Added a detailed NEWS entry for this traumatic change.
 

 Calls to functions defined in pwalign are now redirected there

The following Biostrings functions are now implemented in the new
pwalign package:
  - pairwiseAlignment
  - PairwiseAlignments
  - PairwiseAlignmentsSingleSubject
  - writePairwiseAlignments
  - alignedPattern
  - alignedSubject
  - insertion
  - deletion
  - unaligned
  - aligned
  - indel
  - nindel
  - nedit
  - pid
  - mismatchTable
  - mismatchSummary
  - compareStrings
  - stringDist
  - nucleotideSubstitutionMatrix
  - errorSubstitutionMatrices
  - qualitySubstitutionMatrices

Note that they are still temporarily defined in Biostrings but now
they just call the corresponding function in pwalign. Since this is a
temporary redirect, the user also gets a warning that tells them to use
the fully qualified name (e.g. pwalign::pairwiseAlignment()) to call
the function.
 

 bug fixed, #48
 

 updated vignette
 

 Added hypergeometric test
 

 Version bump
 

 Manually edit output of devtools::document() to avoid documenting usage of defunct code
 

 Code clean up

  - temporarily disbale test
  - clean up some Rd notes
 

 bioC second review
 

 update rd

update the Rd file
 

 Update vignette to emphasize full package nature of BatchQC
 

 updated DESCRIPTION
 

 Notes corrections and update to Matrix version
 

 Merge pull request #64 from nqgurevich/temp2

plotting bug fixes 

 Documentation update for compare_results
 

 Bug fix in comparison plotting
 

 Cosmic v2 signature names consistent format with v3
 

 Add question in every pages
 

 modify version number of Matrix in description
 

 TCGA import error
 

 [change] change slot name of CircSeqAlignTkCoverage.
 

 Removed creating_a_methylation_rse_from_methylation_array_files vignette due to problem downloading files with TCGAbiolinks
 

 minor version bump
 

 more of ctlab/genome -> alserglab
 

 fixed leadingEdge calculation depending on scoreType
 

 Downgraded GSVA version
 

 Merge pull request #756 from mingl1997/devel

prep for BioC release 

 need to fix GSVA functions
 

 edge case fix for FlatFile inputs
 

 fixing Seurat documentation for BioC release
 

 Merge pull request #754 from joshua-d-campbell/devel

Devel 

 Merge pull request #23 from compbiomed/devel

Devel 

 Bugfix in plotHFGC
 

 Merge branch 'devel' of https://github.com/adeschen/enrichViewNet into devel
 

 Merge pull request #19 from adeschen/adeschen-patch-5

Update .Rbuildignore 

 Update news file
 

 Update news file
 

 Update vignette
 

 Update vignette
 

 Update check-bioc.yml 

 Update test-coverage.yaml 

 Update test-coverage github action
 

 Update test-coverage github action
 

 Update test-coverage github action
 

 Update test-coverage github action
 

 Update test-coverage github action
 

 Add unit tests
 

 Update vignette
 

 Use smaller quality image in vignette
 

 Update unit tests
 

 Update error message and associated unit test
 

 Update checkout action in test-coverage github action
 

 Update error message it createEnrichMapMultiComplex() function and associated unit test
 

 update createEnrichMapMultiComplex() function
 

 Use current bioc version in check-bioc action
 

 Clean macos section in check-bioc actions
 

 Force brew update
 

 Force brew update
 

 Force install icu4c
 

 Update XML install on mac os in check-bioc action
 

 Update XML install on mac os in check-bioc action
 

 Add createEnrichMapMultiComplex() function
 

 Update checkout version to v4
 

 Force using Node20 for action cache in check-bioc
 

 Force using Node20 for action checkout in check-bioc
 

 Update doc for extractInformationWhenNoIntersection() function
 

 Update doc for extractNodesAndEdgesInformation() function
 

 Update doc for parentalNapaVsDMSODEG dataset
 

 Update doc for demoGOST object
 

 Update doc for rosaNapaVsDMSODEG object
 

 Update doc for parentalNapaVsDMSOEnrichment dataset
 

 Update doc for rosaNapaVsDMSOEnrichment() function
 

 Update NEWS file
 

 Update doc for extractInformationWhenNoIntersection() function
 

 Update doc for demoGOST dataset
 

 Update doc for rosaNapaVsDMSODEG dataset
 

 Update documentation for removeRootTerm() function
 

 Move the NEWS file to main directory
 

 User smaller version of figure in vignette
 

 Correct indents in vignette
 

 Correct indent in code
 

 Update documentation
 

 Add unit test for createMultiEmap() function
 

 Update vignette
 

 Update check-bioc action to use the devel branch
 

 Update vignette
 

 Update createMultiEmap() function
 

 Add unit test for createEnrichMapMulti() function
 

 Add unit test for createEnrichMapMulti() function
 

 Adding unit tests for createEnrichMap() function
 

 Add line parameter to functions creating emaps
 

 New manageNameDuplicationInEmap() function
 

 Add unit tests for createEnrichMapMulti() function
 

 Update action to include devel branch
 

 Update vignette
 

 Remove old functions and new tests for extractInformationWhenIntersection() function
 

 Rectoring
 

 Update indent
 

 Merge pull request #8 from AGImkeller/bioc_review_2

Bioc review 2 

 Updated NEWS; ready to bump version
 

 Extended package installation checks for optional functionalities and also added them to the SCAE-Constructor
 

 updating version from 0.99.17 to 0.99.18
 

 Updated controlPlots
 

 update JS to use alserglab for TCGA files
 

 Update data_import.Rmd
 

 Rolled back C++20 requirement to C++17
 

 Merge pull request #13 from imbeimainz/size_time_down

Size and time brought down! 

 updated news for version 0.99.3, bumped already
 

 smaller size of elements to buttonify & include in tables, should cut down nicely on the size of the final html document
 

 1.11.106 : modelvar : assert unique values in `fit` and `coef` args
 

 Merge pull request #128 from rformassspectrometry/jomain

Add common_path function 

 Merge branch 'main' into jomain
 

 Merge branch 'main' into jomain
 

 Update R/binning.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 

 feat: calculate sequence with increasing difference between values

- Add function `breaks_ppm` to calculate a sequence of values with increasing
  difference between value pairs.
 

 Version update
 

 Improving server error handling
 

 fixed github issues #3 and #9
 

 fixed version number conflict
 

 fixed illegal version bump
 

 fixed github issue #5... bumped version
 

 fixed github issue #6 about global variables
 

 replaced gloabl phasing matrices by ZP specific R environment
 

 fixed build errors
 

 fixed github issue #1... deviating chromosome annotations chr1 - 1
 

 moved external debugging script into repo
 

 limma 3.59.9

- Fix to detectionPValues() example.
 

 fix the empty GeneName due to org.Hs.eg.db bug
 

 Merge

Merge branch 'main' into devel
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
 

 Merge pull request #36 from SONGDONGYUAN1994/devel

Devel 

 Merge pull request #35 from chexjiang/devel

revise typos 

 Merge pull request #33 from SONGDONGYUAN1994/main

Merge devel 

 Fix bugs in dimensions
 

 Merge branch 'devel' into main
add new cov
 

 Fixed default params for spatial and pseudotime

The quick start guide claims the default params for spatial and pseudotime are NULL. I fixed the code to reflect this issue. 

 Version bump
- Argument names have been changed so need to run check() again
- Also have two fewer notes
 

 Updated many arguments to use camelCase
- Also added type checking for qtle objects
 

 Replace 1:n with seq_along and seq_len
- Also changed some variable names to camelCase
 

 Remove .multistate_pattern_check function
- Function was not used in any source code and couldn't discern the function.
 

 update README
 

 Updated GitHub URL in DESCRIPTION
 

 usage
 

 add ... to as_facets()
 

 added links_data param
 

 add check for unix package


Merge-request: PHANTASUS-MR-44
Merged-by: Alexey Sergushichev <alsergbox@gmail.com> 

 org databases to suggestions
 

 fix undocumented parameter
 

 changed to R 4.4
 

 re-added infinite<-0 handling back to localOuliters and localVariance after running into NA issues
 

 updated install instructions for Bioc release
 

 Update unit tests to account for TrEMBL ID results

- SomaScan.db currently returns both SwissProt (manually
  reviewed/curated) and TrEMBL (uncurated) IDs from UniProt, while the
  SomaLogic online menu tool only uses SwissProt IDs
- future releases of SomaScan.db will (ideally) exclusively return
  SwissProt IDs as well - the current tests comparing online tool and
  SomaScan.db are failing, but these tests are vulnerable to changes
  caused by AnnotationDbi
- tests are now skipped, but will be retained as they will be more
  relevant in the future
 

 update the gleamTest to accept single input.
 

 add multiple instance learning to classification workflow
 

 Resolve https://github.com/LieberInstitute/Habenula_Visium/issues/5 reported by @cyntsc
 

 venn <- vennCount(c(bed, gff))
vennPlot(venn)
 

 add multiple instance learning; various bugfixes
 

 v2.5.16 bugfixes and doc updates
 

 update mi_learn() docs again
 

 updated cv_do() and mi_learn()
 

 Deprecate

 - unresponsive
 

 Switch from aws.s3 to paws.storage for interacting with R2.

This avoids problems with aws.s3::get_object whereby incomplete
downloads do not cause an error, allowing the creation of invalid caches.
paws.storage also seems to be more actively maintained.

Incidentally, the error handling of paws.storage is better, allowing us
to replace prechecks with a simple tryCatch when the key doesn't exist.
 

 documentation update
 

 correct documentation
 

 adjust notes and warnings
 

 new sysdata
 

 roxygenise COXISSign
 

 resolve conflict
 

 add code for COXISSign function
 

 roxygenise COXISSign
 

 update sysdata with dataframe for COXIS_Bonavita
 

 add code for COXISSign function
 

 add test for ICBResponseSign
 

 add ICBResponse_Chen signatures in utilityfunctions
 

 add code for ICBResponseSign
 

 Update fixed files
 

 Fix confilicts
 

 Fix conflicts
 

 add packages in description
 

 update vignette
 

 Merge branch 'LRRC15_CAF' of gitlab.romualdi.bio.unipd.it:stefania/signifinder into LRRC15_CAF
 

 roxygenise LRRC15CAFSign
 

 new sysdata
 

 add LRRC15CAFSign function
 

 Merge branch 'PTEN_MITF' of gitlab.romualdi.bio.unipd.it:stefania/signifinder into PTEN_MITF
 

 add getSignGenes
 

 roxygenise LRRC15CAFSign
 

 new sysdata
 

 add LRRC15CAFSign function
 

 add MITFlowPTENneg_Cabrita dataframe in sysdata
 

 add signature function MITFlowPTENnegSign
 

 fix conflicts
 

 Update of new gsva method
 

 Addition of BreastState_Wu function in SignatureFunction, BreastState_Wu name in UtilityFunction and update sysdata
 

 v1.15.3 -- bump version after Nick's latest commits
 

 Add several unit tests for vis_gene
 

 Make capitalization consistent for layer names
 

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

 Unlabeled and coloured pca plot included
 

 Vignettes has been updated
 

 check whether there are no DEGs has been added to compute 2nd pca
 

 parse_pseudocounts script and function added
 

 Citations updated
 

 v0.99.17
 

 Bump version
 

 version UP
 

 Fixed an error in Bioc daily check.
 

 remove some tests and make vignette smaller
 

 Restored the Leng assay names to normcounts, which is accurate.
 

 Update some details in the user's guide.
 

 Small roxygen fix and devtools::document()
 

 Check and normalize 'center' argument before passing down to matrixStats (#38)

* Check and normalize 'center' argument before passing down to matrixStats

* restore empty line 

 Update merged-pancreas.Rmd

- Courser clustering of donor-integrated data to retain good matching of clusters to proposed cell labels
 

 Updated addEditedAlleles when no nucleotide changes found
 

 reduce plot quality
 

 Add authors to clusterGraph, graph, and DESCRIPTION (#23)

 

 bump version
 

 Update cell-cycle.Rmd

- Migrate to non-legacy `scRNAseq::LengESCData()`.
  - See https://github.com/LTLA/scRNAseq/issues/50
 

 Update more-hvgs.Rmd

- Migrate to non-legacy `scRNAseq::SegerstolpePancreasData()`
  - See   https://github.com/LTLA/scRNAseq/issues/48
 

 fix sp of htmltools + bump version
 

 review changes + bump version
 

 Updated typos in BatchQC_Intro vignetter
 

 add Solomon as a contributor
 

 Fix the confliction issue of complexUpset and ggplot2.
 

 add news file
 

 v0.99.9
 

 Merge branch 'main' of github.com:richardheery/methodical into main
 

 1.11.105 : summarize_fit : add assertion to make sure no duplicate columns
 

 correct tests and new snapshots
 

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

# Conflicts:
#	DESCRIPTION
 

 Merge branch 'feature/EPICv2' into devel
 

 Removed deprecated ggplot code, changed default values for assembly and normlization
 

 Format report text / Implement function for gene symbol retrieval / Code cleanup
 

 Create cluster profile for LSF cluster and updated documentation
 

 Started drafting LSF cluster architecture
 

 Fix typo of probesMMBC in rnb.get.snp.matrix()
 

 Minor reference fix
 

 Fix SNPs anno column names
 

 Improve nv-probe related sections. / Minor fixes
 

 Improve variable name
 

 Code cleanup
 

 Merge branch 'improve/SNPs_filtering'
 

 Improve assembly selection for EPICv1 and 450K platforms / Address bugs
 

 Use SNPs MAF column in probesEPICv2 annotation to filter bad probes
 

 Update RnBeadRawSet-class.R 

minor correction 

 Add TODO markers for EPICv1 hg38 compatibility / Fix syntax for MMBC control probe annotation
 

 Add GEO platform ID of EPICv2 / Improve comments
 

 Improve comments / Uncomment an if-block
 

 Fix get.annotation function for EPIC v2 / Clean code
 

 EPIC v2 update initial commit
 

 0.99.7