Change the Examples.
 

 Update the Description for the biocheck.
 

 Fix examples/tests and reduce package size.
 

 fix ggplot2 label error
 

 fix import and run document()
 

 use MatrixGenerics
 

 Merge pull request #7 from bigomics/fix-normfactor

fix normfactor for low number of genesets (fix issue #6) 

 Merge pull request #376 from rformassspectrometry/jomain

fix: precursorPurity with missing precursor peak in MS1 

 Update
 

 UPDATE
 

 Organize codes.
 

 edgeR 4.9.2
- glmQLFit() with legacy=FALSE now caps any preset dispersions to be <= 4. Previously, large preset dispersions could lead to a segmentation error.
- glmQLFit() with legacy=FALSE no longer automatically estimates the NB dispersion from trended values found in the DGEList object, if present. The results will now be the same whether the DGEList contains dispersion estimates or not.
- Adding DTE and DTU references to intro.Rmd.
- Revise example code for sampleWeights.Rd.
 

 version bump
 

 revert to R version >= 4.3.0
 

 bump version
 

 update bioc version
 

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

 bump version
 

 update bioc version
 

 update bioc version
 

 update bioc version
 

 import enrichit
 

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

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

 bump version
 

 update
 

 update
 

 update
 

 update
 

 update data action
 

 update readme
 

 correct DO url
 

 no deps parsed
 

 update
 

 setup env
 

 correct url
 

 update
 

 fixed installation issues
 

 install bioc pkgs
 

 auto-update data with github action
 

 use enrichit
 

 use enrichit for ORA; and move helper functions to enrichit
 

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

 update bioc version
 

 update
 

 version bump in devel
 

 Merge pull request #17 from NICHD-BSPC/minor_fix

updt R version fr bioc 

 Merge pull request #16 from NICHD-BSPC/bioc-submit2

update repo for bioconductor submission

- added examples to exported functions/objects
- added data to use in examples 

 add examples
 

 add helper func to get upset tbl
 

 add NEWS
 

 add more examples
 

 fix examples
 

 fix unloaded function calls with ::
 

 rename data obj
 

 use data obj in examples
 

 add data, docs & script
 

 updt docs for settings module
 

 add pattern plt docs
 

 updt func enrich docs
 

 add docs/ex fr fuzzy plt
 

 fix biocCheck folder path
 

 add donttest to get_degplot
 

 add missing library(shiny) to ex
 

 add horizon plt ex
 

 add alluvial plt ex
 

 add cnetplot ex
 

 fix sumov plot ex
 

 add docs,ex fr sumov plt
 

 add docs,ex fr ma plot
 

 add pca plot module docs
 

 add func docs
 

 updt scatter plt ex
 

 updt gene plt ex
 

 updt biocViews
 

 fix scatterplot ex
 

 factor out bioccheck to new action
 

 add scatterplot docs
 

 more example fixes
 

 fix examples
 

 add scatterplot examples
 

 use get_gene_counts instead of reshape2::melt
 

 fix add_metadata examples
 

 add BiocCheck action
 

 fix typos
 

 dont filter proj desc if no staged data
 

 repl stop w modal
 

 repl T w TRUE
 

 repl 1:.. w seq_len
 

 rm paste inside message/warning
 

 Version bump in devel
 

 Version bump in devel
 

 Version bump in devel
 

 Version bump in devel
 

 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