fix for named coordinate index
 

 Auto-formatted with Air
 

 update TODO
 

 Merge branch 'main' of github.com:snaketron/ClustIRR
 

 Delete .github/workflows/rdefault.yml

failed .yml 

 Repair and optimize PsiNorm()

A recent change in DelayedArray (in version 0.33.5) broke PsiNorm()
on a sparse DelayedMatrix object and on a SE/SCE object with counts
represented as a sparse DelayedMatrix object.
This commit repairs that and introduces two small improvements to
PsiNorm():
- makes PsiNorm() work on a SparseMatrix object;
- makes PsiNorm() slightly faster by reducing the number of matrix
  transpositions from 4 to 2.
 

 tests: update extracting Tissue information for cell lines in PRISM data
 

 update news and description
 

 bump to 1.13.2
 

 version bumps up
 

 fix bridgeness tests
 

 fixing typos
 

 component wise clustering
 

 update TODO
 

 version bump 1.43.10
 

 version bump 1.43.9
 

 check for large files only in package source dirs
 

 fix various compiler warnings, including removing a lot of dead code
 

 Add 'recycle.along' to internal helper .Arith_SVT1_v2().
Not used yet. This is just preparatory work to support Arith operations
between an SVT_SparseArray object and a tile object.
 

 bug fix: use %in% operator
 

 Revert "bug fix use %in% operator"

This reverts commit bd9cbd569de683358e6b6c5b74f09b43c5f2106b.
 

 bug fix use %in% operator
 

 version bump 1.43.5
 

 syncing with original repo
 

 version bump 1.17.6
 

 HDF5Array 1.35.15

Minor edit to the "HDF5Array performance" vignette.
 

 Vignette "installation" section typo correction
 

 Update CCAFE.Rmd

Change T/F to TRUE/FALSE
 

 Add other binary information (#12)

* Update data_col_sel

* Add evaluated, consultand, proband, carrier, asymptomatic and adopted

* Add error in case of adopted individuals in kinship calculation

* Imrpove shiny col selection

* Fix sex output of fix_parents

* Update tests

* Update snapshots

* Fix test fix_parents

* Update tests

* Use data.frame

* Update linux snapshots

* Add other patterns

* Remove prints

* Update news

* Update dataset

* Fix find_avail_affected

* Remove NA carrier

* Update snapshots

* Improve slicing

* Fix polygn splitting

* Fix legend orientation

* Update tests

* Update snapshots

* Update tests

* Fix linting

* Remove accent

* Update documentation

* Fix ped to pedi

* Add warning error for proband, asymptomatic

* Fix test

* Update snapshots

* Fix vignette

* Set fertility to unordered factor

* Update documentation and tests

* Remove internal

* Fix example

* Update linux snapshots

* Fix example

* Update changelog

* Fix linting

* Update stop messages

* Fix linting

* Fixx test and vapply

* Update snaps

* Update error message

* Update snapshot

* Update snapshots

* Fix par

* Update snapshots

* Update snapshots

* Update ped sticker

* Test shiny

---------

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com> 

 Add fertility status (#10)

* Update steril to fertility and remove terminate as sex

* Update snapshots

* Add infertility symbol

* Fix constructor when no renaming given

* Update news

* Update doc, namespace, linux snap

---------

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com> 

 New development (#8)

* Update title plot

* Separate is informative from useful

* Fix title in tips

* Add tsv support

* Add support for ped data

* Fix data family table

* Remove snapshop of 4.3

* Update snapshot

* Remove old snap

* Fix test

* Add new import test

* Fix documentation

* Fix tests

* Fix indentation vignette

* Ignore Rplots.pdf

* Update linux snapshot

* Fix linting

* Fix tips reactivness checking

* Fix missing space

* Update snapshot

* Set default browser to chrom

* Fox linting

* Update snapshots

* Fix argument data_import

* Use variable environment for github action

* Update to 1.3.1

* Fix GA linux chrome installation

* Fix chrome installation

* Update chrome installation

* Fix environment

* Update snapshot

* Update workflow

* Update workflow

* Change chrome installation

* Simplify chrome installation

* Update workflow

* Fix line length in vignette

* Remove chromote arguments

* Update data download

* Fix linting

---------

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com> 

 Update CCAFE_Extra_Details.Rmd

Replace T/F with TRUE/FALSE
 

 bump v0.99.27, fix missing utils bib
 

 Bump v0.99.26, Fix data documentation add source files
 

 rm unused age_categories sysdata script
 

 Update DESCRIPTION

version bump to trigger new build
 

 Deprecated

  - user requested
 

 Finished updating C functions
 

 Separated R & C threads
 

 Added checks against edgeR
 

 Improved handling of edge cases
 

 Added comments
 

 Shifted overdispersions to C
 

 Bugfix
 

 Fixed version numbers
 

 Refined arguments for digestSalmon
 

 User requested deprecation
 

 typo
 

 Merge branch 'devel'
 

 lms is now maintainer
 

 trigger rebuild
 

 trigger rebuild
 

 Bump version
 

 Parallelize the calculations of spatCor() using BiocParallel
 

 git rm --cached dev/*
 

 ignore dev for clean upload
 

 Reduce image size
 

 version bump
 

 bump v0.99.22 - style code
 

 bump v0.99.21 - Update bib #13
 

 Bump v0.99.20, add tests for plotting functions
 

 Add test for plot_markers_express_ALL
 

 Add test for plot_compsition_bar
 

 suppressMessages in tests
 

 Add test for 1vALL
 

 Fix message for create_cell_colors
 

 Add test for make_test_sce
 

 rm bad line from create_cell_colors test
 

 Bump version 0.99.18, update vignettes
 

 Add introduction to get started vignette
 

 Bump version
 

 import graphics text, bump version 99.16
 

 add revised (and finally complete) normalization & PCA timings for lconway
 

 fixed examples in man pages
 

 Fixed examples
 

 Fixed oxygen annotation to optimize man page generation
 

 Merge remote-tracking branch 'bioc/devel' into devel
 

 Updated LICENSE to new format
 

 Fixed warning in matrixSums C code
 

 Merge pull request #35 from Goultard59/patch-1

Update decontPro.Rmd 

 Merge pull request #31 from campbio/feature/pass_maintainer_role

Feature/pass maintainer role 

 Updated cre status in DESCRIPTION
 

 version bump
 

 Merge branch 'main' into devel. Add rstan updates
 

 Update deprecated Stan syntax
 

 add ambient_counts input
 

 add ambient contamination profile to stan output
 

 Merge remote-tracking branch 'bioc/devel' into devel
 

 updated dplyr function to use everything() to select all cols. Was causing an error in the Heatmap.Rmd article
 

 Merge remote-tracking branch 'bioc/RELEASE_3_20' into devel
 

 Set default interactive to FALSE for plotSeuratElbow
 

 fixed decontX/soupX webapp error
 

 addressed do.call issue
 

 Merge remote-tracking branch 'bioc/devel' into devel
 

 Merge remote-tracking branch 'campbio/devel' into devel
 

 Fixed enrichR bug by attaching package so it connects to database. removed an example in semi_pheatmap
 

 Minor edit to tutorial, getFindMarkerTopTable workaround
 

 Adding Celda module-based analysis tutorial
 

 Fixed dependency issues
 

 Merge pull request #404 from joshua-d-campbell/devel

Updates to celda reports 

 Reduce comptime evalweightfunction
 

 addressed devtools::check warnings
 

 Docfixes, mostly for the new link policy.
 

 Minor clean-up to the marker testing code.
 

 Merge branch 'csoneson-issue-266-bpprogressbar' into devel
 

 Use do.call() instead of lapply() in `bpoptions` (addressing issue #266)
 

 limpa 0.99.4
- Update NEWS.Rd.
- Expand details section of voomaLmFitWithImputation.Rd
- Fix length of Rd usage lines.
- Fix bug in dpc() when some peptides are completely missing in all samples.
- Package title changed to "Quantification and Differential Analysis of Proteomics Data"
- Package description expanded.
- New function plotProtein(), to plot the quantifications for a given protein with error bars.
- Cleanup annotation output from dpcQuant() to remove peptide-level annotation columns
- dpc() now outputs `n.detected` for each peptide.
- dpc() now checks for peptides that are entirely missing.
- plotDPC() now accepts input from either dpc() or dpcCN().
- plotDPC() now estimates jittering amount automatically.
- Add readDIANN() code to vignette.
 

 fix up last few issues with the vignette (#62)

* check if this works?

* reorder 

 bug fix
 

 version bump
 

 remove badge
 

 badges
 

 Vignette link to Bioconductor
 

 Merge branch 'main' of github.com:KatjaDanielzik/MetaboDynamics into main
 

 Delete vignettes/MetaboDynamics.html 

 vignette link
 

 change figure name
 

 Merge pull request #70 from ahl27/master

feat: label hop attenuation for ExoLabel 

 Removes probabalistic edges; updates documentation pages; streamlines verbose argument
 

 update news/description, add references to documentation
 

 Move RcolorBrewer from impports to suggests, version 99.15
 

 Version 0.99.13
 

 Point bug report to github issues, version 0.99.12
 

 Merge pull request #147 from gdrplatform/GDR-2886

[GDR-2886] Update capping_fold param in cap_assay_infinities 

 chore: update capping_fold param in cap_assay_infinities
 

 doc: update capping_fold param in cap_assay_infinities
 

 rm vignette gitignore
 

 Use broad/fine cell types for split, return nested list of broad & fine color pallets. Flip plot, only plot fine ct when split. Update docs.
 

 fix arg name, add pallet example
 

 Update use of cell_type_colors in vignette
 

 Resolve conflict with Bioc
 

 Change Rory email
 

 Update CTD creation functions
 

 feat: add c and coerce methods for XcmsExperiment

- Add `c()` method to combine `XcmsExperiment` objects.
- Add a method to coerce from `XCMSnExp` to `XcmsExperiment` objects.
- Fix references in documentation.
 

 Update NEWS.md
 

 Merge branch 'devel' into jomain
 

 bump version
 

 Address William's comments
 

 Merge pull request #770 from pablovgd/issue705

Added peak quality section to xcms vignette. 

 Added section on peak quality to vignette.
 

 requested changes for PR #768
 

 Merge pull request #767 from pablovgd/issue705

Add internal function to calculate beta metrics 

 Fixed requested changes for PR #767
 

 docs: add documentation for chromPeakSummary generic
 

 fix: peak shape quality calculation for gap filling

- Peak shape quality (similarity to gaussian shape) calculation is now performed
  using the EIC representation of a chromatographic peak, i.e. with intensities
  of mass peaks for the same retention time (but different m/z) summed.
 

 Fixed troubles of 1.39.1, forced C17 standard for ClustalOmega; version number bumped to 1.39.2
 

 Merge pull request #40 from janlisec/devel

Fix for issue #22 

 ...forgot to save text edit
 

 Fix for issue #22 using a new elemental definition set and implementing a test for old and new set.
 

 version bump
 

 update mutation_positions: return a single vector
 

 Version 0.99.3: Fix overly long lines as requested by Bioconductor
 

 Fixed name space
 

 DelayedArray 0.33.6

Binary operations between a DelayedArray object and an array now
raise an error. This is temporary and only to prevent users from
trying to use a tile object (new in S4Arrays 1.7.3) on the left or
right side of the operation, and get the wrong result.
 

 HDF5Array 1.35.13

Minor edits to "HDF5Array performance" vignette (Discussion section).
 

 Try to avoid windows timeout
 

 `chalmers-gem`: for non-human organisms Gene Symbols are used instead of ENSG IDs; updated regex to match those; fixes #116
 

 small doc improvement for DTEG.analysis
 

 Improved documentation and DTEG.analysis design
 

 Added gtf support for db = "refseq" or"genbank"
 

 Improved peak detection
 

 Added argument for height_scaler in shiftPlots
 

 Fixed itemized docs for star align
 

 Merge pull request #98 from gdrplatform/GDR-2873

Gdr 2873 

 doc: appease lintr
 

 chore: bump version and update NEWS.md
 

 refactor: extract tissue info for PRISM data
 

 version bump in devel
 

 update addParquetToMeta() error msg
 

 0.99.19
 

 eval=FALSE to installation chunck
 

 Added installation instruction to the vignette
 

 Fix multiple typos
 

 DESC/NAMESPACE update
 

 `misc`: helper function `fname_from_url`
 

 fix multiple typos and update the documentation.
 

 version bump
 

 v1.3.3 updates
 

 Update to v1.11.2

Includes hotfix change for mouse genome support and updated IRanges dependency version

Merge branch 'master' into devel

# Conflicts:
#	DESCRIPTION
 

 Merge pull request #154 from neurogenomics/fix-mouse-support

Fix support for mouse genome [HOTFIX] 

 Fix support for mouse genome
 

 fixed import warnings
 

 small tweaks
 

 update R dependency
 

 Version bump to expose the new changes to Bioc users
 

 Update for new version of CosMX
 

 Merge branch 'devel'
 

 Use release version numbers
 

 Update utils.R

Update getTechTxFields() to recognise both .csv and .csv.gz CosMX transcript files. 

 Version 0.99.1: add easyTENET wrapper function to simplify use

Also push a step 5 documentation update that didn't make it to the repo.
 

 Change minimum R to 4.5
 

 R version dependency fix R >= 4.5.0
 

 IRanges 2.41.3

New implementations of the viewMins(), viewMaxs(), viewSums(), viewMeans(),
viewWhichMins(), viewWhichMaxs(), viewRangeMins(), and viewRangeMaxs()
methods for RleViews objects.

This is a complete rewrite (including of the C code behind these methods)
that addresses many long-standing (and unnoticed-for-years) bugs in the
previous implementation. This new implementation can also be significantly
faster than the previous one e.g. 5x faster or more for RleViews objects
with millions of views.
 

 fix for https://github.com/Bioconductor/Contributions/issues/3631#issuecomment-2548723782. check() and BiocCheck() Passed.
 

 Updated package versions in tests and examples for latest Miniforge.

Or specifically, the Python 3.12 that comes with the latest Miniforge.
 

 Minor docfixes to keep CHECK happy.
 

 Support diversion to an external fallback R environment.

This is occasionally necessary when the external conda installation is
read-only or when a system installation is used with an external conda.
 

 use molecularProfiles to determine mutation or copy number molecular profile
 

 ci: disable installation of openssl
 

 ci: install pre-compiled openssl in macOS
 

 ci: install openssl on macOS
 

 Fixed a failling unit test
 

 Adress Jo's comments, bump version, add news item
 

 Merge pull request #303 from jorainer/devel

feat: extract electronBeamEnergy MS term 

 Fixed off-by-one indexing issue between R's 1-based indexing and pwiz's 0-based indexing.
 

 feat: extract electronBeamEnergy MS term
 

 added README badge for BioC
 

 Merge pull request #11 from kinnaryshah/devel

update to 1.3.1 with Bioc version  

 added rmarkdown as suggests
 

 removing oldrel bc bioC package
 

 added in all the changes from John
 

 trigger rebuild
 

 update of SystemRequirements; version number bumped to 1.39.1
 

 `translate_ids`: fixed regression in case of identical `from` and `to` column names; might fix saezlab/decoupleR#147
 

 replaced `httr` with `httr2` in dependencies
 

 docs rebuild
 

 patch `httr2` to keep the curl handle on request obj
 

 patch `httr2` to keep the curl handle on request obj
 

 `generic_downloader`: do not fail if the env or reader func is not a namespace
 

 log message before arg processing for OmniPath queries
 

 update inherited changes from VisiumIO
 

 bug fix: missing package anchor in param ... doc
 

 add ref = "Gene Expression" to example and vignette
 

 Support arbitrary matrix types in Y and Offset
 

 make work with -DR_NO_REMAP
 

 Merge branch 'devel' of github.com:KatjaDanielzik/MetaboDynamics into devel
 

 Delete .gitignore 

 bioconductor link in readme
 

 add citation detail
 

 bug fix: change in options for computing neighbourhood lists fixes bug in calculating Moran's I
 

 must move version forward
 

 ensuring use of 3.20, to get r2u
 

 Create Dockerfile 

 Merge pull request #3 from vjcitn/devel

Devel 

 avoid @master on pandoc action
 

 fix typo
 

 take care of installation dependencies
 

 bump container version
 

 moving forward
 

 trying very simple action
 

 Merge pull request #2 from vjcitn/devel

syncing various sources 

 bump version
 

 Update DESCRIPTION

Trigger github action 

 Update check-bioc.yml 

 Update check-bioc.yml 

 bump vers 2021 

 Upgrade version of actions used in arm64 workflow
 

 Version bump
 

 Don't need to specify c99 here
 

 Patch blosc for C23 compiler