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
 

 remove .Rproj file
 

 Merge branch 'devel' of ssh.code.roche.com:scwg/gene-transcriptional-network/activity-inference/epiregulon.extra into devel
 

 edit DESCRIPTION
 

 Merge pull request #129 from stemangiola/fix-bioc-checks

fif checks 

 fif checks
 

 sync
 

 docs(converters): Add log warning messages indicating that converters will be deprecated in favor of those in MSstatsConvert (#120)

* docs(converters): Add log warning messages indicating that converters will be deprecated in favor of those in MSstatsConvert

* docs(parallel-processing): Rename MSstatsSummarizeV2.Rd to MSstatsSummarizeWithMultipleCores.Rd

* switched from WARN log to message 

 version bump 

 docs(pull-request): Add pull request template and automatic dry run builds (#117)

 

 feat(groupComparison): Enable parallel processing for groupComparison function (#110)

* feat(groupComparison): Enable parallel processing for groupComparison function

* refactored single core vs multicore group comparison into separate util functions

* update documentation regarding groupComparisonWithMultipleCores util function

* fix(groupComparison): Remove return statements, define environment() variable, fixed all_proteins_id iterator

* docs: Updated docs to mention that parallel processing only works for Linux/Mac OS 

 Changes for version 3 release

 Committer: Erik Wright <eswright@pitt.edu>
 Changes to be committed:
	modified:   DESCRIPTION
	modified:   R/AlignPairs.R
	modified:   R/BrowseDB.R
	modified:   R/BrowseSeqs.R
	modified:   R/FindSynteny.R
	modified:   inst/CITATION
	modified:   man/AlignPairs.Rd
	modified:   man/BrowseDB.Rd
	modified:   man/BrowseSeqs.Rd
	modified:   man/Clusterize.Rd
	modified:   man/FindSynteny.Rd
	modified:   vignettes/ArtOfAlignmentInR.Rnw
	deleted:    vignettes/BrowseDBOutput.png
	deleted:    vignettes/BrowseSeqsOutput.png
	modified:   vignettes/ClusteringSequences.Rnw
	modified:   vignettes/DECIPHERing.Rnw
	new file:   vignettes/FunctionalRelationships.pdf
	modified:   vignettes/GrowingTrees.Rnw
	modified:   vignettes/SearchForResearch.Rnw
 

 testfile: cellz biosample id prefix change
 

 [FIX] getGenomePairs failed after oma api change
 

 bump
 

 More tweaks to UCSC.api.url() and its man page
 

 remove the now-deprecated plotMedExprs()
 

 compile metadata
 

 version
 

 update documentation
 

 update namespace for SCE objects
 

 update title
 

 update DESCRIPTION
 

 update descriptions
 

 update metadata
 

 Merge branch 'devel' into devel 

 fix version number
 

 rename 'ground truth' to 'reference' annotation labels
 

 small update on data obj col and row names. to update vignette.
 

 Fixing documentation
 

 version bump 1.39.34
 

 version bump 1.39.33
 

 filter out invalid blank parents
 

 remove magick pkg and fix note
 

 Merge pull request #113 from PhanstielLab/hicsquare_rot

Hicsquare rot 

 genome label updates for compatibility with new plotHicSquare parameter
 

 add new files
 

 Update data_import.Rmd
 

 Merge pull request #27 from EnesSefaAyar/master

Acquisition protocol update 

 fix Acquisition protocol
 

 Merge pull request #92 from jessmcc22/devel

Updated BatchQC Intro to reflect current state of shiny app 

 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
 

 Merge pull request #91 from jessmcc22/devel

Added log only normalization option 

 Added log only normalization option
 

 fix building errors, replace open/close gdsn ops with acquireGDS per updated GDSArray
 

 modify vignette to demonstrate use of 'geneSetSizes()' in limma example
 

 restore dependency on scMultiome
 

 add missing imports
 

 v0.99.14
 

 Add docs change
 

 Fix selection of left-most central acceptor, add documentation
 

 1.11.102 : fukuda20.proteingroups.txt : bitbucket -> extdata
 

 1.11.101 : plot_sample_nas : imputation blocks had to be identified BEFORE imputation
 

 NEWS update
 

 update news
 

 Fix typo in vignette 

 Version bump
 

 Update reference
 

 update
 

 Update segerstolpe-pancreas.Rmd

- Migrate to non-legacy data
  - See https://github.com/LTLA/scRNAseq/issues/48 and https://github.com/OSCA-source/OSCA.workflows/pull/5
 

 Version bump
 

 Update nestorowa-hsc.Rmd

- To accommodate changes in `scRNAseq::NestorowaHSCData()`
  - FACS data moved from the `colData` to its own `altExp`
  - See https://github.com/LTLA/scRNAseq/issues/47#issuecomment-2049038702
 

 updated effective samp size calc and documentation
 

 printing number of samples while indexing counts
 

 fix missing fgsea files bug
 

 fix documentation errors
 

 pull master
 

 update for DESeq2

update for DESeq2 and CEDAR DE methods
 

 update try on version

update try on version 1.1.0
 

 change R version
 

 version
 

 Update r.yml 

 Merge pull request #161 from rcastelo/160-warning-missing-link-or-links-in-documentation-object-gsvard-dgcmatrix

fix WARNING Missing link or links in documentation object 'gsva.Rd': … 

 1.11.100 : Fix `systematic_nas`
 

 fix: add parameter rtimeDifferenceThreshold for ObiwarpParam

- Add a parameter `rtimeDifferenceThreshold` for `ObiwarpParam` to allow
  increasing the tolerance to define *gaps* in the sequence of retention
  times. This fixes issue #739.
 

 docs: fix typos mentioned by Carl
 

 tests: remove obsolete line to stop parallel processes
 

 ci: ensure packages are indeed installed from source
 

 ci: install also RCurl
 

 ci: force installation of MsCoreUtils from github
 

 ci: install packages from source
 

 ci: force installation of MsCoreUtils from github
 

 Fix quoting of Orcid
 

 fixes
 

 Merge branch 'devel' into lama 

 Squashed commit of the following:

commit c37baa789f0b55768ba43362ce19d32cadaef110
Author: jorainer <johannes.rainer@gmail.com>
Date:   Mon Mar 18 07:59:02 2024 +0100

    fix: update required Spectra version

commit 2faed9073ad90cb7aa785ca1ba565fd99dbd7eca
Author: jorainer <johannes.rainer@gmail.com>
Date:   Fri Mar 15 14:58:39 2024 +0100

    fix: require ProtGenerics 1.35.4

commit 086999d759fce9129993f39924a202f0d472a651
Author: jorainer <johannes.rainer@gmail.com>
Date:   Thu Mar 14 14:46:02 2024 +0100

    refactor: cleanup NAMESPACE and dependencies and documentation

    - Re-save data object.
    - Fix documentation and unit tests following the move of `MSnbase` from Depends
      to Imports.

commit 97d7d4c8c86e637893b50d8340385045ba410ad7
Author: jorainer <johannes.rainer@gmail.com>
Date:   Thu Mar 14 13:54:53 2024 +0100

    docs: replace inst/NEWS with NEWS.md

commit a455e6b229c0d0c4d1501effcd6a0f12d96b85e9
Author: jorainer <johannes.rainer@gmail.com>
Date:   Wed Mar 13 09:54:18 2024 +0100

    refactor: clean up namespace

    - Remove not required packages.
    - Move packages from Depends to Imports.

commit 28e4ca7c0732ef20b3aed3ea9864c55d8b9c0009
Merge: 19b1b9ab 90c30b8e
Author: jorainer <johannes.rainer@gmail.com>
Date:   Fri Mar 8 16:09:04 2024 +0100

    Merge branch 'devel' into jomain

commit 19b1b9ab5debbb1faf880809f0e8c7b3d51bccd2
Author: jorainer <johannes.rainer@gmail.com>
Date:   Tue Feb 27 11:04:15 2024 +0100

    refactor: ensure backward compatibility of parameter objects

commit 40c09c00480e310ce8b187210bab01558869ff5c
Merge: 17b487fb 48ac5e0c
Author: jorainer <johannes.rainer@gmail.com>
Date:   Tue Feb 27 11:01:02 2024 +0100

    Merge branch 'devel' into jomain

commit 17b487fb2884162b2b0cac3be9979e4546c412a0
Merge: c36018be 1cf7cda4
Author: jorainer <johannes.rainer@gmail.com>
Date:   Mon Feb 5 14:49:22 2024 +0100

    Merge branch 'devel' into jomain

commit c36018be05da2d96f0592007ca8444ca36d0665c
Author: jorainer <johannes.rainer@gmail.com>
Date:   Thu Feb 1 15:43:19 2024 +0100

    fix: call updateObject for some Param classes in as.list
 

 fixes
 

 fix
 

 reorganise
 

 Update XcmsExperiment.R
 

 Merge branch 'devel' into lama
 

 changes
 

 Update adjustRtime.Rd
 

 Use verbose conversion as demanded by Matrix
 

 Update documentation
 

 Merge pull request #43 from rformassspectrometry/jomain

feat: add spectraSampleIndex function 

 feat: add spectraSampleIndex function

- Add `spectraSampleIndex()` function.
- Update documentation to use `()` for functions.
 

 fix indent
 

 parallel threads set to 1
 

 version update
 

 add makeDGE checks, fix documentation, change p-value threshold to 0.05
 

 fixed kbl tables in the reports for 2D analysis
 

 fixed the issue when there are no significant sets
 

 Regenerated docs for v2.13.2
 

 Fixes to examples for DEG. Fix and simplify code in call to runWilcoxon. Fix runFindMarkers by setting some unused variables to NULL.
 

 Merge pull request #403 from salzcamino/master

Updates to CeldaCG_PlotResults rmd 

 require multipanelfigure package in report plotting RMD
 

 Merge pull request #401 from joshua-d-campbell/master

Bioc fixes 

 Fixed maintainer duplicate
 

 Updated examples and tests to use 'hvf' instead of 'hvg'. Some examples needed to be updated to more clearly define different use cases for selecting hvfs
 

 Merge pull request #741 from akshayarav/devel

Workflow Changes 

 removed test files
 

 Merge pull request #750 from mingl1997/devel

Improved Matrix versioning and HTAN output 

 Update DESCRIPTION 

 Select genes now working after cluster
 

 Change names for marker plot and make tab available after clustering
 

 Add req to  beginning of plotting
 

 Select marker genes now working
 

 Add panel tab for Marker Genes
 

 Merge branch 'devel'
 

 Removed manual installs in GA workflows
 

 added namespace
 

 Fixed Seurat FindHVG
 

 Fixed bugs with filtering of Seurat V5 objects
 

 Updated docs for 2.12.2
 

 update function documentation
 

 Line 27 of test-featureSelection error fixed
 

 test-clustering now passing
 

 Change all relevant occurrences of runFindMarker and getFindMarkerTopTable
 

 Change all relevant occurrences of runUMAP
 

 Fix runFeatureSelect.R match.arg
 

 test-seuratFunctions fixed regarding workflow changes, still failing

- Fails even on most recent devel changes on fork, need to ask question
 

 Fix test-dimensionReduction, now passing
 

 Implement Differential Expression Analysis workflow changes

- Change runDeAnalysis to now take in inSCE object first, and changed method default
- No changes made to plotDEGHeatmap
 

 Implement workflow changes for Clustering, plot function skipped
 

 Implement workflow changes for Dimension Reduction

- Change functions scaterPCA and plotDimRed
 

 Implement workflow changes for getTopHVG
 

 Merge pull request #740 from mingl1997/devel

Updated description and Seurat functions 

 Merge pull request #21 from compbiomed/devel

Devel 

 Merge branch 'devel' into devel 

 Updated docs for v2.12.1
 

 Merge pull request #738 from salzcamino/master

plotSeuratGenes 

 git push origin masterMerge branch 'compbiomed-devel'
 

 Merge pull request #20 from compbiomed/devel

Merge pull request #735 from mingl1997/devel