Merge branch 'master' of https://github.com/saeyslab/FlowSOM into devel
 

 Update Plot1DScatters: character vector as input for metacluster parameter (compatibility with metacluster levels after running UpdateMetaclusters)
 

 Updated version number in NEWS
 

 Depricated PlotFileScatters and aligned the x-labels to the top.
 

 PlotMFIHeatmap function added and included in FlowSOMmary
 

 Merge commit

Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	DESCRIPTION
#	inst/NEWS
 

 added Plot1DScatters
 

 Replaced geom_text with annotate in FlowSOMmary
 

 Added .data$ in MajorityLabels function
 

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
 

 Added GetMajorityLabels function
 

 Added parameters for read.FCS in PlotFileScatters
 

 Added alpha parameter to plotFlowSOM
 

 Fix typos in FlowSOMmary
 

 - Update to the plot metacluster labels in FlowSOMmary
- No longer supress warnings in GetFeatures
- Add outlier count to matrices returned by GetFeatures
 

 made GetFlowJoLabels more efficient
 

 Small adaptations to make the GetFlowJoLabels function more robust
 

 Fixed colored metacluster centers when using Plot2DScatters
 

 updates to plotOutliers
 

 Added PlotOutliers and documentation
 

 Merge branch 'master' of github.com:saeyslab/FlowSOM
 

 Updating the outlier detection - will still be further updated
 

 allow resampling in AggregateFlowFrames
 

 Solve merge conflict
 

 Align version number with Bioconductor
 

 Update to AggregateFlowFrames for nicer handling of iterative aggregation  (+ according visualisation in FlowSOMmary). AggregateFlowFrames will now introduce 0 values if a channel is not present in one of the fcs files. If channels is not provided as an argument, the channels of the first file are used.
 

 Merge branch 'master' of github.com:SofieVG/FlowSOM
 

 Added abbreviations to PlotDimRed "colorBy"
 

 Reversed PlotDimRed to scattermore and added support for custom colors and color scale limits to it
 

 Add support for flowSets in AggregateFlowFrames.
 

 percentage_positives in GetFeatures now works with a FlowSOM with updated metacluster labels
 

 Change default value of map to TRUE in SOM so original functionality remains the same
 

 Bugfixes to pass BioConductor check and now normal ggplot colors are used in Plot2DScatters when ggpointdensity is not installed
 

 Update version number to be in sync with Bioconductor
 

 Added possibility to provide additional arguments to the read.FCS function in SaveClustersToFCS() function
PlotFileScatters now accepts other File ID columns, not anymore stricted to "File"
 

 Added a warning in UpdateDerivedValue when using FlowSOM on an FCS with NA value
 

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	FlowSOM_Cheatsheet.pdf
 

 Plot2DScatters: title is fixed, extra warning when wrong manual colors are used, add marker/channel names on plots
+ Updated cheatsheet
 

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
 

 NewData clones prettyColnames from the original fsom object
 

 Test
 

 Added height and width parameter to PlotFileScatters
Fixed bug in PlotFileScatters
 

 Added colsUsed and prettyColnames description in GetMetaclusterCVs
 

 Increased version number
 

 Adapted PlotManualBars function so that it works after using UpdateMetaclusters
 

 Updated CheatSheet and added code from UpdateDerivedValues for metaclustersMFIs to UpdateFlowSOM
 

 Combined the RelabelMetaclusters, ReassignMetaclusters and ReorderMetaclusters finctions into one UpdateMetaclusters function.
 

 Added checkNames = FALSE in MetaclusterMFIs
 

 Update to avoid @ call in GetMarkers
 

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	DESCRIPTION
 

 Version bump
 

 Updated PlotManualBars, Plot2DScatters and FlowSOMmary so that it works with relabeled metaclusters.
 

 Fixed the cluster/metacluster issue in PlotManualBars, part 2
 

 Fixed the cluster-metacluster issue
 

 Added the FlowSOM R Cheatsheet
 

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
 

 PlotFileScatters: makes duplicated filenames unique and now works with output of AggregateFlowFrames
 

 Added ReassignMetaclusters to NAMESPACE
 

 Fixed issue with FlowSOMmary
 

 Fixed warnings with ggtexttable in FlowSOMmary
 

 Increase version number
 

 Merge

Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	R/4_metaClustering.R
 

 Added the option to change yLabel in PlotFileScatters to markers and/or labels, added error message to RelabelMetaclusters when no metaclusters are available, edited NEWS and description
 

 Added function RelabelMetaclusters
 

 Allow TRUE/FALSE vector as input for GetMarkers / GetChannels
 

 Fix to make sure print also works on FlowSOM object created by ReadInput only.
 

 Changed year in NEWS
 

 Added examples to NClusters, NMetaclusters, AddAnnotation. Used flowSOM.res instead of fsom in all examples
 

 Added color support to AddLabels
 

 Added GetCounts and GetPercentages
 

 Set star size to 0 if node is empty
 

 Included a print function.
Outliers calculated not only when mapping new data but now also in the base model (stored in fsom$outliers).
PlotNumbers now has an extra argument so it can also show metaclusters.
For some unknown reason rerunning devtools::document() changed the newlines in all the man files...
 

 Fixed the PlotManualBars
 

 Added check whether meta argument is provided in GetMetaclusters, and na.rm arguments in GroupStats.
Tried to fix some issues with the vignette.
 

 Adapt the SaveClustersToFCS function to have some more options in where the file is saved, and also add the metacluster and the x y coordinates of the tree as additional columns
 

 Fiixed the PlotManualBars function
 

 Fixed warnings in the R check due to examples in deprecated functions, updated the NEWS file and small changes to vignette.
 

 maxNodeSize is now relative to the value calculated from AutoMaxNodeSize.
 

 Adapted FlowSOMmary to also work with a FlowSOM model with empty clusters. Also some slight changes to improve the package check.
 

 Merge branch 'FlowSOM_v2' of https://github.com/saeyslab/FlowSOM into FlowSOM_v2
 

 Use new functions in the examples of the deprecated ones
 

 Small bugfix in GetChannels + UpdateFlowSOM now changes brackets in fsom$prettycolnames to <>
 

 Corrected a few typos in GroupStats
 

 Fix for dropping empty MC MFIs
 

 Fix to update metacluster MFIs
 

 Merge branch 'FlowSOM_v2' of https://github.com/saeyslab/FlowSOM into FlowSOM_v2
 

 Added deprecated functions
 

 Added colsUsed and prettyColnames to GetMetaclusterMFIs
 

 added rownames to the median expression metacluster MFIs
 

 Update R requirement
 

 Small updates:
- Added plot with backgroundvalues to FlowSOM function example
- use fr_append_cols instead of cbind in aggregateFlowFrames
- Added ... argument to aggregateFlowFrames, passed to read.FCS
- Added get_data argument in GetFlowJoLabels, so the compensated/transformed data can also be returned
- Some updates to work with newest flowWorkspace/CytoML version
- Apparently some newlines added in the man pages
 

 Fix colors when using more than 12 metaclusters in PlotOverview2D
 

 Fix to make better node sizes, also with empty nodes.

Added option to scale pie pieces in PlotStars to either each marker individually (as was the case before) or to an equal scale for alle markers (new default).

Merge branch 'devel'

# Conflicts:
#	DESCRIPTION
 

 Update to make sure that empty nodes are counted as well when updating the node size. Change 0 node size to 0.00001 for better plotting accuracy.
 

 fix pass parameters from PlotGroups to PlotStars
 

 Update to make sure FlowSOM works with the current release version of flowWorkspace (parseWorkspace has moved to CytoML)
 

 Update to flowWorkspace devel version
 

 Merge branch 'master' of https://github.com/SofieVG/FlowSOM
 

 Merge pull request #24 from exaexa/scaling-fix

Fix creating scaled.scale and scaled.center 

 Fix creating scaled.scale and scaled.center

R attr()s do not get preserved when assigning data into a sub-range of a larger
frame (even if the range is just "whole data"); for that reason attr(fsom$data,
"scaled:scale") is not created after a recent update of scale handing. This
attempts to reconstruct a reasonable scaled.scale/scaled.center in both new
cases.
 

 * Fix issue with running NewData function when there are more or less columns than originally (not impacting the columns used for the FlowSOM calculations)

* Fix issue when applying the AggregateFlowframe function multiple times.

* Fix issue in documentation

* Fix issue where sdValues where not updated
 

 Increased version number to stay in sync with the bioconductor version.
This version bump corresponds to the changes in PCA initialization as proposed by Miroslav Kratochvil.
 

 explain the sdev-scaling
 

 Merge pull request #20 from exaexa/codebook-fix

Fix the logic of checking codebook size 

 o The ReadInput function can now also take a matrix as input.
o Made input of the NewData function more general (can now take any input of the
ReadInput function).
o Included a TestOutliers function which checks the average distance of the cells
to the cluster centers (using the median and MAD measures) and returns how many
cells seem to be further then expected from the cluster center.
o Fixed the bug that only the first file-specific compensation matrix was taken
into account in the ReadInput function.
 

 GetMFIs: added colsUsed and prettyColnames

colsUsed    logical. Should report ONLY the columns used to build the SOM
prettyColnames   logical. Should report pretty column names instead of standard column names
 

 Fixes as suggested by Samuel Granjeaud
 

 Added a keepOrder parameter to the AggregateFlowFrames function. If TRUE, the
cells of the random subsample will be ordered in the same way as they were
originally ordered in the file. Default = FALSE for backwards compatability.
This will be especially useful if the whole file is selected in the subsample,
in which case indices keep corresponding to the original ones.
 

 PlotLabels method now propagates 'main' argument to plot.igraph

* Same issue as with `PlotNumbers` in the previous commit, but for
  `PlotLabels` this time
 

 o added get_markers and get_channels functions for easier access
o added PlotOverview2D function, which gives an overview of multiple
  PlotCluster2D plots.
 

 More bug fixes
 

 Bug fixing in CV function
 

 Forgot DESCRIPTION and NAMESPACE
 

 Added font size and correct scaling when using thresholds.
 

 New functions to get the cluster and metacluster labels for every cell from a FlowSOM object.
Fix for fcs output of AggregateFlowFrames function.
Fix for PlotGroups p-value correction.
 

 Merge branch 'master' of https://github.com/SofieVG/FlowSOM
 

 Updated the CountRes function for more plotting options and rownames in the pctgs
 

 Added nClus argument to MetaClustering and adapted documentation
 

 Delete rds file
 

 Merge branch 'master' of https://github.com/SofieVG/FlowSOM
 

 Update README.md 

 Update README.md 

 merged: README
 

 Update README.md 

 Updated documentation.
 

 Updated version, including some bug fixes and extra functionality.
Some parameter names have been renamed, so not fully compatible with older scripts!
 

 Update to FlowSOM version 1.1.1
 

 added: install script
 

 Include functionality to indicate differences between groups: CountGroups and PlotGroups functions
 

 Initial commit
 

 Create README.md 

 Version accepted for Bioconductor
 

 Added examples to the documentation
 

 remove extra functions and update of documentation
 

 update version of EP
 

 v1.3.2
 

 bump version
 

 remove IRanges from DESCRIPTION/imports (no import in NAMESPACE)
 

 update docker version 

 bioc-check 4.5 and devel
 

 version number in NEWS-0.99.9to1.7.1-matchBiocVersion
 

 version 0.99.9-FixBreakingChangesXGBv3-updatesAllDoc
 

 Add xlim and ylim for cellinfo and gene exprs plot
 

 bug fix: bad counts order
 

 another sapply
 

 fix bug in inspectDigests
 

 bump version
 

 Added shQoute for mergeFastq
 

 Fixed training_non_default_regression_models vignette
 

 rename functions

due to update in rols dependency
 

 Bump version to trigger rebuild.
 

 Forgot to set eta when running t-SNE.
 

 Ignore testthat artifacts.
 

 Bugfix to get the maximum distance for subsampling neighbors.
 

 Summary quantiles are now stored in a nested data.frame.

This is a bit easier to extract programmatically as users don't have to
re-assemble the column name. In particular, we avoid discrepancies in the
precision of the float->string cast between C++ and R. Now, users can traverse
columns of 'quantiles' in the same order as 'compute.summary.quantiles'; the
column names are also created in R instead of C++ for consistency.
 

 Add Aryee 2025 CTCF footprinting
 

 Add CTCF footprinting paper from Aryee lab, https://doi.org/10.1101/2023.10.20.563340
 

 Try RELEASE_3_16
 

 portable atanpi()
 

 remove set.seed from proast
 

 fix documentation in new functions
 

 Bump version
 

 Remove unused .format_string()

This is now implemented in C
 

 Fix split size for format_unicode()
 

 Read string function in C code
 

 Remove readBin() from loop
 

 Move vlen_utf8 codec directly in format_chunk
 

 adding check on pvalue for adding DESeq results
 

 v1.25.0 -> .1
 

 fix typo
 

 merge main
 

 changed bbhw preprint refs to published version
 

 Bioc 3.22 release version bump
 

 Remove Author/Maintainer fields, use only Authors@R; bump to 0.99.9
 

 bump to 0.99.7
 

 use simplified link for combined class and constructor docs
 

 Updated dynamic programming (general)
 

 Subscribe to bioc-devel; fix duplicate export MCF7_TNF; bump to 0.99.5
 

 Update vignette for Seurat 5.x: replace slot with layer
 

 Remove SeuratWrappers dependency
 

 version bump
 

 reduce example size
 

 Merge remote-tracking branch 'upstream/devel'
 

 upload package
 

 upload package
 

 Merge branch 'devel' of github.com:tgac-vumc/StatescopeR into devel
 

 Adjusted BLADE code to pytorch version (https://github.com/tgac-vumc/Statescope/blob/master/src/BLADE_Deconvolution/BLADE.py) and made vignette less minimal
 

 Merged from master

Merge branch 'master' into devel

# Conflicts:
#	DESCRIPTION
 

 Updated from qs to qs2 with TBB support check
 

 Fixed another bug for end GRanges
 

 Exported more S4 generic overwrite getters
 

 Bump version for Bioc devel
 

 Merge pull request #29 from ebecht/devel

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

 Fixed vignette to turn off evaluation of packages installation
 

 minor formal changes, faster examples
 

 Biostrings 2.79.3: Repair compatible_seqtypes/get_seqtype_conversion_lookup

Repair low-level utilities Biostrings:::compatible_seqtypes() and
get_seqtype_conversion_lookup() when at least one of the supplied
sequence type is "ModDNA" or "ModRNA".

This regression was introduced in previous commit (commit b15bffb,
Biostrings 2.79.2) and was breaking the Modstrings package. See
https://github.com/Bioconductor/Biostrings/issues/132
 

 lint and tidy up vignette
 

 update workflow actions
 

 Merge branch 'devel'
 

 v1.41.1: updated test_convert
 

 fixed deprecation error caused by Seurat
 

 build: rename codecov.yml to codecov.yaml 

 chore(deps): update actions/upload-artifact action to v6 (#178)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> 

 update vignette
 

 update of EventPointerBAM
 

 delete rproj
 

 update readme.
 

 sia to ia
 

 add geros funtions, clean up package
 

 correct suffixes for single tool analysis
 

 dynamic and condensed onput
 

 version with indiv file uploads
 

 making sia reactive
 

 update docu
 

 add diff dds slot
 

 ass highlights and spider
 

 reindent
 

 limpa 1.3.2
- Case study vignette with DIA-NN data
 

 igblastr 1.1.8: Add extract_codons() and translate_codons()

Also rename argument 'max_codons' of function translate_fwr4()
to 'max.codons'.
 

 Fix version number for Bioconductor devel
 

 Merge branch 'main' into feature/beta-smoother-tm-centering 

 updating readme
 

 update contributing.md
 

 complie demo data into R data
 

 Docs: fix roxygen issues and reorganize sources for Bioconductor submission
 

 version_bump to trigger bioc build
 

 Bumped version after reverting commits which broke graphical tests.
 

 Revert "Pushing snapshots to github to try and resolve R CMD build errors"

This reverts commit f16d4fec4f2eb12dc12c0ee502c1cd8aec430d94.
 

 Updated snapshots because of failing test on mac-os
 

 refactor: use Rf_ prefix for R API calls (#138)

 

 fix version (again)
 

 rm so,o
 

 version bump
 

 Merge pull request #6 from Vitek-Lab/feature-anomaly

Feature anomaly 

 fix filter_few_obs processing
 

 fix(summarizePSMs): Fix line that summarizes PSMs
 

 bug(Fragpipe): Fix converter to be backwards compatible to anomaly model changes
 

 Merge pull request #5 from Vitek-Lab/feature-spec-qval

fix spec bug 

 Apply moderation changes and bump version
 

 Update DESCRIPTION 

 tests: update tests
 

 introduce a netParseDate() function to abstract the libcurl dependency away from the udc logic
 

 network stuff used by utc should compile on windows now
 

 remove internet.[ch] as they are no longer needed
 

 feat: use NA as value instead of string 

 docs: remove non-default function arguments in prepareSignature
 

 docs: change the vignette installation instruction to Bioc
 

 dont bioc check
 

 try again
 

 try earlier
 

 new try fix gha
 

 try installing quarto
 

 putting in docs and error, resolves #95
 

 new version bump
 

 tempdir remode from examples
 

 Slightly scale the median to avoid issues with float imprecision in the tests.

Otherwise, we'd be checking for float equality for the observation with
distance equal to the median, and the outcome depends on the precision of the
calculation; this might result in slightly different results between our C++
and the R-based reference calculations in our test suite.
 

 Added relevant system headers for completeness.
 

 trackDb track file path is relative to the genome directory
 

 rewrite networking stack on top of libcurl (again)
 

 Fix DESCRIPTION and CITATION, bump to 0.99.8
 

 Updated the vendored tatami_stats.
 

 Try to install fansi from source
 

 Manually clear cache
 

 Fix documentation and loading of example data
 

 igblastr 1.1.7

Add utility functions translate_J_alleles(), J_allele_has_stop_codon(),
and translate_fwr4().

Rename auxdata column CDR3_stop to cdr3_end.
 

 Fix warning message
 

 Reoxygenate
 

 Remove LazyData from DESCRIPTION
 

 Print notification when falling back to an unknown matrix

- Provide options for turning this notice into a warning or error.
- Require a more recent assorthead to use the latest tatami_r.
 

 Consistent bedGraph terminology
 

 Updated installation instructions for official Bioconductor devel version
 

 Updated vignette
 

 Updated to 0.99.10
 

 Allowed filtering of non-zero thresholds; improved filtering sample number logic
 

 Suppressed redundant messaging; internal param change
 

 Added eBayes `trend` and `robust` options, changed the input data filtering to allow non-zero thresholding, added diagnostic plots option.
 

 Moved FDR filter functions to this file
 

 Added option for using simplied sample display names
 

 Updated to 0.99.10
 

 By default, FDR calcs now return the true BH-corrected FDR values.  A legacy option is provided to return to the method used in Southall et al 2013.
 

 Changed default max_overlaps to 10
 

 Document fill_value string fix in NEWS
 

 Add test for #94
 

 Replace dash in v3 codec names
 

 Add test for vlen-utf8 v3
 

 Version bump to 1.0.1
 

 fix a typo.
 

 new version bump added
 

 corrected examples
 

 examples fixed
 

 error in example fixed
 

 date updated
 

 Merge pull request #55 from drighelli/enhancements

# Changes in version 1.1.2

* adding volume instead of area for MERFISH.
* refactoring log2CountArea to log2DensitySignal
* added size and alpha arguments to plotCellsFovs
* added scaleBar argument to plotCellsFovs, plotCentroids, plotPolygons and plotZoomFovsMap
 

 Merge branch 'devel' into enhancements 

 fixing news versioning
 

 every check is ok
 

 enhancing documentation of computeQCScore about randomness and seed setting
 

 adding scale bar to plots
 

 fixing version in news file
 

 fixing epsilon for log2 ctrl tot ratio
 

 bumping version, adding notes on serious bug fixing
 

 modifying epsilon in spatialPerCellQC
 

 bug fixing coldata cell_id alignment with countmat cell_id
 

 updating to biocrelease
 

 Clarify installation instructions for SpaceTrooper

Updated installation instructions for SpaceTrooper package. 

 version bump
 

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

 Updating visuals of readme
 

 igblastr 1.1.6

Add function compute_auxdata() to compute the auxiliary data for a
set of germline J gene allele sequences.

Rename functions get_igblast_auxiliary_data() and
load_igblast_auxiliary_data() to get_auxdata_path() and load_auxdata(),
respectively. The old names can still be used but are deprecated.
 

 Merge pull request #213 from toby-clark4/p-fix

fixed 0 p-value inf values 

 build: update Rbuildignore to ignore more unnecessary files 

 chore(deps): update actions/checkout action (#175)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> 

 chore(deps): update actions/checkout digest to 8e8c483 (#173)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> 

 docs: fix writing errors uing vale 

 1. Remove .Rproj from version control 2. Update .gitignore, DESCRIPTION
3. Add extdata description
 

 restrict to feature in VisiumIO
 

 update RoxygenNote
 

 wrap text to 80 char width
 

 version bump 1.7.5
 

 version bump 1.31.4
 

 Update TCGAutils Quick Reference link and image 

 Update README.md 

 Update README.md 

 Update README.md

add note for STAR mapping parameter things 

 Update README.md 

 Update README.md

fixed typo 

 build conda environment from .yml file 

 Update README.md

fix typos in the conda installation section 

 Update NormalizationMethods.R 

 Update README.md 

 Update README.md

Fixed some typos. 

 Fix vignette, version bump 0.99.5
 

 Remove .Rproj, update docs, and bump version to 0.99.1
 

 Mention fixes in NEWS
 

 Fix long Rd line
 

 Replace aes_string() by aes()
 

 Fix vignette, version bump 0.99.4
 

 various package adjustments - version bump 0.99.3
 

 bug fix: plot cluster plots time point in correct order
 

 wrapped_curl_perform() returns an actual HTTP status code
 

 version bump
 

 ucscSchema() no longer returns an invisible value
 

 udpate news
 

 bump cache
 

 fixing
 

 fix CVParam
 

 updates_for_bioc_review3
 

 updates_for_bioc_review1
 

 updates_bioc_review
 

 updates_bioc1
 

 updated_Tutorial_Oct
 

 updated_readme
 

 updated_oct8
 

 Readme updated
 

 Update based on Bioconductor review
 

 updated examples
 

 example improved
 

 examples updated
 

 Updated contributor email, mutiple fixes suggested by BiocCheck::BiocCheck()
 

 Merge branch 'master' into devel
 

 Update check-bioc.yml cache v4 

 update vignette and README
 

 Update links
 

 Merge pull request #5 from khoroshevskyi/master

Updated bedbase ids and docs 

 Fixed missing files and incorrect links
 

 Clarify about mouse gaps
 

 Update readme, AH107305
 

 Bump version
 

 Import tail
 

 Use evaluation from S4Arrays to capture subsetting indices
 

 Add cache-version to fix macOS cache collision
 

 Remove unnecessary steps and update actions
 

 Remove unused amd64 workflow
 

 Remove outdated workflow
 

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

 Use %notin% operator
 

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

 handled corner case where network is empty in reduce_solution_network
 

 built new doc
 

 added double threshold function
 

 corrected the reduce_solution_network function
 

 Update README.md 

 Update README.md