Merge branch 'devel'
 

 Merge branch 'master' of github.com:yduan004/signatureSearch
 

 feat: support windows; use HDF5Array
 

 Fix for removed variance modelling functions.
 

 KnowSeq V1.1.15
 

 Fixing barcode in the gistic2 query
 

 Fix GISTIC reading
 

 Update prepare.R

Because of the folder structure (and the previous change, keep.copy=FALSE), if we choose to run (for idat methylation files) GDCprepare several times or if we just run GDCprepare on some samples more than once, on the current state we will have the problem of either keep moving the files up until the base folder (eg. the default "GDCdata") or potentially having some idat files somewhere between the base folder and the file_id folder.

Since "readIDATDNAmethylation" only applies to files that are within the "Raw_intensities" folder anyway, this change makes it so that files that were to be moved outside this folder are not actually moved.

A more elegant solution would be better but this works for now. 

 passing check on R 4.0
 

 update news
 

 Fixed core heatmap
 

 Merge branch 'bugfix'
 

 Reoxygenated, updated NEWS.
 

 Split off coassignment calculations from bootstrapCluster.
Robustified bootstrapCluster to missing clusters in bootstrap.
 

 Added listing of defunct functions, closes #10.
 

 Bumped version and date.
 

 Added listing of latest defunct functions to assist transition.
 

 Add extractAt() method for BSgenome objects

A cleaner/faster replacement for getSeq(). The plan is to deprecate
getSeq() at some point.
 

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

 Bumped version, updated NEWS.
 

 Reorganized combineMarkers docs.
 

 Add a summary effect size to combineMarkers output.
 

 ExperimentHub load error, add localHub=TRUE option
 

 update readme for v1.2.0
 

 v1.17.1 merge commit
 

 update with previous commits of 1_19
 

 desc
 

 Update DESCRIPTION 

 Update README.md 

 Merge pull request #6 from cnk113/master

Accepted pull from cnk113: ported over Seurat V2's MultiCCA, removed PMA. Thanks! 

 small fixes
 

 Update DESCRIPTION 

 bum
 

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 

 pkgdown updates
 

 Add CytoExploreR_exports
 

 load flowCore
 

 load flowWorkspace
 

 Update .travis.yml for issue with travis build script
 

 Merge branch 'cytoset' of github.com:RGLab/openCyto into cytoset
 

 Update test reference for cytoverse API change
 

 resolve pull conflicts
 

 more friendly error messasge for reporting empty dims in csv
 

 Update .travis.yml to access cytoset branches
 

 Update gating-testSuite.R for cytoverse API and new-format gs
 

 merge cytoverse
 

 Remove flowClust calls from add/remove_pop tests for speed
 

 bump to 2
 

 Add ImmunoOncology biocViews term
 

 skip recompute for ocRectRefGate
 

 update
 

 update based on new cytolib
 

 bump
 

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 

 Fix rrcov CovMcd import
 

 Coerce cytosets to flowSets in vignette
 

 load flowCore in example code since now it is on imports
 

 Move dependencies to Imports section
 

 Merge trunk in to cytoset

Merge branch 'trunk' into cytoset

# Conflicts:
#	DESCRIPTION
#	R/gaussNorm.R
#	R/normalize-methods.R
#	R/warpSet.R
 

 add warpSet.cytoset support #23
 

 Merge branch 'trunk' into devel
 

 Merge branch 'cytoset' into trunk
 

 convert legacy gs_bcell_auto
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 

 bump
 

 rm CYTOLIB_VERSION keyword when comparing to flowframe
 

 add test case for rename marker to empty string
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 Merge branch 'pkgdown' into cytoset
 

 pkgdown updates
 

 doc consolidation
 

 doc consolidation
 

 Add gh_pop_get_stats_tfilter
 

 Some required updates to DESCRIPTION/NAMESPACE
 

 Rebuild pkgdown branch off of cytoset branch
 

 fix test case regarding to time channel scaling
 

 assign the dummy legacy max_val for logTrans
 

 flowjo_flog --> flowjo_log_trans
 

 Add .onAttach message about cytoset changes
 

 Some vignette metadata formatting
 

 Update for cytolib::LdFlags->cytolib::cytolib_LdFlags
 

 Restore some doc and namespace changes
 

 Revert "Update logtGml2 for 9e5a282"

This reverts commit a0d1931cbe7a5dc448d929e0879260af9b07e27c.
 

 Update logtGml2_trans doc example for 9e5a282 and a0d1931
 

 fix gh_get_transformations for fasinh
 

 update flog in R
 

 update according to the refactored cytolib
 

 make sure pd is synced to disk during load_cytoset_from_fcs
 

 fix old api call
 

 add test case to ensure meta won't be flushed to disk automatically for cytoframe
 

 addd cytoframe-suite
 

 fix typo
 

 define cf_scale_time_channel API
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 write dummy replacement method [[<- for gs to enable the operations like 'markernames(gs[[1]]) <- newv'
 

 Load flowCore in some examples and tests
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 Update .travis.yml for issue with travis build script
 

 make sure to clone gslist since gslist_to_gs call now points to the original gs
 

 deprecate GatingSet() with gh_apply_to_new_fcs in test case
 

 refactor gh_apply_to_new_fcs
 

 add more tests to transformation of gs
 

 fix [ method for gs
 

 add gh_apply_to_new_fcs and its test case
 

 add stats comparison for new GatingSet based on the existing gating hierarchy
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 fix some more cytoverse merge issues
 

 bump
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 initial merge cytoverse with manual resolving conflicts
 

 Import graph::nodes() for plot_diff_tree()
 

 Update .travis.yml
 

 rm flowJo parser
 

 Re-order .travis.yml to fetch proper cytolib
 

 Fix subset.GatingSet()
 

 revert the change(mistakenly) to Makevars in regard of c++fs
 

 allow symlink directories in FCS searching
 

 fix test case where cols in pdata change the order on mac
 

 Merge remote-tracking branch 'origin/cytoset' into cytoset
 

 conditional linking to fs lib based on compiler
 

 undef FALSE to resolve RcppExports.cpp compiling warning (error on osx)
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 restore recompute = FALSE argument to keep 'add' backward compatible
 

 fix getCompensationMatrices.GatingSet
 

 Change default value for dataset argument to load_cytoframe_from fcs to enable helpful warning
 

 resolve pull conflicts
 

 Add check for duplicate guid in parseWorkspace
 

 Revert "Add pre-check for duplicate guids before parsing samples in parseWorkspace"

This reverts commit 8b976040a37d92a7c157b2f213931ae7b4fbf24d.
 

 Update comments and cleanup guid strings in parseWorkspace
 

 Allow parseWorkspace to parse workspace opened from cwd
 

 fix test error
 

 fix doc
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 Update DESCRIPTION 

 Add guid slot to GatingSetList
 

 resolve cherry-pick conflicts
 

 fix test-compensate
 

 add convert_legacy_gslist
 

 pass which.lines correctly to c parser to speed up test cases of big FCS
 

 add validity checks on tree structures for parser
 

 refine sampleRef xpath to skip ManuallyIncludedSamples node
 

 optionally mute workspace type print
 

 revamp get_sample_groups so that it is lightweight and does not traverse entire xml
 

 merge
 

 add swap_colnames
 

 write test case for load_cytoframe_from_fcs where which.lines is specified
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 Update docs for added cytoset/cytoframe APIs
 

 replace references to csApply with lapply
 

 importFrom dplyr group_by
 

 update CytoML section
 

 normalizePath in save_gs
 

 create s3 for getSamples
 

 pass M to logicleTrans constructor properly for logicleGml2
 

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 

 Create S3 generic for parseWorkspace methods
 

 Fix typo in cf_write_h5
 

 use gh.check_ungated_bool_node
 

 normalizePath in load_gs
 

 take care of even older legacy gs archive.
 

 remove recompute option from .addGate
 

 resolve merge
 

 add print message for missing FCS. #268
 

 link to RcppParallel through importing it so that tbb shared lib is automatically loaded by RcppParallel and make symbol available at runtime
 

 add lock for getTransformation calls. #268
 

 wrap the loop logic into separate function to be able to use thread
 

 Defunct plotGate and eliminate legacy viz pkg dependencies
 

 modify search_for_fcs to avoid creating temporary cs container thus avoid the extra omp lock. #268
 

 update keywords during gs_transform_data
 

 update flowCore_PnR keywords to reflect the transformation for the load_legacy
 

 fix merge gs test cases
 

 fix and pass addGate testsute
 

 fix transform method for gs
 

 fix subset.cytoset
 

 do in-place compensation for gs
 

 update doc
 

 add h5_set_error_handler to redirect h5 error print to R error console
 

 refactor cytoFrame/cytoSet to eliminate the leading capital letter
 

 replace CXX1X with CXX11
 

 fix setKeyords Rcpp api
 

 add test cases for cytoframe
 

 use gs id as the default h5_dir
 

 add subset.cytoSet
 

 filter PnX keywords on the subsetted cytoFrame
 

 add test case for cytoset
 

 add flowFrame_to_cytoframe
 

 fix compensate methods
 

 merge swap_data_col commit
 

 import read.AnnotatedDataFrame
 

 fix external comps
 

 fix external comps
 

 support external compensation
 

 R API for gs contructor based on gating template of existing gh
 

 do in-place update in colnames<- and markernames<- for gs/cs to avoid triggering the classical cascade effect of R replacement method [[<-
 

 keep pData order consistent with sampleNames API
 

 fix load_gslist
 

 skip derived parameters. #262
 

 drop dep on cytoCore
 

 add getter/setter for gs guid
 

 rewrite recompute in c++
 

 add coerce function from fs to cs and vice versa
 

 fix the Rcpp API name conflicts