Adding imports
 

 Add proteinId slot for peptide datasets
 

 Updates for BiocManager

  - syntax ERROR
 

 version bump
 

 update of the documentation and change of the NEWS file
 

 some code formatting
 

 Minor bugfix allowing empty annotation without crash in output
 

 Minor fix where function wasn't properly used. Update tests to do global run of SummarizedExperiment
 

 Crash for SummarizedExperiment as argument fixed and full NA rows automatically filtered out with a warning
 

 Correct vapply validation check for correlation counts calculated among groups
 

 Minor bugfix where slice index selection in RT range widened ended up with one-off index
 

 major commit including small bugfixes, code refactoring and performance improvements
 

 update of the maintainer
 

 - SVM can now calculate a score which can be used for ROC plots.
- Handling of training indices for data transformation fixed.
- Added missing mean function to subtractFromLocation code.
- featureSetSummary slot access bug eliminated.
 

 Add DelayedSubassign class for representing delayed subassignments

This brings the number of concrete DelayedOp subclasses to 8.
The DelayedOp class hierarchy now is:

  Node type                        Represented operation
  ------------------------------------------------------------------
  DelayedOp (VIRTUAL)
  ------------------------------------------------------------------
  * DelayedUnaryOp (VIRTUAL)
    o DelayedSubset                Multi-dimensional single bracket
                                   subsetting.
    o DelayedAperm                 Extended aperm() (can drop and/or
                                   add ineffective dimensions).
    o DelayedUnaryIsoOp (VIRTUAL)  Unary op that preserves the
                                   geometry.
      - DelayedUnaryIsoOpStack     Simple ops stacked together.
      - DelayedUnaryIsoOpWithArgs  One op with vector-like arguments
                                   along the dimensions of the input.
      - DelayedSubassign           Multi-dimensional single bracket
                                   subassignment.
      - DelayedDimnames            Set/replace the dimnames.
  ------------------------------------------------------------------
  * DelayedNaryOp (VIRTUAL)
    o DelayedNaryIsoOp             N-ary op that preserves the
                                   geometry.
    o DelayedAbind                 abind()
  ------------------------------------------------------------------
 

 consensus_0.99.17
 

 consensus_0.99.15
 

 citation_and_sticker
 

 Added missing arguments to \usage statements. Removed missing \links from \item descriptions.
 

 optimization in 2-bit array decoding
 

 Package deprecation
 

 Package deprecation
 

 Fixed import issue
 

 Updated .Rbuildignore
Replaced data.table with readr
Removed incomplete functions
Added examples
Added importFrom statements
Updated reading for PCV10; with an attempt to be backwards compatible
Updated getPcDatabasesNames for recent file name changes
Added additional headers to deal with PC API issues: XML vs JSON return
Switched to query parameter for PC API calls with httr rather than URL creation
Removed skip_on_bioc since now in testthat
Expanded pcFormats
Expanded checkInputFile with additional checks
Updated pathways.txt.gz example file
 

 Merge branch 'master' of https://github.com/cannin/paxtoolsr
 

 Moved results creation for large files so that the code can find nodes
 

 Added convertToDataFrameWithListOfVectors (opposite also included)
Removed default version in downloadPc2 (current no longer works)
Deleted idMapping since it was removed (also from vignette)
Added readSifnxSmall for small SIFNX
 

 Merge branch 'master' of https://github.com/cannin/paxtoolsr
 

 Added readCombinedSifnxFile
 

 Updated Travis CI
 

 Updated Travis CI
 

 Added additional commands
Added hack for downloadSignedPc since GitHub does not support LAST-MODIFIED
Added additional parameter to filterSif
 

 Merge branch 'master' of https://github.com/cannin/paxtoolsr

* 'master' of https://github.com/cannin/paxtoolsr:
  Update README.md
  Update README.md
 

 Update README.md 

 Fixed bug in readPcPathwaysInfo()
 

 Updated documentation
Fixed variable name bug
 

 Merge branch 'master' of https://github.com/cannin/paxtoolsr

* 'master' of https://github.com/cannin/paxtoolsr:
  Added getPcDatabaseNames Added more options to filterSif Updated SignedPC URL Added default option to toGSEA Updated how URLs are generated in topPathways

# Conflicts:
#	DESCRIPTION
#	R/filterSif.R
#	man/filterSif.Rd
 

 Added getPcDatabaseNames
Added more options to filterSif
Updated SignedPC URL
Added default option to toGSEA
Updated how URLs are generated in topPathways
 

 Update README.md 

 Updated version and test
 

 Moved tests to tests/testthat
Minor documentation changes
 

 Updated documentation
 

 Fixed bug with filterSif edgelist
 

 Added the ability to filter by edgelist
Added getShortestPathSif
Added parameter for getting directed igraph network
 

 Fixed bug in graphPc call
 

 Changed DESCRIPTION
 

 Update README.md 

 Minor
 

 Changed .Rbuildignore
 

 Updated .travis.yml
 

 Updated README
 

 Added .travis.yml
 

 Changed CITATION
Added verbose flag to download functions
Fixed bug for downloading files outside of cache
Added function for downloading signed PC
 

 Merge branch 'devel'

* devel: (35 commits)
  Updated DESCRIPTION and documentation
  Hide warnings caused by http progress() Added support for PC2 archives Minor documentation changes
  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
  Changed .gitignore
  Re-did documentation
  Change R dependency Added documentation to skip_on_bioc()
  Comment out entire fromPsimi test
  Commented out fromPsimi test, testthat skip() does not work with Jenkins
  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
  Added updates to several functions
  Updated DESCRIPTION
  Added convertSifToSpia.R file Updated documentation
  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
  Split functions
  Commented skipped tests
  Use file.info rather than file.size
  Minor
  Minor
  Minor
  ...

# Conflicts:
#	DESCRIPTION
#	R/pathwayCommons.R
#	R/paxtools.R
#	man/downloadPc.Rd
#	man/getPc.Rd
#	man/graphPc.Rd
#	man/idMapping.Rd
#	man/searchPc.Rd
#	man/topPathways.Rd
#	man/traverse.Rd
 

 Hide warnings caused by http progress()
Added support for PC2 archives
Minor documentation changes
 

 Merge branch 'devel' of https://bitbucket.org/cbio_mskcc/paxtoolsr into devel
 

 Changed .gitignore
 

 Change R dependency
Added documentation to skip_on_bioc()
 

 Commented out fromPsimi test, testthat skip() does not work with Jenkins
 

 Added updates to several functions
 

 Added convertSifToSpia.R file
Updated documentation
 

 README.md edited online with Bitbucket 

 README.md edited online with Bitbucket 

 README.md edited online with Bitbucket 

 Split functions
 

 Use file.info rather than file.size
 

 Minor
 

 Minor
 

 Updated documentation
Attempt to make sure file.size() from base can be found
 

 Changed readSifnx
Added readSifnx tests
 

 Changed DESCRIPTION
 

 Added colClasses to fread
 

 Minor
 

 Added tests
Remove NAs from search data.frame
Added check to not overwrite cache map
Added split SIF by pathway function
 

 Changes from paxtooolsr 1.1.11 Bioconductor changes
 

 Updated version
Added examples
Added test stubs
Refactored reading formatted responses
Added utils functions
 

 Updated NEWS
 

 Added new dependencies for reading faster
Added additional functions to simplify dealing with content
Added caching of downloads
 

 Updated NEWS
 

 Changed DESCRIPTION, description section
 

 Changed DESCRIPTION Minor
 

 Minor DESCRIPTION change
 

 README.md edited online with Bitbucket

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@99286 bc3139a8-67e5-0310-9ffc-ced21a209358
 

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 Merge branch 'work'

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 Change DESCRIPTION

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 Changed DESCRIPTION

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@99218 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Updated to paxtools 4.3
Added better Java error messages
Added the ability to switch PC versions
Updated to PC version 6

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@97662 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Added CITATION file

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@96214 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Increment version number

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@96040 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Bumping versions after creating 3.0 release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@95443 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Adds GenomicInteractions/ PSEA/ ALDEx2/ polyester/ MSGFplus/ derfinder/ derfinderPlot/ derfinderHelper/ regionReport/ FEM/ MSGFgui/ IdeoViz/ proBAMr/ ASGSCA/ PAA/ paxtoolsr/ flowcatchR/ to the repos.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/paxtoolsr@94975 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 v1.7.6 -- 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
 

 v1.15.3 -- 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
 

 improving robustness of HmdbEntry, which failed if underlying XML model is modified; now more predictions are in place, and a failover to returning a list is present
 

 setting github in sync with bioc
Merge remote-tracking branch 'upstream/master'
 

 testing merge
 

 Deprecated classes and methods in BioC 3.7 have now become defunct in BioC 3.8.
 

 - ClassifyResult object now store the trained classifiers. They may be reused in a future classification task using the function named previousTrained.
 

 New code for aggregation
 

 New code for aggregation
 

 modify usermanual
 

 New code for aggregation
 

 Continue Win32 debugging efforts on cyclone optimizations.
 

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

 Allow use of number of SNNs directly as the edge weight.
 

 * edgeR 3.23.4
- Bug fix to column name returned by decideTestsDGE().
- Improved error messages from DGEList().
- Note added to readBismark2DGE() help page.
- Edit to readBismark2DGE code (not user-visible).
 

 Fixed PCA plot tooltips show incorrect values with ComBat and SVA
 

 Reduce memory usage when realizing a sparse DelayedArray to disk

On-disk realization of a DelayedArray object that is reported to be sparse
(by is_sparse()) to a "sparsity-optimized" backend (i.e. to a backend with
a memory efficient write_sparse_block() like the TENxMatrix backend imple-
mented in the HDF5Array package) now preserves sparse representation of the
data all the way. More precisely, each block of data is now kept in a sparse
form during the 3 steps that it goes thru: read from seed, realize in
memory, and write to disk.
 

 Updated Description
 

 Added survivalFS functions
 

 Add files via upload 

 Enhance DelayedArray dim() setter

In addition to allowing dropping "ineffective dimensions" (i.e.
dimensions equal to 1) from a DelayedArray object, the dim()
setter now allows adding "ineffective dimensions" to it.
 

 attempt to clarify
 

 version bump and updated NEWS file
 

 test annotations in the absence of package
 

 fixed annotateEntrez with correct usage of the parameter
 

 more tests: brush, lasso, custom, empty colData
 

 point out a test that requires a working internet connection
 

 cover a bit more of codetrack
 

 typo
 

 add ::: to internal function calls in tests
 

 updated the README
 

 Clarified documentation for Top in combineMarkers.
 

 fix
 

 version bump
 

 fix clinical
 

 bug fix
 

 Add comment
 

 Enhance "aperm" method for DelayedArray objects

In addition to allowing dropping some of the "ineffective dimensions"
(i.e. dimensions equal to 1) from a DelayedArray object, aperm() now
allows adding "ineffective dimensions" to it.
 

 version bump
 

 updatin compendium with new dataset (without Red flagged samples)
 

 Merge branch 'master' into RELEASE_3_7

 

 Merge branch 'RELEASE_3_7'

 

 remove .Rproj.user from github
 

 Delete unnamed-chunk-5_af1f59610059ae069f8dc9e8fd46c527.rdx 

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 Delete __packages 

 Delete unnamed-chunk-7-1.pdf 

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 Delete .Rhistory 

 Delete powerTCR.fls 

 Delete powerTCR.tex 

 add parallelization imports
 

 remove vignette cache
 

 version bump
 

 version bump
 

 version bump
 

 Merge branch 'master' into RELEASE_3_7

 

 Merge branch 'master' of https://github.com/PoisonAlien/maftools
 

 Update LICENSE 

 Added vignette on Mus musculus
 

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

 update news with url
 

 new gh devel version
 

 Fixed a bug with zoom with extra seqlevels

 

 Update DEsingle.R 

 Update NEWS 

 Update DEsingle.R 

 Clarified documentation for design= in pairwiseTTests.
 

 verion bump
 

 no docs on bioc
 

 update docs
 

 update news
 

 update site with latest version
 

 missed a few
 

 vectorise reduce --- should speed up base case
 

 update stretch per comments in #49
 

 rename
 

 ungroup signature fix
 

 update docs
 

 update appveyor
 

 symlink NEWS.md for pkgdown
 

 fixes #42
 

 Another warning removed
 

 Changed buffer sizes to remove warnings
 

 Changed the scalling factor in index-builder to better suite the new index structure
 

 Updating CITATION
 

 update metadata.csv
 

 minor clean-up

- whitespace
- use more precise terminology to describe HDF5 & dense matrix
 

 Updated docs to describe TENxBrainData20k.
 

 Updated metadata maker to include 20k subset.
 

 update the version number.
 

 fix a issue of circle type in lollipop plot (pdf is different from png version)
 

 edit ignore
 

 fix heatmap plot
 

 Fixing the cluster within groups for heatmap
 

 Update NEWS
 

 Move from NEWS to NEWS.md
 

 Reduce complexity
 

 Improve efficiency of code in vignettes
 

 First the development badges then the Bioconductor badges
 

 Update notifications of appveyor
 

 Increment version number 

 Update README with an example
 

 Use covrpage for reporting tests
 

 Check spelling
 

 Update documentation
 

 Merge branch 'master' of github.com:llrs/BioCor
 

 Update test

  - output column removed
 

 drug-gene interactions
 

 minor fix
 

 Update of importCufflinksFiles
 

 Remove deprecated args from read.bismark
 

 20 Sep 2018: limma 3.37.6

- Bug fix for cumOverlap(), which was under-counting overlaps in some
  cases. cumOverlap() now uses Holm's method for p-value adjustment
  and computes an overall p-values by Simes method.
 

 Complete merge

Merge branch 'master' of github.com:grimbough/rhdf5

# Conflicts:
#	DESCRIPTION
 

 Registration of S3 methods
 

 Version bump
 

 Swap malloc for R_alloc
 

 Merge changes in master branch

Merge branch 'master' into write-64bit

# Conflicts:
#	R/h5write.R
 

 Fixed the issue of not quiting when the annotation format is wrong
 

 Also make unlist() fail more graciously on an IRanges object
 

 Chanegd some return values from align() and subjunc()

Hope to be last commit before copying code to RELEASE_3_7
 

 version bump 0.99.7
 

 updated inst/extdata