version bump for rebuild
 

 Rename NEWS to NEWS.md 

 Update documentation. Fix various warnings and errors. Bump version.
 

 Merge pull request #99 from dburkhardt/master

Correcting README typo 

 Updating Vignette so that it works in Bioconductor according to Brian Ripley and Luigi Marchionni
 

 add tests for seed/thread consistentcy
 

 don't reorder rows/cols in distributed CoGAPS
 

 Pigengene:multi map
 

 Minor fixes to quickCluster tests for altmatrices.
 

 Reverted to min.size=100 for quickCluster.
 

 Update computeSumFactor tests for new behaviour.
 

 Bugfixes for below-sizes clusters, corrected library norm.
 

 Updated computeSumFactors docs about library size norm.
 

 Changed the order of latex packages according to Brian Ripley's suggestion
Merge remote-tracking branch 'upstream/master'
 

 Modified order of latex packages according to Brian Ripley's suggestions
Merge remote-tracking branch 'upstream/master'
 

 modify title in MV plots for Imputation
 

 Centralized choice of cluster and its references in text.
 

 modify title in MV plots for Imputation
 

 version bump
 

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

 removing U from the chromosomes onjects in fly
 

 adding annotations for fly: dm3 and dm6
 

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

 updating annotation use for dm3 and dm6
 

 added param and functionality to return early the list of top ranked genes with hi loadings
 

 fixing up travis settings
 

 More work on h5mread()
 

 version bump
 

 add github details gathering functionality
 

 version bump and update vignette
 

 More work on h5mread()
 

 display set sizes
 

 updated version & docs
 

 updated docs and version
 

 remove unneccesary copy
 

 simpler config
 

 Rename simple_h5read() -> h5mread(), and more work on it
 

 spectral matching documentation update
 

 Spectral matching documentation update (v1.9.1) (#16)

* updated documentation for spectral matching

* more spectral matching documentation

* purityD averaging update for grouping across multiple lists, also updates for documentation

* removed hardcoding for ppm for groupPeaksEx

* removed hardcoding for ppm for groupPeaksEx

* cleaning up documentation

* removing old readme

* updating readme

* updating readme

* updating readme

* Update readme

* Updating shields

* update readme

* (re)-create travis yaml

* updating travis for codecov

* cleaning up tests

* removed codecov check

* update descript and news with new release

* updated version to match bioconductor

* update links in readme

* update readme

* update readme

* update shield links

* added more shields

* update bioconda reference

* Remove mirror code ref
 

 update docs
 

 version bump
 

 version bump
 

 back to release
 

 sm unit test change
 

 added back unitests
 

 version bump 

 removed file
 

 test that updates
 

 database bug fix
 

 added function to fetch pubchem ids from compound names
 

 updated documentation for new params
 

 implemented the possibility to choose the specific topGO method, on top of the classic algo
 

 Updated NEWS
 

 Minor documentation updates.
 

 work on exportJuicerbox
 

 bump
 

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

 Merge branch 'trunk' into devel
 

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

 suppress rd for internal functions. #184
 

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

 Update README.md 

 Merge branch 'trunk' into devel
 

 update test case. #136
 

 Update write.FCS to handle very large flowFrames
 

 update_release
 

 Updated description
 

 Bug fix: added new terms to sample vocabularies
 

 Updated sample.cs.obo and sample.do.obo with new terms
 

 Added new sample dictionary
 

 Changed version to trigger bioconductor build
 

 Update version to trigger biocondutor
 

 Removed Rproj file
 

 removed .Rproj.user directory
 

 Added sample obo ontology
 

 Added a short vignette explaining the contents of the package
 

 changed version to trigger webhook
 

 OnassisJavaLibs
 

 fix merge conflict
 

 clean up merge conflict
 

 v2.0.1 check for old peakFilter() behavior
 

 NEWS and DESCRIPTION for latest version
 

 Version 1.1.1
 

 commenting error code in vignette 

 Added human_anno 

 update2_november2018
 

 update sessionInfo in doc
 

 fix regression bug in plot spectrum1
 

 add none imputation method
 

 Add filterMsLevel,Spectra and coerce,Spectra,MSnExp

- Add filterMsLevel,Spectra method.
- Add coerce,Spectra,MSnExp method (issue #370).
- Add related unit tests and documentation.
 

 Merge branch 'master' into spectra_methods
 

 Merge branch 'master' into spectra_methods
 

 Install pkg before running pkgdown::build_site()
 

 new devel version
 

 Add as,MSnExp,Spectra and as,Spectra,list #370
 

 changes in vignette
 

 text annotation with correct width
 

 New master version
 

 test
 

 New master
 

 Small improvement to "coerce2" method for DataFrame objects
 

 use formal expand args
 

 wip: ID translation with unit tests
 

 add unit tests for translation
 

 rename resultFrame to rframe
 

 wip: barcode auto recognition and translation
 

 bump
 

 add swap_cols argument to .addGatingHierarchies
 

 hanle external comp properly
 

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
 

 pass external compensation to GatingSet method for template cp
 

 alevin work
 

 print working properly inside BiocParallel
 

 Fixing conflict
 

 updating get_hubs function
 

 Updating RELEASE version
 

 change author's email address
 

 par(mfrow) is corrected
 

 parse error message from GREAT
 

 bump version
 

 correct version numbering
 

 updated version
 

 forcesegmentsontemplate added
 

 1.0.5 fix for non UMI data
 

 Merge remote-tracking branch 'origin/RELEASE_3_8'

Currently local master:1.1.2, local RELEASE_3_8: 1.0.4
I want to set local master to be 1.0.4.
 

 Merge branch 'master' into RELEASE_3_8

They are all identical (master and RELEASE_3_8), hence I merged them.
 

 1.0.2
 

 Modified default choice of ref.clust in computeSumFactors.
 

 title case in DESCRIPTION
 

 Add coordinate mapping use-case vignette
 

 removed separator line from DESCRIPTION
 

 added travis
 

 added travis
 

 Use of setAs for coercion.
 

 Added as.Pairs function.
 

 edits
 

 bumping version #
 

 Nidhi's edits
 

 renamed files
 

 combined database version
 

 fix vignette missing block
 

 Merge branch 'master' of http://github.com/hcbravolab/metagenomeFeatures
 

 fixed warning roxygen warning message
 

 fixing merge conficts

Merge branch 'vignette-revision'

# Conflicts:
#	vignettes/Exploring_a_MgDb.Rmd
#	vignettes/database-explore.Rmd
#	vignettes/retrieve-feature-data.Rmd
 

 fixed typo
 

 revise text
 

 rebuilt documentation
 

 Merge branch 'vignette-revision' of https://github.com/HCBravoLab/metagenomeFeatures into vignette-revision
 

 fixed typo of variable name

Also made select params consistent 

 revised text incorporating phyloseq
 

 update source documentation & vignette
 

 revised and added mgFeatures
 

 Merge pull request #48 from HCBravoLab/biocCheck

Bioc check 

 rebuild documentation
 

 removing purrr import
 

 updated result and compressed data
 

 updated docs & version
 

 removed benchmarking code'
 

 fixed dot operator
 

 initialization of s doesn't need to square Z1
 

 Merge branch 'master' into sparse_cogaps
 

 added helper function to build retina subset
 

 Merge branch 'develop' of github.com:FertigLab/CoGAPS into develop
 

 merge
 

 Merge branch 'sparse_cogaps' of https://github.com/FertigLab/CoGAPS into sparse_cogaps
 

 added data
 

 added shifted dot product
 

 Merge branch 'develop' into sparse_cogaps
 

 Merge branch 'develop' into sparse_cogaps
 

 working versions of three different iteration schemes
 

 renamed internal bytes class to nbytes due to Rcpp
 

 1.1.2
 

 1.0.3
 

 1.0.1
 

 update in srv_ConvertData
 

 Switched back to computeSumFactors for the xtra workflows.
 

 Switched MNN workflow back to using computeSumFactors.
 

 Switched back to computeSumFactors for UMI workflow.
 

 Updated NEWS.
 

 Purged simpleSumFactors tests.
 

 Rebuilt NAMESPACE, updated DESCRIPTION.
 

 Expanded quickCluster tests for new behaviour and options.
 

 Further changes to defaults, altered behaviour of 'd'.
 

 Added non-rank-based clustering to quickCluster.
Allow changing of graph clustering algorithm.
Altered defaults for quickCluster.
 

 Commented on speed advantages of splines.
 

 Fix a bug in power estiamtion (cumsumBorder.cpp), which make results
incorrect when k not equal to one. 

 Merge remote-tracking branch 'upstream/RELEASE_3_8'

# Conflicts:
#	DESCRIPTION
#	NEWS
#	R/generate_pwms.r
#	R/swing.r
 

 update to vignette
 

 make viewPWM visible
 

 big fix
 

 unit test clean-up
 

 merge
 

 padd outline to grid.boxplot()
 

 add sanity check
 

 set adjust_annotation_extension to NULL
 

 update
 

 add dev.null() to get rid of white page
 

 check arguments from old versions
 

 update
 

 vignettes added
 

 remove old vignettes
 

 update
 

 update code for adjusting oncoprint
 

 update
 

 adjust color order on barplot
 

 fixed device issue under rstudio
 

 update travis.yml
 

 documentation checked
 

 update
 

 merge
 

 fixed several bugs
 

 update
 

 update
 

 R CMD check passed
 

 udpate
 

 update
 

 update
 

 merge
 

 merge
 

 Merge branch 'master' of https://github.com/jokergoo/ComplexHeatmap
 

 imporved according to the package reference
 

 small bug fix
 

 support qq, glue and tibble
 

 oncoPrint is vectorized
 

 vignette check passed
 

 a backup push
 

 adding heamtaps by columns generally works now
 

 add documentations
 

 backup
 

 improved HeatmapAnnotation class
 

 add AnnotationFunction class
 

 vignette revised
 

 merge
 

 Merge branch 'master' of https://github.com/jokergoo/EnrichedHeatmap
 

 generate vignette
 

 update
 

 merge
 

 merge
 

 updaet with new legends
 

 Merge pull request #57 from nhejazi/fix-bioccheck

Improve consistency with  Bioconductor standards 

 remove use of sapply
 

 Documented new --cores and --parallel flags for Coverage.R
 

 tris changes
 

 fixed reactivity for some components, e.g. melting temp, dimerization (used rv_primers instead of primer.data)
 

 warn for tris buffer different from 0
 

 updated doc for tris buffer
 

 Bumped version number, date.
 

 Transitioned xtra workflows to use simpleSumFactors.
 

 Transitioned MNN workflow to use simpleSumFactors.
Removed bit about batchShift for now.
 

 Switched UMI workflow to use simpleSumFactors.
 

 Updated index numbers.
 

 bug fixed
 

 Remove examples in DrugVsDisease and generateprofiles
 

 Removing print