User requested deprecation
 

 add Title: to DESCRIPTION

- oops, somehow deleted on last commit
 

 Update DESCRIPTION 

 Update check-bioc.yml 

 Merge pull request #129 from cvanderaa/master

refactor: adapted subsetting to behave as MultiAssayExperiment (issue #128) 

 Merge pull request #126 from cvanderaa/master

refactor: optimized 'infIsNA' and 'zeroIsNA' 

 test: fixed the tests to pass R CMD checks
 

 refactor: optimized 'infIsNA' and 'zeroIsNA'
 

 docs: link to WSBIM2122 chap 8
 

 ci: untabify yml file
 

 fix conflict
 

 doc: use quantile norm
 

 only run action using bioc docker on linux
 

 change to push
 

 set biocversion to 3.12
 

 use macOS with r 4.0
 

 fix syntax error
 

 try again macOS-latest
 

 comment matrix
 

 ci: install libgit2 and use osx
 

 Update check-bioc.yml

remove win and osx 

 fix: temporarily use median-norm
 

 Merge pull request #1 from drighelli/devel_R1

Devel r1 

 fixing error in utils parseCode
 

 revision 1
 

 volcano server
 

 Deprecate

 - unresponsive
 

 Deprecate

  - unresponsive
 

 Merge branch 'master' into RELEASE_3_12 

 Latest version of cyanoFilter after feedbacks from Bioconductor
 

 Update for ensembl 103
 

 Merge branch 'master' into master_bioc

* master:
  variable not found issues
  Update write_constraints_6.R
  these drops should be gone, otherwise matrix dimensions change
  Update write_objective_function_all.R
  Update DESCRIPTION
  Update checkMeasObj.R
  Updated author roles
  Update maintainer of the package
  Update README.md
 

 Merge pull request #39 from saezlab/gabora-drop-issue

variable not found issues 

 Update write_constraints_6.R

cc1 is not found in certain cases 

 these drops should be gone, otherwise matrix dimensions change
 

 Update DESCRIPTION

New contributor roles, fixing verson for syncing with bioconductor 

 Updated author roles
 

 Updated gh page
 

 Merge pull request #19 from christianholland/master

Release of new GitHub page 

 Setup of gh page
 

 Resolved conflict between NAMESPACE and DESCRIPTION

Addresses warnings from http://bioconductor.org/spb_reports/cellmigRation_buildreport_20210308041031.html#machv2_buildsrc_anchor. Still trying to (blindly) get it to build on macOS.
 

 Version bump
 

 Bumped patch version
 

 Moved kableExtra to Imports
 

 Merge branch 'master' of github.com:epurdom/clusterExperiment
 

 Thanks to Lain (INRAe) and Team W4M for this PR, fixing argument passing to annotatedDiffreport()
 

 Merge pull request #68 from Lain-inrae/transmit_annotateDiffreport_params_to_groupCorr

[WIP - waiting for !66 ]Transmit annotate diffreport params to group corr 

 Parameters that annotateDiffreport takes are transmitted to groupCorr function.

Related unit tests have been redacted.
 

 Fixed up documentation around direction=.
 

 Migrated advanced QC topics from Basic book into a new chapter. (#2)

 

 Merge branch 'master' of https://github.com/compbiomed/tbsignatureprofiler
 

 Create new COVID signatures vignette for website
 

 Update news and version number
 

 Correct signature documentation ordering to match objects
 

 Clarify vignette
 

 Fix lintr
 

 adding saveCols to results and lfcShrink
 

 bugfix: network flavor parameter added in plot_network
 

 mboost
 

 Version sync
 

 Omit automatic testing 

 Further notifications on updated maintainer email

(cherry picked from commit 7bcb9abaf3314496167337a1f352fc739a998dc6)
 

 Update the citation 

 Include news and version bump
 

 Omit spaces in test data header
 

 Fix tests to include Limma intensity trend
 

 Statistical report also allow PNG. Allow intensity trend in Limma.
 

 Draft both PNG report and sample setup display
 

 Minor issue where matrix was dropped to vector
 

 Fiddled with the title and license.
 

 Bugfix for test for the time being.
 

 Removed accidentally committed file.
 

 Added a quickCorrect function to wrap the usual workflow.
 

 change default alphaValue

in man files
 

 bug fix #115: multigraphs and repeat nodes
 

 docs for #114
 

 fixed typo for #114
 

 bug fix #114
 

 add citation file
 

 update viggnette with single cell
 

 Merge remote-tracking branch 'upstream/master'
 

 move devel to master branch
 

 Fixed conflicts in version change
 

 Fix badges
 

 Fix links
 

 Fix pkgdown.yml
 

 Disable macOs and windows until rjava setup can be figured out
 

 Add xquartz for macOS testing
 

 try with macOS
 

 Update java config for windows and remove pkgdown
 

 Fixed table display
 

 try --no-multiarch for windows
 

 Add cairo to fix macOS issue
 

 Try with r release for windows and macOS
 

 forced push commit
 

 force commit
 

 update badges
 

 Remove kableExtra
 

 Clean up ignored files
 

 Fix links
 

 Add tinytex
 

 Add github actions
 

 Reflow
 

 Add badges workflow
 

 Version bump to 1.7.0
 

 Fix link
 

 changed title
 

 update citation
 

 remove the axis of first geom_tile
 

 Bug Fix
 

 Bug Fix
 

 bugfix for return_unprocessed PE
 

 ssvConsensusIntervalSets bugfix if min_number = 0
return_unprocessed supresses fragLens calculation
return_unprocessed same variable names between bam and bamPE
 

 Updated to PANTHER.db v1.0.11 based on pantherdb.org v16
 

 Update: version bump for Bioc build
 

 Fix: changed all(..., na.rm=TRUE) to all.equal call
 

 Update: version bump for Bioc build
 

 Update: Version bump for Bioc build
 

 Fix: Incorrect check of length(dots) in SurvivalExperiment constructor
 

 FFix: Version bump for Bioc build
 

 Merge branch 'master' into development
 

 Fix: examples and tests passing with new data and SurvivalExperiment column names
 

 Fix: all tests passing again
 

 Fix: removed stray print statemnts from testing code
 

 Update: passing checks
 

 Updated BiocManager install for release and devel 

 Fix: unit tests working since randomSeed changes
 

 Fix: removed all set.seed calls inside functions at requirest of Bioc reviewer; updated documentation to indicate the seed is no longer set localling inside functions
 

 Merge branch 'master' into development
 

 Development version passing tests and checks after merge with master
 

 Version bump for Bioc build
 

 Fix: missed a conflict in merge with master
 

 Fix: Modified examples to run faster on Windows
 

 Update: validateModel when model has subtypes working; forestPlots also working
 

 Add: validateModel now calcualtes per subtype statistics if  subtypes have been assigned to the predoction cohorts
 

 Update: modified validateModel method for PCOSP class to also compute subtype specific model performance if a model has subtype annotations
 

 Add: trainModel method for GeneFuModel class whichs throws and error telling users this functionality is not implemented
 

 Add: unit tests for trainModel, predictClasses and validateModel methods for ClinicalModel class
 

 Add: final check in SurvivalExperiment constructor tests for 100% coverage of that file
 

 Add: tests for automatic column type coercion in SurvivalExperiment constructor
 

 Add: unit tests for ClinicalModel constructor
 

 Add: unit tests for RGAModel constructor
 

 Fix: Resolved error introduced by adding model class name to column name for risk predictions
 

 Add: unit tests for RLSModel constructor
 

 Fix: error in .generateTSPModels due incorret subset placement
 

 Add: units tests for SurvivalExperiment coercion and SurvivalModel constructor
 

 version inc to 0.99.8
 

 cosmetics to produce a meaningful error message
 

 Version 1.47.2
 

 Correct argument description in man-page (plus typos)
 

 Changes version to 2.1 and updates NEWS
 

 Add a new section (ASpli overview) in vignette
 

 ASpli.R and Aspli.Rnw in inst/doc and ASpli.pdf
 

 Las junturas con NA son removidas pero no pudimos identificar por que aparecen los NA
 

 Changes locus overlap from exon overlaps to gene range overlap
 

 Fixes issue #6 binGenome function may assign incorrect bins at the start and the end of each gene
 

 Adds bams on the fly for jCounts
 

 Changes system2 call for system
 

 Changes target data frame to accomodate only one extra column with full call to aligner. Calls aligner in readCounts, builds bai, reads it and drops bam and bai if required
 

 Adds alignFastq and dropBAM to gbCounts
 

 Export zellkonverterAnnDataEnv

Formally known as anndata_env
 

 Convert metadata to dict in SCE2AnnData()

Fixes #40
 

 Add SparseDataset support to NEWS

Fixes #37, #41
See PR #41
 

 Support H5AD-backed matrices during the conversion.
 

 Package deprecation

  - unresponsive
 

 Rbuildignore rawrr.Rmd
 

 replace path
 

 vignette cosmetics
 

 test case for tic of EH4547
 

 RawFileReaderLicense.doc -> RawFileReaderLicense.txt
 

 replace slash with file.path
 

 BiocStyle edit cosmetics
 

 MIT to CeCILL
 

 Merge release 0.99.2
 

 Numbered notes
 

 Reverting to the latest vignette

Reverting to the latest vignette
 

 REF URL fixed

REF URL to: https://www.data-pulse.com/dev_site/cellmigration/ 

 Changed version back to match Bioconductor submission
 

 Updated docs (including version)
 

 Merge branch 'issue-69-vignette' of https://github.com/ocbe-uio/cellmigRation into issue-69-vignette
 

 Update all_extra.R

Added details about the datasets 

 Wor-around for vignette multi-thread issue

- set all threads=1 (no parallelization at building);
- add reccommendations to paralleliza by setting the threads argument to a value bigger than 1 

 Set threads to 1 (fixes #69), removed whitespace
 

 Merge branch 'issue-36-tests' into develop
 

 removing tiff file

extdata not needed anymore 

 Reimplemented testthat units as RUnit tests
 

 Merge branch 'fix-check' into develop
 

 Version bump
 

 Solved conflicts between BiocNewVersion & develop
 

 Fixed vignette code

Fixed few lines in the vignette that were raising an exception.
Briefly, in the former Vignette version, the 'x3' object was analyzed using wrong diameter and lnoise values -> no tracked cells -> exception. Argument values were updated. 

 Updated package version - bioc compatible
 

 Rebuilt README.md
 

 Added recipe for building README.md
 

 Add new files
 

 Ignoring deployment info
 

 Improved formatting
 

 Added TODO
 

 Merge branch 'issue-66' into develop (#66)
 

 "Improved text"
 

 Merge branch 'split-shiny-files' into develop (issue #65)
 

 Split away server file
 

 Moved Shiny deployment to Makefile
 

 Ignoring Makefile on package
 

 Fixed syntax error
 

 Changed all indentation to 4 spaces
 

 Merge branch 'break-wide-lines' into develop
 

 Broken wide lines on man files (issue #61)
 

 Breaks wide lines on all .* files
 

 Some formatting improvements (issue #34)
 

 Changed installation instructions (issue #34)
 

 Merge branch 'issue-57' into develop
 

 Merge branch 'issue-58' into develop
 

 Merge pull request #41 from ocbe-uio/LoadTiff

Replaced sapply 

 Merge branch 'solve-checkout-notes' into develop
 

 Excluding the inst folder from the package
 

 Renamed NEWS file
 

 Renamed function using period (issue #31)
 

 MOre fixes
 

 Fixed another sapply
 

 Another sapply in ForwardMigration
 

 Fixed a sapply in ForwardMigration
 

 Another sapply fix
 

 Another fix of sapply
 

 Replaced a bunch of sapplies
 

 Merge branch 'develop' of https://github.com/ocbe-uio/cellmigRation into develop
 

 Merge master' into develop due to mistake on PR base for #40
 

 Another sapply fix
 

 Merge pull request #52 from ocbe-uio/wsaPreProcessing2

Wsa pre processing2 

 Merge pull request #50 from ocbe-uio/rmPreProcessing5

Rm pre processing5 

 Merge pull request #48 from ocbe-uio/rmPreProcessing3

Rm pre processing3 

 Merge pull request #46 from ocbe-uio/rmPreProcessing

Rm pre processing 

 Merge pull request #44 from ocbe-uio/optimizeparams

Optimizeparams 

 Merge pull request #42 from ocbe-uio/cntrd_fix

Cntrd fix 

 Merge pull request #55 from ocbe-uio/wsaPreProcessing5

Wsa pre processing5 

 another fix
 

 New fix
 

 Replaced a sapply in wsaPreProcessing
 

 Merge pull request #40 from ocbe-uio/visualizeTrcks

Fix in visualizeTrcks 

 Final two sapply-s replaced in rmPreProcessing
 

 Another replacement of sapply in rmPreProcessing
 

 Another fix in rmPreprocessing, replacing sapply
 

 Removed a sapply in CellTracker
 

 Fix in track()
 

 Fix in cntrd
 

 Replaced sapply
 

 Fix in visualizeTrcks
 

 vapply and seq_len fixes in LinearConv2
 

 Changed biocViews
 

 Merge branch 'release-1.0' into develop
 

 Version bump