From Version 1.3.3 to Version 1.3.4
 

 updated image data ebicat37 and abicat38 to data ebicat_37 and ebicat_38
 

 v bump 1.9.5
bugfix for strand sensity bam fetch overlapping stranded qgr
added error if qgr id duplicated.
 

 Merge pull request #22 from LTLA/master

Added draft of random matrix methods for choosing PCs. 

 Slightly more correct Gavish-Donoho implementation.
Added effective limit on variance to attributes.
 

 Version bump - 2.15.2, fixed double name
 

 rerendered docs - last time local
 

 removing circleCI continuous integration
 

 Merge branch 'master' into devel
 

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 

 Make ggsave work for ggcyto_GatingLayout objects
 

 Update README.md 

 update issue template
 

 Merge branch 'master' of https://github.com/RGLab/openCyto
 

 Update README.md 

 update bug report template
 

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 

 Merge branch 'master' into devel
 

 add optional 'tmp' argument to convert_legacy_gs to customize the working dir during converting when the default system temp is full
 

 Update README.md 

 Merge branch 'master' of github.com:RGLab/flowWorkspace
 

 Merge branch 'master' of github.com:RGLab/flowWorkspace
 

 add test case for RGLab/cytolib#36
 

 Merge pull request #190 from itskathylam/patch-1

Update README.md 

 Update README.md 

"trunk" branch no longer exists; provide an example of using a commit SHA 

 #189: Make rectangleGate upper bounds inclusive, matching flowWorkspace behavior
 

 update test case. #187
 

 bump the computed(from data) range value for the missing PnR keywords. #187
 

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 

 Fix author
 

 Update README.md 

 update issue template
 

 bump
 

 Update LICENSE 

 add option skip_faulty_node to gating
 

 add recursive version of removeNode()
 

 merge
 

 simplify installation
 

 not sure
 

 Fix error in dorothea confidence levels parameter

Fix error with dorothea confidence levels parameter
 

 restore
 

 Ignore DimPlot add-ons meant for discrete data when data is numeric

Add tests that check if these are ignored when needed.

Also updates the `.msg_ifV()` internal function to simply `.msg_if()`, and moves it to 'utils.R'
 

 Updated `importDemux()` documentation

Reorganized the details & multi-lane sections to hopefully make the documentaation clearer and easier to follow.
 

 Fixed bug caused by a change in gwascat.
 

 Include warnings for deprecated functions
 

 Website
 

 swap_undirected: keep also the original orientation of undirected interactions
 

 import_intercell_network: docs updated
 

 merge conflicts resolved
 

 vignettes: updated some details, build successful
 

 replaced nsources, nrefs in print_interacions
 

 import_intercell_network seems to work
 

 updated version
 

 count_resources/references methods
 

 updated import_intercell_network drafted
 

 option to remove resource labels from references
 

 option to provide arguments for omnipath_download
 

 import intercell adjusted to new intercell data and new import_omnipath
 

 filter_by_resource added to cache loading routine
 

 import...interactions methods finished
 

 renamed arguments updated in docstrings; default fields
 

 query_string reference extended
 

 Signor -> SIGNOR in examples
 

 refactoring download methods, vol 3
 

 refactoring download methods, vol 1
 

 new function: get_resources -- gonna replace all `get_..._databases` functions
 

 cosmetic changes on function headers
 

 Revert "website"

This reverts commit 6fc327d2e7e36376d687bad2d81cc61b3f2b9636.
 

 website
 

 use roxygen2 to generate the help file.
move multiple package from Imports to Suggests.
 

 1.18.3
 

 droplevels
 

 lift over the snpchip 6.0 coordinates for compatibility with gwascat
 

 add dims for sparse and CFA=scaledTPM
 

 update doc
 

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

 fix URL
 

 Vignette update
 

 Version bump to match upstream
 

 Merge branch 'RELEASE_3_11' of git.bioconductor.org:packages/CellBench
 

 minor edit
 

 bump IRanges version requirement
 

 coverage() now supports 'method="naive"'

This is in addition to the already supported methods "sort" and "hash".
This new method is a slower version of the "hash" method that has the
advantage of avoiding floating point artefacts in the no-coverage regions
of the numeric-Rle object returned by coverage() when the weights are
supplied as a numeric vector of type 'double'.
 

 coverage() methods now supports 'method="naive"'

This is in addition to the already supported methods "sort" and "hash".
This new method is a slower version of the "hash" method that has the
advantage of avoiding floating point artefacts in the no-coverage regions
of the numeric-Rle object returned by coverage() when the weights are
supplied as a numeric vector of type 'double'.
 

 Bumped version and date.
 

 bug fix: issue with rownames on tibble for oncoPrint plots
 

 cnvEQTL: support window=NULL for genome-wide testing
 

 From Version 1.3.1 to Version 1.3.2
 

 update doc
 

 From Version 1.2.4 to Version 1.2.6
 

 Fixed bugs due to dplyr 1.0.0 breaking changes.
 

 update vignettes
 

 fixed roxygen doc for data
 

 Updated NEWS
 

 Merge branch 'RELEASE_3_11' into develop
 

 added referece to the paper
 

 update doc
 

 added setSeed param for reproducible research
 

 update doc
 

 From version 1.1.13 to Version 1.1.14
 

 From Version 1.1.12 to Version 1.1.13
 

 From Version 1.1.11 o Version 1.1.12
 

 From Version 1.1.10 to Version 1.1.11
 

 From Vesrion 1.1.9 to Version 1.1.10
 

 From Version 1.1.8 to Version 1.1.9
 

 Version1.1.7 to Version 1.1.8
 

 updated vignettes
 

 updated vignettes
 

 Version 1.1.5 to Version 1.1.6
 

 Updated getPlots function. Also motifs found in the background sequences are  now reported in the output.
 

 Version 1.1.3 to Version 1.1.4
 

 Version 1.1.2 to Version 1.1.3
 

 updated vignettes
 

 updated man doc
 

  In plotMotifs function:
To avoid infinity as a value for fold change, 1 was added to number of occurences
of each motif found in the foreground and background target sequences before
the normalization.
 Added angle param for the rotation angle of the axis labels.
 Added removeNegLog2FC param to remove the RBPs having a negative log2FC.
 In volcanoPlot function:
Added geneSet param that allows to show only specified host gene names.
 

 Version: 1.1.0 to Version: 1.1.1
 

  Version: 0.99.13 to Version: 0.99.14
 

 Bug fixes to tests

- Due to the new version of GO.db, tests were failing
- Now all tests pass
 

 Update: Merged package still passes BiocCheck
 

 Update: Expanded CoreGx vignette, as per reviewers request
 

 bugfix for file_paths and file_attribs error if data.table
v bump 1.9.3
 

 1.9.2 v bump for build
 

 addressed seq over 1:N NOTE.
 

 un R_REMOTES_NO_ERROS_FROM_WARNINGS
 

 bug fix pathway name doens't exist anymore
 

 New Version
 

 New Version
 

 w	modified:   ../DESCRIPTION
 

 My informative commit message describing the change
 

 Delete DoFEMbi.R 

 consistent deltaPsi calculation; update of NEWS
 

 fixed remaining pajd typos
 

 option to exclude non standard chr also from existing count cache
 

 fixed typo in padjVals
 

 check for empty split read object
 

 Merge remote-tracking branch 'bioconductor/master'
 

 minor fix
 

 bug fix: correct strandSpecific counting
 

 Re-export scuttle utilities to ensure scater:: still works.
 

 Renamed quickPerCell subset.fields= to avoid subset= clash.
Bugfix to deprecated pseudo-count argument.
 

 Added n_region_splits to ssvFetchSignal and implemented
 

 fix spelling error
 

 travis dep libgsl-dev
 

 Another attempt to fix links in Rd files to quieten R CMD check on Windows

- According to Martin, this is the 'simplest solution', which lets the help system resolve the location dynamically (https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016552.html)
 

 bump version
 

 bump version
 

 re-render help files with roxygen 7.1.0
 

 'git clean -i' needs to see *.o and *.so files
 

 Clarifies floating point precision artefacts returned by coverage()
 

 Merge pull request #1 from seversond12/RELEASE_3_11

-update RELEASE version number 

 -update RELEASE version number
- fixed bug due to deprecated SingleCellExperiment function isSpike()
	- vignette was altered to reflect change in syntax
	- single function in estimate_noise.R was altered to reflect change in syntax
	- data objects were altered so SingleCellExperiment objects stored in them would reflect updates to SingleCellExperiment package
- adjusted version appropriately for bioconductor bump
 

 Bump version with fixed merge conflicts
 

 bug fix: is_a to isa
 

 Merge remote-tracking branch 'upstream/master'
 

 Downgrading required R version
 

 Fix for .findKNN_all_k tests; added NEWS about findKNN
 

 Bumped version and date.
 

 Bumped version and date.
 

 version bump for master
 

 Merge upstream
 

 fix left_join issue
 

 Merge branch 'pablo-rodr-bio2-newshinyplots'
 

 fir n() error
 

 fix tibble error
 

 2.19.2: Updated ctb: added Magellan and exprTk and clarified contributions
 

 fix n() error from dplyr
 

 Update maintainer in DESCRIPTION file
 

 User requested deprecation
 

 User requested deprecation
 

 Package deprecation

  - Unresponsive
  - Software removed in previous release
 

 Package deprecation

  - Unresponsive
 

 Merge branch 'master' of git.bioconductor.org:packages/Mulder2012

Conflicts:
	DESCRIPTION
 

 v1.19.1
 

 Fix-conflicts
 

 Merge branch 'tscan'
 

 Docfixes, reoxygenated.
 

 Ensure cells assigned to branch points show up in all paths.
 

 Initial draft of utility to test for differences in pseudotime.
 

 Reoxygenated, updated NEWS.
 

 Added more test scenarios for clusterMST pseudotime.
 

 Added preliminary tests for *ClusterMST functions.
Bugfix to avoid unnecessary randomness.
Extra check for consistent clusters and centroid inputs.
 

 Update test-auxilliary-functions.R
 

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

 Update README.md
 

 bug fix: fixed buildPedigree function
 

 Merge remote-tracking branch 'origin/master'

 

 Merge pull request #1 from jlab-code/RELEASE_3_11

Release 3 11 

 update RELEASE version number
 

 bumped version and date, updated NEWS.
 

 Massive reoxygenation to account for scuttle migration.
 

 Fixes to replace imports from migrated functions.
 

 Removed tests that were migrated to scuttle, updated remainders.
 

 Purged Rcpp as it is no longer necessary.
 

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

 Cleaned up Makefile to use OSCA's master.
 

 Just compute the Rand index directly if requested.
 

 Reoxygenated.
 

 Generalized bootstrapCluster to work with any comparison function.
 

 Added tests for clusterRand.
 

 Updated dependencies.
 

 Updated and streamlined vignette.
 

 Bugfixes everywhere for the integrated scuttle code.
 

 Replace linear model fitting code with scuttle's version.
Streamlined code for correlation internals.
 

 Switched all imports from scater to scuttle.
Updated various calls to scuttle utilities.
 

 data_frame to tibble
 

 - adjusted SingleCellExperiment use to accommodate recent changes that made isSpike defunct
	- specifically switched to altExp as recommended by SingleCellExperiment authors
	- this change was refected in the data objects as well as in the estimate_noise functions and the vignette markdown document
- compressed the data objects to be smaller
 

 Version bump for bug fix
 

 Return tibble instead of base R data frame; this is causing trouble in a newer version of testthat
 

 version bump for release 3.11
 

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

 Fixed maintainer
 

 bump
 

 Update LICENSE 

 flowjo_to_gatingset alternatively takes cytoset as data input #100
 

 importFrom flowWorkspace cytoset
 

 Update LICENSE 

 bump
 

 #99: Implement subset by filtering expression in flowjo_to_gatingset
 

 bump
 

 Update docs
 

 Let gatingset_to_flowjo use binary or docker
 

 add skip_faulty_gate arugment to flowJo parser. #96
 

 Make docker availability check work with Windows
 

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 

 Update LICENSE 

 bump
 

 #327: Appropriately add flowJo_fasinh transformation
 

 Merge branch 'master' of github.com:RGLab/flowWorkspace
 

 Remove residual author tag from cytoframe doc
 

 update csv metadata file
 

 update metadata helpers
 

 Updating version number
 

 updating required packages in .travis.yml
 

 User requested deprecation
 

 merge latest
 

 bug fix
 

 bug fix: handle no blocks in LD and no genes associated with pathway
 

 todo
 

 version back to 1.7
 

 updated news
 

 less messages in example
 

 update email. update tests
 

 update to 4.0.0
 

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

 Push new devel version to BioC
 

 Fixed plotEIC legend not labelling m/z's that didn't have assigned adducts
 

 Removed erroneous line for data file
 

 Update xsAnnotate.R 

 bump version
 

 by default quiet is TRUE when downloading files
 

 characterORconnection got renamed character_OR_connection in BiocGenerics