouper

      Commit: e7b9eb30e670b0212723094370332ec2b5d7f49d

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-10 20:59:05 -0700

      Commit message:


	  
		
 Add bioconductor build info to README
 
    
  
    

      Package: plotGrouper

      Commit: d7cf2f0fe7e6e707ce019d3b15b3b231bd442895

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-10 10:40:34 -0700

      Commit message:


	  
		
 Merge pull request #61 from jdgagnon/develop

fix non-ascii quotes in readme file 
    
  
    

      Package: plotGrouper

      Commit: 55e16d536efe782ab9f63e0f78bad194c90aecf2

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-10 10:40:07 -0700

      Commit message:


	  
		
 fix non-ascii quotes in readme file
 
    
  
    

      Package: plotGrouper

      Commit: e16a7120dcf9057b7e926f038a1fd050843eedd1

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-09 21:53:04 -0700

      Commit message:


	  
		
 Merge pull request #60 from jdgagnon/develop

updated sessionInfo() 
    
  
    

      Package: plotGrouper

      Commit: b2dcb15414d230d135f6d03b0d55713840c7c244

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-09 21:48:10 -0700

      Commit message:


	  
		
 updated sessionInfo()
 
    
  
    

      Package: plotGrouper

      Commit: d7d7ad1df92951f286e5ea0a60e57f8ffe9907d4

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-09 12:55:55 -0700

      Commit message:


	  
		
 Merge pull request #59 from jdgagnon/develop

Version bump 
    
  
    

      Package: plotGrouper

      Commit: 118ca7fae2498edd5dd52fca84307da975e85a7a

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-09 12:55:24 -0700

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: plotGrouper

      Commit: 43ef35b55dc24ede9e78eed678fca7de00cec463

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-09 11:06:19 -0700

      Commit message:


	  
		
 Merge pull request #58 from jdgagnon/develop

Use png with transparency for GitHub page. 
    
  
    

      Package: plotGrouper

      Commit: 8c5cb47c414721b57c330133707b644e0e5877e2

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-09 11:04:53 -0700

      Commit message:


	  
		
 Use png with transparency for GitHub page.
 
    
  
    

      Package: plotGrouper

      Commit: 18a5c4ac5ea3fb5469bfff31fccf76c269c66e75

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-07 12:30:13 -0700

      Commit message:


	  
		
 Merge branch 'master' of https://github.com/jdgagnon/plotGrouper
 
    
  
    

      Package: plotGrouper

      Commit: 419fa7aee55943d6a65d9c4c306ed9803e49a188

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-07 12:29:54 -0700

      Commit message:


	  
		
 Cleanup master
 
    
  
    

      Package: plotGrouper

      Commit: acb7a3130c2b89e3e1b75fe0638b41ac3221cb4e

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-07 12:25:51 -0700

      Commit message:


	  
		
 Merge pull request #57 from jdgagnon/develop

allow Rproj on github 
    
  
    

      Package: plotGrouper

      Commit: 7185636f9d99ecb5cc7777b5ec86a9fb045d868b

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-07 12:24:01 -0700

      Commit message:


	  
		
 allow Rproj on github
 
    
  
    

      Package: plotGrouper

      Commit: d69bb2a75184372f31cf15184cdc4f9f534f87a0

      Author:  John Gagnon <john.gagnon.42@gmail.com> 

      Date: 2018-09-07 12:18:16 -0700

      Commit message:


	  
		
 Merge pull request #56 from jdgagnon/develop

Develop 
    
  
    

      Package: plotGrouper

      Commit: 2b9cff991ce0e070d6406d4cf08e00b825ab4dc1

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-07 12:17:50 -0700

      Commit message:


	  
		
 Fix README logo
 
    
  
    

      Package: plotGrouper

      Commit: 3dc28c091fbe85dc9fb14f4f6985266dea07fc95

      Author:  jdgagnon <jgagnon@Johns-MacBook-Pro-3.local> 

      Date: 2018-09-07 12:16:43 -0700

      Commit message:


	  
		
 Fix logo in readme
 
    
  
    

      Package: DelayedArray

      Commit: 31cc4290fdd72acd1d9de796cbda4df16b43211e

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2018-09-12 16:18:18 -0700

      Commit message:


	  
		
 Workers now inherit DelayedArray user-controlled global options

In the context of BiocParallel::bplapply() and family, workers now inherit
the user-controlled options defined on the master. Workers can also modify
the inherited options or define new user-controlled options but this does
not affect the options defined on the master (one-way communication).
This mechanism works with nested levels of parallelization i.e. if workers
start subworkers and so on.
 
    
  
    

      Package: flowWorkspace

      Commit: b5745306a5113db947071bc0afca9bab5d5e6dfe

      Author:  mikejiang <wjiang2@fhcrc.org> 

      Date: 2018-09-12 15:31:15 -0700

      Commit message:


	  
		
 Merge branch 'trunk' into devel
 
    
  
    

      Package: flowWorkspace

      Commit: ae7097d307dea6480182dbf3b5d1c372c87eb46f

      Author:  mikejiang <wjiang2@fhcrc.org> 

      Date: 2018-09-12 15:30:47 -0700

      Commit message:


	  
		
 bump
 
    
  
    

      Package: flowWorkspace

      Commit: 7a8527e8c34e601b5b5983df883ce5d781f15156

      Author:  mikejiang <wjiang2@fhcrc.org> 

      Date: 2018-09-12 15:10:50 -0700

      Commit message:


	  
		
 fix typo. #242
 
    
  
    

      Package: debrowser

      Commit: f5aa3b5442b360a6c3ce02c16e4fff4840a2931c

      Author:  Alper Kucukural <alper.kucukural@umassmed.edu> 

      Date: 2018-09-12 18:14:57 -0400

      Commit message:


	  
		
 Merge branch 'RELEASE_3_7'
 
    
  
    

      Package: debrowser

      Commit: b8da70c0a78104e950ff29e7914f25ac3ae81479

      Author:  Alper Kucukural <alper.kucukural@umassmed.edu> 

      Date: 2018-09-12 18:13:08 -0400

      Commit message:


	  
		
 Bug fixes
 
    
  
    

      Package: methylKit

      Commit: 77aa6c7acf9845c869fa60ce7b34b7252dd50113

      Author:  alexg9010 <alex.gos90@gmail.com> 

      Date: 2018-09-12 23:14:36 +0200

      Commit message:


	  
		
 update NEWS and version bump to 1.7.7
 
    
  
    

      Package: methylKit

      Commit: dcac7ee0d34a95bb0809b68cb3fdbb7f32770560

      Author:  alexg9010 <alex.gos90@gmail.com> 

      Date: 2018-07-17 17:53:41 +0200

      Commit message:


	  
		
 omit .checkTabixFileExists for destranding
 
    
  
    

      Package: methylKit

      Commit: aee5da5712746ccd88b914d042ded29c38276683

      Author:  alexg9010 <alex.gos90@gmail.com> 

      Date: 2018-06-18 10:54:16 +0200

      Commit message:


	  
		
 update NEWS and version bump
 
    
  
    

      Package: methylKit

      Commit: 46833e3e8abc352106c6841a21cab6cbff5e16ee

      Author:  alexg9010 <alex.gos90@gmail.com> 

      Date: 2018-06-18 10:35:15 +0200

      Commit message:


	  
		
 update documentation
 
    
  
    

      Package: methylKit

      Commit: 14fc0281054613abeee91258c958c926a49f6692

      Author:  Alexander Gosdschan <alexg9010@users.noreply.github.com> 

      Date: 2018-06-16 11:29:16 +0200

      Commit message:


	  
		
 Update methSeg.R

Remove duplicate check for sample size. 
    
  
    

      Package: methylKit

      Commit: 6a4dc7d3f336967d2f0ed5964a7efe94a09e1a25

      Author:  alexg9010 <alex.gos90@gmail.com> 

      Date: 2018-06-14 18:06:17 +0200

      Commit message:


	  
		
 Updates to @katwre pull request:
- changed parameter name from `estimate.params.density` to `initialize.on.subset`
- allow for values higher than 1, which directly yields number of samples
- priorize Mclust argument `initialization`
- check for to few samples, 9 seems to be the magic number
- add tests
 
    
  
    

      Package: methylKit

      Commit: d84a677f2e120e699affb5b38b4eb27d66544561

      Author:  Kasia Wreczycka <katarzyna.wreczycka@mdc-berlin.de> 

      Date: 2018-06-14 13:17:50 +0200

      Commit message:


	  
		
 fix previous commit
 
    
  
    

      Package: methylKit

      Commit: 17bfae99df33b9e9156c628b787bd96949dd4add

      Author:  Kasia Wreczycka <katarzyna.wreczycka@mdc-berlin.de> 

      Date: 2018-06-14 12:48:21 +0200

      Commit message:


	  
		
 remove if clause
 
    
  
    

      Package: methylKit

      Commit: d87f446e47c22800c7267d748312040b2ab9ef79

      Author:  Katarzyna Wreczycka <katwre@gmail.com> 

      Date: 2018-06-13 16:51:58 +0200

      Commit message:


	  
		
 added estimate.params.density param to methSeg
 
    
  
    

      Package: MultiAssayExperiment

      Commit: 1556af77e4c06abae42c8f8673be2b267c277e46

      Author:  LiNk-NY <mramos09@gmail.com> 

      Date: 2018-09-12 17:35:32 -0400

      Commit message:


	  
		
 update c method to allow MultiAssayExperiment concat, add tests
 
    
  
    

      Package: MultiAssayExperiment

      Commit: c9bbe7272ec1e51797752a887a513cc0210dc415

      Author:  LiNk-NY <mramos09@gmail.com> 

      Date: 2018-09-12 17:34:35 -0400

      Commit message:


	  
		
 bug fix: use a named vector when merging replicates
 
    
  
    

      Package: MultiAssayExperiment

      Commit: 536db3c7c2ea89f7a3e85f1352e623546f2081b3

      Author:  LiNk-NY <mramos09@gmail.com> 

      Date: 2018-09-12 17:33:19 -0400

      Commit message:


	  
		
 update format, remove unchanged metadata from replaceSlots
 
    
  
    

      Package: MultiAssayExperiment

      Commit: 7f32e967bf7a293ebbdeb931daba59b5207a968a

      Author:  LiNk-NY <mramos09@gmail.com> 

      Date: 2018-09-10 20:51:36 -0400

      Commit message:


	  
		
 update wercker.yml file again
 
    
  
    

      Package: MultiAssayExperiment

      Commit: f2c7aa86413d5a84919eb2c5eb5c46b44505c7e6

      Author:  LiNk-NY <mramos09@gmail.com> 

      Date: 2018-09-10 20:46:04 -0400

      Commit message:


	  
		
 update wercker.yml file
 
    
  
    

      Package: MultiAssayExperiment

      Commit: 94eee7859da597ddb7cb6faf5aac0c4ad61591a1

      Author:  LiNk-NY <mramos09@gmail.com> 

      Date: 2018-09-10 18:06:35 -0400

      Commit message:


	  
		
 Merge branch 'master' of github.com:waldronlab/MultiAssayExperiment
 
    
  
    

      Package: MultiAssayExperiment

      Commit: cdd69545bab74c36dd2488089af9d6f57cc570f0

      Author:  LiNk-NY <mramos09@gmail.com> 

      Date: 2018-09-10 18:05:52 -0400

      Commit message:


	  
		
 bug fix: avoid Inf by using min on TRUEs, closes #249
 
    
  
    

      Package: ORFik

      Commit: e762b10e58746f210d9bb10340c068646c1a0e89

      Author:  Kornel Labun <kornellabun@gmail.com> 

      Date: 2018-09-12 18:50:29 +0200

      Commit message:


	  
		
 Merge pull request #55 from JokingHero/orfScannerUpdate2

Orf scanner update2 
    
  
    

      Package: ORFik

      Commit: 45f1f13e9f334887eef3c1bc4ca1d56bdd540034

      Author:  Kornel Labun <kornellabun@gmail.com> 

      Date: 2018-09-12 18:50:11 +0200

      Commit message:


	  
		
 Fix description 
    
  
    

      Package: ORFik

      Commit: 05d68446822b350d98d8c773501a2f276b6a36a9

      Author:  Roleren <hauken_heyken@hotmail.com> 

      Date: 2018-09-12 18:30:17 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: ORFik

      Commit: 9b7468152f699c24d61bb3f23a806c034bfe1385

      Author:  Roleren <hauken_heyken@hotmail.com> 

      Date: 2018-09-12 18:26:10 +0200

      Commit message:


	  
		
 added more docs, some logic fixup on orfScanner
 
    
  
    

      Package: DelayedArray

      Commit: e4534a7c0ffdc5d738958b706b6617d0f7859c6a

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2018-09-12 08:39:19 -0700

      Commit message:


	  
		
 Add TODO for "is_sparse" method for DelayedUnaryIsoOpWithArgs objects
 
    
  
    

      Package: DMRcaller

      Commit: 0744d4ec2d136df04a873b0fcbf07f9282c8946c

      Author:  nrzabet <n.r.zabet@gen.cam.ac.uk> 

      Date: 2018-09-12 15:39:05 +0100

      Commit message:


	  
		
 bug fix
 
    
  
    

      Package: DMRcaller

      Commit: e6585817fc7493fc7c95c0a99a6ee2593dcc843c

      Author:  nrzabet <n.r.zabet@gen.cam.ac.uk> 

      Date: 2018-09-12 15:36:17 +0100

      Commit message:


	  
		
 bug fix
 
    
  
  


</div>

</div>