T/F replaced with TRUE/FALSE
 

 version bump
 

 Readme update; upload to Zenodo
 

 Merge branch 'RELEASE_3_13'
 

 version bump 1.11.4
 

 sync version

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

# Conflicts:
#	DESCRIPTION
 

 pupup RoxygenNote
 

 deprecate

 - unrepsonisve
 

 deprecate

 - unresponsive
 

 deprecate

 - unresposnive
 

 Changed maintainer and version bump for BioC build
 

 deprecate

 - unresponsive maintainer
 

 deprecate

 -- unresponsive maintainer
 

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

 Deprecated

  - maintainer unresponsive
 

 deal col>12 and offset dimension
 

 update NEWS.md
 

 fix file download efficiency
 

 fixed undocumented param
 

 replaced wrong || 

 fixed missing quote 

 fixed missing miRNA column
 

 added RleList import
 

 version bump
 

 dataset -> data set
 

 p-value correction by ncol
 

 docs updated, typos fixed, version bump
 

 docs updated, typos fixed
 

 ramr.ranges -> amr.ranges
 

 verbose for slow functions
 

 docs updated
 

 reproducibility by %dorng%
 

 docs updated
 

 updated with simulate* methods
 

 new default for data.samples
 

 docs updated
 

 simulateData method code, unit tests
 

 simulateAMR documented and tested
 

 @seealso updated
 

 verbose defaults
 

 cleaner Import
 

 released at bioc
 

 Forget again to change the version.
 

 Forgotten to change the version number.
 

 update docs
 

 fix vector logical check
 

 update docs
 

 Merge remote-tracking branch 'upstream/master' into geom_range
 

 bump version up
 

 fix a bug
 

 Previous error in saving test files.
They should be saved with saveRDS instead of save function (with the option compress='xz').
Now the tests pass. We also had to re-save the data in /data with the same compression.
We also cleaned the data.R file. The names for the datasets are now the same as the saved files (in the data folder).
Because of this, we had to change the corresponding names in the examples and in the tests.
 

 bump version
 

 added rmarkdown in Suggest
 

 Update test-gh-actions.yml 

 Merge pull request #8 from ManonMartin/master

added the GHA to test for HPA version 

 debug bioc cmd check
 

 added the GHA test for HPA version
 

 feat: function to get version from hpa website
 

 Bump version number
 

 Bump version for citation and description changes
 

 Fix citation
 

 Add biorxiv citation
 

 Update version
 

 add unit test for single cluster est/sim
 

 rmv lazy data; add statmod to suggests; version bump
 

 Version bump.
 

 Update .gitignore.
 

 Use HTML vignette.
 

 Fix checking object class.
 

 Fix: accidentally left 1000 repeasts for model training in the vignette
 

 vignette single cell example
 

 Fix: disabled error check for factor columns in survival_time
* Support has been added for attepting a coercion, then erroring only if it fails to yield the expected types
* Modified the event_occurred error test to check for the new error message
 

 Fix: CohortList no longer drops mDataType
* Also added factor handling to SurvivalExperiment for surival_time and event_occurred columns
* Verison bump for BioC
 

 bump up version
 

 fix error in DESCRIPTION because of rmarkdown dependency
 

 Explicitly import grid dependencies to avoid conflict bewtween grid::pattern and Biostrings::pattern.
 

 bump version 2.5.7
 

 update API protocol from website
 

 remove extra output from error vignette
 

 added rmarkdown to Suggests to resolve changes in knitr
 

 add rmarkdown to Suggests in DESCRIPTION per changes in knitr
 

 Merge pull request #248 from vjcitn/vince_M1_file

needed on M1 mac 

 added reference to vignette; added rmarkdown to Suggests
 

 fix in evaluatePrediction(); version number bumped to 1.27.1
 

 fix of plot() method; version number bumped to 2.21.1
 

 Add rmarkdown in Suggests:
 

 v-0.99.7
 

 v-0.99.6
 

 v-0.99.4
 

 v-0.99.2
 

 multiple fix to examples and vignettes
 

 minor, message omitted
 

 default assembly
 

 added attachManifest
 

 updated the users guide
 

 fixing recent issue with soft dependency of rmarkdown in knitr. Version bump to rebuild.
 

 version
 

 commit1_17June2021
 

 Fix: bug in computeLimmaDiffExpr
* The protocolData of a SummarizedExperiment is not subset in subsetTo (nor should it be)
* Added a workaround where I delete it in the function for now
* Ultimate solution will be to remove protocol data in ORCESTRA
 

 Merge branch 'master' of github.com:bhklab/ToxicoGx
 

 Fix: removed GHA for Windows and macOS single workflows are broken
* Updated the GHA badge in README.md
 

 update NEWS
 

 Aligning versions

Making sure versions are aligned with the current bioconductor releases
fixing build issues with sce conversion
prepping for expanding functions - yeah I said it, not just check out the dev branch
 

 bug fix: my bug fix
 

 Start to reintroduce malloc
 

 Add rmarkdown to Suggests

       - changes in knitr require explicit declaration
 

 update cite
 

 added link to scanmirapp 

 fixed misreported slicing and bug in unlist Rle
 

 removed final gc
 

 changed merging of Rle fields
 

 fixed wobble display, changed sequence display to RNA
 

 relaxed TDMD end binding rule
 

 added get8merRange 

 simplified TDMD rule
 

 Merge branch 'jomain'
 

 fix: fix LC-MS/MS vignette and unit tests (issue #564)
 

 Revert "Bump BioC test environment to 3.15"

This reverts commit 5c4cae7330ef5d74883d056636acf9e96c22f097
which was obviously the wrong approach.
 

 Merge branch 'master' into jomain
 

 Removed blank line to fix broken DESCRIPTION file
 

 Minor adjusts in metadata. Version bump.
 

 remove censoring option (that was never functional)
 

 fixed a wanring.
 

 fixed the bug of multiple boolean values in "if"
 

 moving rmarkdown dependency to Suggests
 

 Update DESCRIPTION
 

 Update Coding Practice

Yeah that's right, just formating based on devtools and bioccheck to commit to bioconductor, not particularly sexy
 

 Update utils.R

fix lengthDF function for multichains 

 Fix grabMeta()

Added conditional assessment of colnames in meta data 

 Update README.md

fix spelling 

 Update README.md 

 Merge branch 'dev' into master 

 CombineTCR() issue

Issue with situation in which given two contigs of a barcode - one is assumed TCRA and the other is assumed TCRB
 

 Update utils.R

Fixed _ use in length call
 

 Update utils.R

Refined parseBCR to ensure all light chains are properly recorded
 

 Update clusterTCR.R

Removal of Vgene addition
 

 Update vignette.Rmd
 

 Updating Diversity Downsampling
 

 Merge remote-tracking branch 'origin/RELEASE_3_12'

Trying to figure this out
 

 Merge pull request #70 from ncborcherding/master

Sync merge for bioconductor 

 Update diversity.R

Add bootstraps to diversity estimates
 

 Update seuratFunctions.R

Fixing attributes
 

 Update vignette
 

 update utils
 

 Merge pull request #61 from ncborcherding/refine

Setting the Dev back 

 Update README.md 

 Devtools::check()
 

 Update clusterTCR.R
 

 Create clusterTCR.R

Use to cluster TCR chains by edit distance.
 

 Update README.md 

 Fix parseBCR 

 adding da truth

10x output changed for productive chains
 

 Update seuratFunctions.R
 

 Updating calling of BCR clonotypes

Modified the way BCR clonotypes are called by:
1) Caclulating normalized edit distance using Levenshtein method
2) For CDR3 nucl with <= 0.15 normalized distance, a igraph is formed where the compoenents are called to create an effective clonotype cluster by global convergence
Note) This substantially increases the amount of time for combineBCR() but is so much better approach so I am cool with it for now.

In addition updated the NEWS, DESCRIPTION and startrac.R to reflect updates or edits in examples.
 

 Update utils.R

Adding dplyr import 

 Merge branch 'master' into dev 

 Update README.md 

 Update DESCRIPTION 

 Merge pull request #14 from scfurl/master

Support for Monocle3

Had to update the DESCRIPTION to include monocle3 into dependencies. Will test the contributions this week. 

 Update DESCRIPTION
 

 add support monocle3 (2)
 

 Version bump
 

 Adapted namespace imports to account for changes in BiocGenerics; version number bumped to 1.25.1
 

 fix: add .github folder to gitignore
 

 feat: export/import CHARGE in correct format (issue #16)
 

 Update version bump
 

 fix iso code
 

 'biocthis' version 1.3.1 generated GHA
 

 Add test cases for 'plotMutSites' function; Minor code reformat
 

 Enable plot functions for 'parallelSites'
 

 The first 'stable' path as default 'lineagePath'
 

 move checks on family to method instead of internal function

Adding the two.stage argument introduced a bug where if 'family'
was not a character string, fitNullModel would fail.
One of the family checks requires the two.stage argument, which
is not passed to the internal .fitNullModel function. Move these
checks to the data.frame method instead (in the form of another
internal function). The internal function now assumes that
'family' is in the form of a function all (e.g., 'gaussian()'),
so modify unit tests accordingly.
 

 bug fix: allow MatrixGenotypeReader in pcrelate

GenotypeData objects created with MatrixGenotypeReader would fail
since there was no readGeno method defined. Fix this by adding a
method.
 

 change description
 

 Merge remote-tracking branch 'origin/main'
 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Update DESCRIPTION 

 Update DESCRIPTION 

 Update DESCRIPTION 

 Update DESCRIPTION 

 version bump
 

 Fix issue #141
 

 Fix issue #141
 

 logfile is disabled if the `omnipath.logfile` config option is `"none"`
 

 misc: `as_type` - convert variable to the type of another
 

 PrePPI: processing dbs and pubs columns
 

 docs: PrePPI scores
 

 example in kegg_pathway_annotations docs
 

 v3.1.1
 

 go annotations: using comment character instead of skip
 

 update API
 

 encapsulate single args in lists for @Bioconductor/AnVIL#37
 

 Update version number to 3.0.8 to start the rebuild
 

 Fix bug: The CalculateRI can't fit dose-response curve if all the response values are exactly same.
 

 update version number to 3.0.6 to initiate rebuild
 

 updated fractions
 

 Update utils_fractions.R 

 Update utils_fractions.R 

 Update utils_fractions.R 

 bug fix: wrapperWPM without any special wells not possible
 

 version 2.1.3
 

 fixed ref name zanotelli dataset
 

 version 2.1.1
 

 Added markdown as suggested package
 

 update news
 

 deal with corrupt cache; jump to 1.7.2
 

 Merge pull request #5 from bhklab/development

Fix: bug in validateModel,ClinicalModel,SurvivalExperiment-method 

 Merge branch 'master' into development
 

 Fix: Update GHA to fix PR merge conflict 

 Fix: deleted old GHA workflow file
 

 Testing `biocthis` GHA workflow 

 Changed R version in GHA workflow 

 Bugfix in row annotation code
 

 v1.21.1; correct check for BiocParallel params #148
 

 Fixed bug in mutation that caused (in very particular cases) individuals to reach bigger sizes than allowed.
 

 Merge remote-tracking branch 'origin/main'
 

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git add FEVV/man/
git commit -m "Fixed conflicts in version change"
git push upstream master
 

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git add FEVV/man/
git commit -m "Fixed conflicts in version change"
git push upstream mastere commit.
 

 restore original code
 

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git commit -m "Fixed conflicts in version change"Q
 

 Update DESCRIPTION 

 Update DESCRIPTION 

 Revidesemote-tracking branch 'origin/main'
 

 Update DESCRIPTION 

 Update DESCRIPTION 

 Update DESCRIPTION 

 update conf to be compatible with bioconductor
 

 allow to filter on full length for topanat analysis
 

 solve bug of filtering on sex, strain, celtype for releases before Bgee 15.0