Bumped z version. Updated date.
 

 Removed unnecessary "require" calls.
 

 Package deprecation
 

 Package Deprecation
 

 Package deprecation
 

 Merge remote-tracking branch 'upstream/master'

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#	R/addAttributeList.R
#	R/checkInputFile.R
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#	R/convertSifToSpia.R
#	R/convertSifnxIds.R
#	R/convertToDF.R
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 Added sub-pathway names to readPcPathwaysInfo
Renamed pathways.txt.gz
Changed documentation to force version information in downloadPc2
 

 toCytoscape added
 

 Minor
 

 Update .travis.yml 

 Updated Travis CI
 

 Fixed bug in reading 1 entry GMT files
Minor documentation fixes
 

 Added parameter to toSifnx
Fixed bugs that repeats pathway names in splitSifnxByPathway and loads unnecessary packages
Added function to split SIF into GMT
 

 Changed default behavor of filterSif ids to only include IDs asked for
 

 Update README.md 

 Added argument passing to read* functions in getPc
Fixed bug with empty genesets in readGmt
Merge multiple pathway info tables into one
 

 Added feature to pass additional parameters to read* functions
 

 Added convertIds
Fixed issue with mediatorIds in filterSif
Added removePrefix and returnDetailed to readGmt
Added function to read PC pathway information
 

 Added tests
Added checks for file existence on read* functions
Added error checks and verbose flag to getShortestPathSif
 

 Update README.md 

 Update README.md 

 Fixed bug to use make use of archives for all downloads
 

 Minor
 

 Fixed issue in filterSif only looking in one direction for edgelist
 

 Fixed bug to add in MEDIATOR_IDS column in convertToDT
Fixed test
 

 Expanded convertToDT
Added additional filtering mechanisms to filterSif
Expanded loadSifInIgraph
Added addAttributeList
Added getShortestPathSif
Added small sinful example
 

 Added README with location of paxtools Java sources
Added description of cache folder
 

 Revert
 

 Updated .travis.yml
 

 Added codecov badge
 

 Updated README
 

 Updated README
 

 Updated code related to file downloads
 

 Removed old files
 

 Updated DESCRIPTION and documentation
 

 Fixed bug in searchListOfVectors for queries with one element
 

 Added graphPc single gene example
Fixed multiple datasets in graphPc
Switched to using PC_URL system variable
 

 Re-did documentation
 

 Comment out entire fromPsimi test
 

 Updated to Paxtools 4.3.1
Added several tests
Updated toSifnx and removed fromPsimi due to changes in Paxtools 4.3.1
Changed to* methods to make use of read* methods
Switched back to using pathwaycommons.org URL
Fixed bug in searchListOfVectors
Added new package require checks for parallelized pathway splitter
Vignette update
 

 Updated DESCRIPTION
 

 Added helper functions, including: convertSifIds, convertToDT, covertToPathwayList, extractIds, filterSif, getCacheFiles, getSifInteractionCategories, loadSifInIgraph, mapValues, readGmt, searchListOfVectors.
Separated several functions from the combined utils.R file
Fixed errors in documentation for graphPc and pcGraphQueries
 

 README.md edited online with Bitbucket 

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 Commented skipped tests
 

 Minor
 

 Minor
 

 Minor
 

 Removed unused argument
 

 Added skip_on_bioc
Updated documentation
 

 Added colClasses to fread
 

 Major updates
 

 Changed fetch example to use package data
 

 Added second SIFNX
Added tests
 

 Updated documentation
 

 Merge branch 'master' into devel

* master:
  Updated NEWS
  Changed vignette to use quicker examples Changed DESCRIPTION
 

 Changed vignette to use quicker examples
Changed DESCRIPTION
 

 Updated documentation
 

 Removed PC dependent tests for paxtools functions
Added skip_on_bioc()
Updated vignette to use glycolysis pathway that can be converted to gene set
Added fill=TRUE to read.table commands in paxtools.R
 

 Change DESCRIPTION, Description entry
 

 Updated DESCRIPTION
 

 Minor changes

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 Changed NEWS

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 Added Rstudio files

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 Fixed topPathways() bug 
Fixed fetch() example/test
Changed title

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 Use BiocStyle on vignette

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 Transitioned to Pathway Commons Version 5 (PC2 v5)
Changed downloadPc to download from PC2 v5
Changed code to validate Pathway Commons webservice requests 
Added table of contents to vignette 
Added description for traverse() in vignette
Changed R dependency to 3.1.1 to match Bioconductor 3
Added function to download a single file extended SIF, splitSifnx
Added the ability to download GMT in downloadPc
Added function to read GMT files 
Added tests for new functions

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 Bump package versions prior to creating the 3.0 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@95439 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 v1.3.3 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 

 v1.15.5 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 

 v1.15.2 -- change from devtools::session_info() to sessioninfo::session_info() as requested by Jim Hester now that https://github.com/r-lib/sessioninfo/issues/14 has been resolved
 

 Small update to fix 1.3.8 - see NEWS
 

 testing version bump
 

 Merge pull request #2 from vjcitn/newvincelocal

Newvincelocal 

 Update for aggregation
 

 fixed code for when maxK is high
 

 Updated citation of the package.
 

 test
 

 Update Export file tools
 

 modify usermanual
 

 adjusting R version and version bump
 

 Bumped version, date; updated NEWS.
 

 Updated docs and tests for new 'type=' in buildSNNGraph.
 

 Minor edits to combineMarkers Top explanation. 

 Fixed date
 

 Add TENxMatrix to list of supported realization backends
 

 Corrected DESCRIPTION
 

 Just version update
 

 Merge remote-tracking branch 'origin/master'

# Conflicts:
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 version bump; site rebuild
 

 Merge pull request #236 from csoneson/testthat

Test coverage and minor updates. Version 1.1.8 

 typo
 

 test table links when certain settings are not initialised yet
 

 .regenerate_unselected_plot independent of session
 

 test if transmitted selection are detected
 

 complete testing of ECM; move ECM code to appropriate file; move generics definition to new AllGenerics
 

 full coverage of codetrack
 

 fully cover plotting.R
 

 test heatmap code
 

 bold panel types and add custom panels
 

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

 fix
 

 fix merge
 

 fix clinical
 

 update fulviu affiliation
 

 oops, misplaced parenthesis
 

 Small code reorg
 

 increment R and version bump
 

 updating RF-models with the models trained without red flagged smples
 

 version bump
 

 Merge remote-tracking branch 'upstream/master' into RELEASE_3_7

 

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 update get_bootstraps man file to comply with build
 

 remove superfluous files in vignettes/ to fix build error
 

 remove cache from vignette
 

 version bump
 

 version bump
 

 update remotes
 

 fix for unlisting
 

 oncogenic pathways
 

 Added zebrafish
 

 update denependency
 

 remove docs
 

 Fix unit tests (issue #360)
 

 version bump on maintainer request
 

 Update README.md 

 Update DESCRIPTION 

 Update DEtype.R 

 Bumped version number, date.
 

 Reverted cyclone C++ code back to last working version.
 

 updating vignette
 

 update docs
 

 merge master
 

 Fix wrong MS OBO terms for smoothing and baseline correction

- Fix wrong MS OBO CV terms for data smoothing (MS:1000592) and baseline
  correction (MS:1000593).
 

 better name
 

 updates rlang exports; closes #50
 

 new `n_distinct()` function
 

 rename
 

 bring back bedtools tutorial
 

 groups/group_vars/ungroup per notes in #32
 

 build machine wants stuff
 

 update news
 

 Merge branch 'master' of https://github.com/sa-lee/plyranges
 

 Change the warning message in subread, subjunc and featureCounts() when the annotation file has format issues.
 

 Removed many warning messages from gcc 8.1
 

 Changed data type in sprintf to remove warnings
 

 Updating dev version number
 

 Fix for default value of useLegacy parameter
 

 Merge branch 'with_20k'

- Thanks to Aaron Lun
- closes #5
 

 Bumped version number, date, rebuilt NAMESPACE.
 

 Added TENxBrainData20k with generalized SCE creation code.
Roxygenated imports/exports.
 

 Added make-data code for 20K subset.
Updated make-data.R, avoid use of TENxGenomics class.
 

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

 version bump 0.99.5
 

 update dependencies
 

 Merge branch 'master' of https://github.com/tiagochst/ELMER
 

 Add a bullet to the news
 

 Simplify the combineScores* functions
 

 Increment version number 

 Improve wording
 

 Improve the documentation
 

 Add a section about GeneOverlap
 

 Update README installation names

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

# Conflicts:
#	DESCRIPTION
#	README.md
 

 Expose my .Rprofile
 

 Normalize the description
 

 Correct spelling mistakes
 

 Appveyor only on changes
 

 Update also the README for BiocManager
 

 Remove Maintainer and Author role 

 version-bump
 

 address #186
 

 Update to the version 1.9.3
 

 Package Deprecation
 

 20 Sep 2018: limma 3.37.7

- Reverting the p-value adjustment in cumOverlap() back to the
  original directed Bonferroni method, because it is more powerful
  when the number of Ids contributing to the significant overlap is
  small.
 

 consensus_0.99.17
 

 Fix test that fails only on Windows
 

 Improved handling of 64bit integers (#24)

- Provides the option to write R-doubles as 64-bit integers in `h5create()` & `h5write()`
- No longer converts short ints and signed 32-bit ints when using `h5read()` and `bit64conversion = "double|bit64` - these stay as native R-integers.
- Fixed bug that would try to use `integer64` when `bit64conversion = "int"`
 

 Remove print statement
 

 Try to improve clarity for handling 64-bit integers
 

 First tests with writing 64-bit integers
 

 Make [[, as.list(), lapply(), and unlist() fail more graciously
on a GenomicRanges object
 

 Changed visualization for methylation distribution visualization
 

 Use NA instead of NULL for missing genome builds
 

 added phenoage and skin and blood age
 

 Merge remote-tracking branch 'upstream/master'
 

 update to the new EH snapshot at 2018-09-19
 

 Don't import all of data.table
 

 Warn against intercept in design=.
 

 Reverted cyclone optimizations to pass CHECK for Win32.
 

 Removed unnecessary utility functions.
 

 update news and pkgdown site
 

 remove old installR4P.R script
 

 Merge branch 'master' of git.bioconductor.org:packages/RforProteomics into devel
 

 fix rmd typo
 

 add mention of biocpkgs::contribs in footnote - see https://github.com/lgatto/biocpkgs/issues/2
 

 version number fixed
 

 Vignette update
 

 vignette fixed
 

 MissingDataMap included
 

 missing value treatment added
 

 v 1.1.4 vignette fix
 

 Updated cluster checks for new findMarkers output.
 

 Fixed conflicts in version change