mail and note fixes
 

 update NEWS
 

 Merge branch 'devel' of git.bioconductor.org:packages/RnBeads
 

 Added reshape to Depends
 

 final fixes for reduced time
- examples fixed with rda
- simplified vignette
- added rd doc for new rda files
 

 #92 pass stderr and stdout to system2 call
 

 bump down version
 

 make package buildable on bioc-submission
 

 update test
 

 Fix to reduce RCMD build time
 

 Merge branch 'bioc_devel'
 

 merge current dev into bioc_dev
 

 NEWS and version update
 

 added anno_gr_keys argument passing for feature annotation when whole pipeline is executed
 

 fixed some stuff after merge: 1) arg min_len  2) too high node threshold for the collapse similar
 

 local old version for paper
 

 splicejnc strict added
 

 version issue
 

 update man pages
 

 raise version to 6
 

 only add line
 

 fix normalizeRC test
 

 refactor: replace msdata by MsDataHub
 

 rm one of the double depends
 

 add more tests
 

 add _PACKAGE
 

 paste in stop error handling
 

 fix line breaks, error handling and add files for testing
 

 add content
 

 document data acquisition
 

 fix = assignements and 1:2 to seq
 

 rm print
 

 Fix documentation links
 

 do not unlist 'facet' columns when constructing tibbles

- fixes bug introduced when all 'organism' dataset entries have a
  single organism
 

 Merge remote-tracking branch 'origin/main' into devel
 

 update NEWS.md
 

 add pkgs to error output in checkInstalled
 

 re-add dependance for zlibbioc to windows build, as it seems to not build otherwise
 

 Update annotation seqinfo class with GenomeInfoDb
 

 Merge pull request #37 from lu000016/master

fix a typo in doc 

 bumped version
 

 Merge branch 'devel' into RELEASE_3_21 

 bumped version
 

 bump version for RELEASE
 

 Fixes needed for Bioconductor 3.22 release (#99)

* bump x.y.z version to even y prior to creation of RELEASE_3_20 branch

* bump x.y.z version to odd y following creation of RELEASE_3_20 branch

* bump x.y.z version to even y prior to creation of RELEASE_3_21 branch

* bump x.y.z version to odd y following creation of RELEASE_3_21 branch

* import OS detecting functions from basilisk

* update bioc version in github action

* switch r version to use

* add news and description

* reset windows environment

* Update basilisk.R

* Update basilisk.R

* Update basilisk.R

* Update test-plotting.R

* fix example

* last move away from basilisk.utils

* try pinning 'scvelo==0.3.3' for all three os

* switch github action macos runner to match BBS (macos-arm 13)

* fix conditions to match all macOS runners

* fetch R version appropriate version of units for macos

* downgrade llvm to last know version supported by llvmlite

* remove extra steps apparently not needed for macos runners

---------

Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Co-authored-by: A Wokaty <andres.wokaty@sph.cuny.edu>
Co-authored-by: Kevin Rue <kevinrue@users.noreply.github.com> 

 Fixed conflicts in version change
 

 formally deprecate all vdiffr functions, and attempt to work around data.table melt and dcast issues
 

 version bump
 

 Merge branch 'main' into devel
 

 Add citation.cff
 

 bumped version
 

 edits to visualization vignette
 

 polish up data vignette
 

 specify name of msigdbr arguments
 

 version merge
 

 Merge remote-tracking branch 'upstream/devel'
 

 Update to Bruker signature 

 update to bruker support email 

 Deprecated
- unresponsive
 

 Deprecation

 - unresponsive
 - emails bounced
 

 Deprecated

  - unresponsive
 

 updating the news and version bump 0.99.1
 

 fixes for bioconductor
 

 refactor: force immediate loading of Python libraries
 

 add last missing dependencies
 

 bump version
 

 bump version number to build E-GADGETS update
 

 Merge pull request #2 from SciomeLLC/dev

Vignette modifications and bug fix for missing data preprocessing 

 fixing bug in missing data preprocessing
 

 Final change to markdown -- change from David and Clare
 

 Minor additions from Clare
 

 Modifying vignette to clarify global permutation tests vs. not
 

 GenomeInfoDb to Seqinfo
 

 GenomeInfoDb to Seqinfo
 

 bump version
 

 Version update and adressing warnings.
 

 Testing Coralysis logo rendenring size
 

 Testing Coralysis logo rendenring size
 

 Testing Coralysis logo rendenring size
 

 parallel seqDigest()
 

 improve formalize function
 

 Fixed coverage badge in README
 

 Bump version
 

 Add funding
 

 Updating the README.md file
 

 add the demonstration mapping with ellmer
 

 Rename progressbar.
 

 docs: add labels to vignette code chunks
 

 ci: set RETICULATE_PYTHON_ENV to .Rprofile for macOS
 

 ci: next try to fix macOS GHA
 

 ci: create a virtual env for macOS
 

 refactor: use py_require instead of manual library installation

- Change to the new suggested `py_require()` functions from *reticulate* (issue
  #81).
 

 ci: use dependencies = TRUE
 

 ci: macOS install python with brew
 

 ci: use reticulate to install Python on macOS
 

 Remove std::cout.
 

 Bump version to 0.99.5
* Fix ORCID
 

 Bump version to 0.99.3
* Fix WARNING and some of NOTES for bioconductor checking
 

 Bump version to 0.99.1
 

 remove rtype arg from bfcdownload
 

 allowing messages to be true
 

 adding magick dependency
 

 Bump version to 0.99.2
 

 Merge branch 'devel' of github.com:LieberInstitute/DeconvoBuddies into devel
 

 Add option to plot a boxplot or violin plot with "plot_type"
 

 Resolve merge conflict in .gitignore and complete merge
 

 latest_changes
 

 Ignore RStudio project files
 

 Save changes to .gitignore and .Rproj before switching branches
 

 version bump 2.21.4
 

 update CRAN binaries URL in Dockerfile
 

 clean up references in vignette
 

 add Zheng2016-au bib entry and reference in vignette, closes #83
 

 update r-base in environment.yml 

 view3dStructure for multiple sequences.
 

 import genome and genome<- from Seqinfo
 

 Avoid ODR violations from copy-pasted struct definition.

Interesting that this wasn't picked up in the ~5 years that it was
introduced, but I guess that newer compilers are less cavalier about it.
 

 add package argument to lifeCycle
 

 fix: switch to pak::pkg_name_check()
 

 GHA checking using bioc devel instead of release
 

 Fixed NEWS file
 

 Merge branch 'devel' of git.bioconductor.org:packages/msqrob2
 

 Merge pull request #70 from alyst/fix_top_features

Fix topFeatures() 

 topFeatures(): cleanup filtering and sorting
 

 Forgot a comma
 

 link documentaions.
 

 version bump
 

 fix(dataProcessPlots): Convert pixels to inches for pdf plots (#167)

 

 Fix data.table bug in .logMissingness after data.table 1.17 update (#164)

 

 v1.37.4: minor modification: minor documentation update
 

 add citation to publication (#71)

* add citation to publication

* formatting changes 

 Remove data-raw folder, update DESCRIPTION
 

 Update DESCRIPTION for commit 'Depends on Seqinfo instead of GenomeInfoDb' and version bump
 

 Update package-level documentation
 

 Add test_data2.R to data-raw, update DESCRIPTION
 

 Merge pull request #167 from gdrplatform/GDR-2908

Gdr 2908 

 fix: update var name (II)
 

 chore: bump version and update NEWS.md
 

 doc: reoxygenate
 

 refactor: average biological replicates
 

 version bump
 

 Merge pull request #787 from salzcamino/master

Update runEnrichR examples 

 Merge branch 'compbiomed:master' into master
 

 fixing errors
 

 Update NEWS and vignette
 

 Fix version bump: 1.29.2
 

 add new Rd
 

 deleted file 

 uodated vignette and DESCRITPION
 

 TFEA.ChIP v1.19.2: Meta-analysis, wrapper workflow, database update, and performance enhancements (#4)

* Added new functionalities, updated regulatory data, and improved performance

* version bump

* Extended TFBS, missing else & mouse translation

- Extended TFBS database with 63 new ChIP-Seq experiment added.
- Missing else condition in txt2GR corrected.
- mouse (mus musculus) gene ID translation to human Entrez Gene IDs implemented.

* Update DESCRIPTION

version bump

* namespace update

* version bump

* substitute for loops with applys, expand documentation, and other corrections

* minor bug in plot_RES solved

* R version dependency

* minor bug in plot_RES

* TF gene symbols updated

* plot_ES bug fixed

* version

* plot LOR instead of OR

* adds metadata to getCMstats function

* GSEA_run compures weighted score, output tables include metadata, plot_CM plots log(OR)

* bug at plotting log(OR) solved

* bug in GSEA_EnrichmentScore solved

* getCMstats modified to include distances

* Solved bug in GR2tfbs_db

Now ChIP-Seqs that don't have any peaks assigned to genes are eliminated from the output list.

* Update All-functions.R

* plot_CM function modified to accept new table containing log2OR and log10.adj.pval columns

* Bug in GSEA_run fixed

* database updated, includes distant TFBS, all documentation and test units updated

* update example datasets and its documentation

* example data updated

* correction in dataset documentation

* man pages updated

* version bump

* Unit test error solved. Checking if biomaRt host is available before translating mouse IDs

* bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

* bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

* bug in GR2tfbs solved (extracting ChIP-seq IDs)

* Added mouse to mouse ID translation and updated database

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

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

* update: TF ranking & faster GSEA_run

* Warning solving: extra man page removed

* bug solved in get_chip_index (encode ChIP selection)

* multiple boolean variable error solved

* multiple boolean variable error solved

* multiple boolean variable error solved

* Bug in preproccessInputData solved (DESeqResults to data.frame)

* New gene-TR database. See NEWS file

* New gene-TR database. See NEWS file

* tests updated

* bug in GeneID2entrez examples solved

* testing issue in test_contingency_matrix solved

* bump x.y.z versions to even y prior to creation of            RELEASE_3_9 branch

* bump x.y.z versions to odd y after creation of RELEASE_3_9    branch

* trimming whitespaces in gene IDs in preprocessInputData()

* trimming whitespaces in gene IDs in preprocessInputData()

* bug fix in GeneID2entrez: toupper() call moved to h2h section

* version bump

* bug fix in preprocessInputData: toupper() call added to h2h section

* error in GeneID2entrez solved

* Citation file added

* bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

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

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

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

* bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

* bump x.y.z version to odd y following creation of RELEASE_3_12 branch

* Simplified plotting functions and data objects stored

* bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

* bump x.y.z version to odd y following creation of RELEASE_3_13 branch

* bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

* bump x.y.z version to odd y following creation of RELEASE_3_14 branch

* Pass serialized S4 instances thru updateObject()

* Version 2.1.1 upgrade

* Corrected version number

* Corrected version number

* patched error on BioC builder

* Version bump

* updated vignette

* updated vignette

* upgraded version

* new changes

* updated vignette and db

* changed vignette and fxs

* changed NEWS

* Delete vignettes/.Rhistory

---------

Co-authored-by: Laura Puente-Santamaria <lpsantamaria@iib.uam.es>
Co-authored-by: LauraPS1 <lpsantamaria@iib.upm.es>
Co-authored-by: luis <lpeso@iib.uam.es>
Co-authored-by: vobencha <valerie.obenchain@roswellpark.org>
Co-authored-by: vobencha <vobencha@gmail.com>
Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
Co-authored-by: Hervé Pagès <hpages.on.github@gmail.com> 

 changed NEWS
 

 updated vignette and db
 

 upgraded version
 

 updated vignette
 

 Version bump
 

 patched error on BioC builder
 

 Corrected version number
 

 Version 2.1.1 upgrade
 

 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
 

 Simplified plotting functions and data objects stored
 

 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch
 

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

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 

 error in GeneID2entrez solved
 

 version bump
 

 trimming whitespaces in gene IDs in preprocessInputData()
 

 trimming whitespaces in gene IDs in preprocessInputData()
 

 bump x.y.z versions to even y prior to creation of            RELEASE_3_9 branch
 

 bug in GeneID2entrez examples solved
 

 New gene-TR database. See NEWS file
 

 Bug in preproccessInputData solved (DESeqResults to data.frame)
 

 multiple boolean variable error solved
 

 bug solved in get_chip_index (encode ChIP selection)
 

 Fixed conflicts in version change
 

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

 Added mouse to mouse ID translation and updated database
 

 bug in GR2tfbs solved (extracting ChIP-seq IDs)
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
 

 version bump
 

 correction in dataset documentation
 

 update example datasets and its documentation
 

 Bug in GSEA_run fixed
 

 Update All-functions.R 

 getCMstats modified to include distances
 

 bug at plotting log(OR) solved
 

 adds metadata to getCMstats function
 

 version
 

 TF gene symbols updated
 

 R version dependency
 

 substitute for loops with applys, expand documentation, and other corrections
 

 Merge branch 'master' of https://github.com/LauraPS1/TFEA.ChIP
 

 Update DESCRIPTION

version bump 

 version bump 

 resolve
 

 fixing infRepsImporter for oarfish & piscem
 

 improvements to allow outline plots
 

 update import used to run the function create_TxDb
 

 increase version number
 

 Merge remote-tracking branch 'upstream/devel'
 

 Merge pull request #12 from KlausVigo/devel

Devel 

 Update DESCRIPTION 

 added a function to swap the minor edges of an evonet object
 

 merge
 

 Remove BisqueRNA.
 

 add sticker for mastR
 

 Added workflow image into README.
 

 Update package: with mutiple code re-written
 

 version bump 063025
 

 Bumped version to trigger rebuild.
 

 pinned versions done
 

 bug fix
 

 Updated script that processes gnomAD data
 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 Merge branch 'updated_method' into develop
 

 updated each bgeecall functions imports with only the external packages and functions needed. Notably to avoid intersect function being taken from Biostring instead of IRanges
 

 Updated Rd files and added missing ones
 

 Merge branch 'updated_method' of github.com:BgeeDB/BgeeCall into updated_method
 

 added exception handling when intergenic don't receive reads
 

 Removed unused comment
 

 Corrected use of correct class attributes (attribute read_size_kmer_threshold is in class myKallisto;etadata and not myAbundanceMetadata)
 

 updated read_size_kmer_threshold with the correct class AbundanceMetadata instead of myKallistoMetadata
 

 Added code to retrieve random libraries from SRA for new Species
 

 Corrected ensembl metazoa ftp link
 

 Added generation of reference intergenic regions by removing outliers found with transcriptomic evidence
 

 Updated kallisto to use small index depending on the threshold set in the KallistoMetadata instead of a hardcoded 50
 

 Corrected format error in merging libraries
 

 Added generation of initial intergenic regions
 

 Added weighted pValue merging option for both the mean and median method
 

 Added outliers removal to intergenic abundances using Tukey's method (interquantile range)
 

 corrected error collect_padjValues not found
 

 removed the taking of the minimum pValue for merging approches
 

 modified read size threshold for small kmer use
 

 updated functions headers
 

 Added new pvalue caclulation method
 

 Add Mastodon 

 bump version
 

 Merge branch 'BIOC_master'
 

 bump version
 

 rename intergenic directory
 

 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
 

 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
 

 Add badges 

 Merge branch 'RELEASE_3_13'
 

 bump version
 

 Merge remote-tracking branch 'upstream/devel'
 

 added processing comment to listcolumns
 

 Add Seqinfo to imports in DESCRIPTION
 

 renameSeqlevels is now exported by GenomeInfoDb package
 

 Added curl download