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test_find_clusters.R to accommodate variability
in label assignments given by FindClusters across different
systems (#9641)group.by parameter to
FindAllMarkers, allowing users to regroup their data using
a non-default identity class prior to performing differential expression
(#9550)image.type parameter to
Read10X_Image enabling VisiumV1 instances to
be populated instead of instances of the default VisiumV2
class (#9556)IntegrateLayers to respect the
dims.to.integrate parameterstroke.size parameter to DimPlot (#8180)RunLeiden to use the leidenbase
package instead of leiden; deprecated the
method parameter for RunLeiden and
FindClusters; updated RunLeiden to reset
random.seed to 1 if the value is 0 or less (#6792)RunPCA to use the BPCells-provided
SVD solver on BPCells matrices; updated
JackStraw to support BPCells matrices (#8271)RunPCA to avoid converting BPCells
matrices into dense matrices - significantly reduces the function’s
memory usage when running on BPCells matrices (#8966)RunSLSI to support BPCells
matricesDietSeurat so that the layers
parameter is respected (#8197)RunUMAP to support umap-learn
version >= 0.5.0 (#9559)LoadXenium and ReadXenium to
accommodate the output from XOA v3.0; updated
LoadXenium to provide more fine-grained control over the
datatypes parsed in, including nucleus segmentation masks, segmentation
methods, and other experimental metadata; updated
ReadXenium to load cell_feature_matrix.h5 when present in
favor of the MEX format files; updated ReadXenium to load
.parquet files using arrow instead of .csv.gz files to
support XOA 3.0 (#8604)LoadXenium to accommodate datasets without “Blank
Codeword” or “Unassigned Codeword” matrices(#9135)ReadXenium to properly parse multiple molecular
outputs at once (#8265)features parameter to LeverageScore
and SketchDataSketchData’s ncells parameter to
accept integer vectorSpatialDimPlots to display spatial
coordinatesBuildClusterTree to
PseudobulkExpression(..., method = "aggregate") instead of
AverageExpressionSpatialPlot to properly handle images with shared
cellscluster.name parameter to
BuildNicheAssayVisiumV2 class, inherits
SeuratObject::FOV, returned by
Load10X_SpatialLoad10X_Spatial to support loading Visium HD
datasets - added bin.size parameterRead10X_Coordinates to handle new
tissue_coordinates.parquet filesshape parameter to SpatialPlot and
wrappers: SpatialFeaturePlot and
SpatialDimPlotimage.scale parameter to SpatialPlot
and related functions:
SpatialFeaturePlot/ISpatialFeaturePlot and
SpatialDimPlot/ISpatialDimPlotimage.name parameter to
Read10X_Imagescale parameter to
Radius.VisiumV1spot.radius attribute for
VisiumV1 instance returned by Read10X_Image —
replace scale.factors$fiducial with
scale.factors$spotRead10X_Coordinates and
Read10X_ScaleFactorsSpatialPlot to properly handle mutli-assay
Seurat instancesPercentAbove to discount null values (#8412)log parameter to FeatureScatterclip.range for
SCTransform when ncells is less than the size
of the passed datasetAverageExpression to handle features
vector when layer="scale.data" and
return.seurat=TRUEfc.slot parameter to
FindMarkersSCTransform to handle
vars.to.regress (#8148) and
(#8349)SCTransform to handle fetching residuals (#8185)SCTransform.StdAssay to pass extra arguments to
sctransform::vst(). Fixes #875PseudobulkExpression by adding ‘g’ to cell
names that started with numeric valuesPseudobulkExpression by adding each variable
specified in group.by as columns in the object metadata
when return.seurat=TRUEDimPlot and FeatureScatter which
were breaking when using the split.by argument with a
variable that contained NAsBridgeCellsRepresentation to construct a dictionary
representation for each unimodal dataset.BuildNicheAssay to construct a new assay where each
feature is a cell label. The values represent the sum of a particular
cell label neighboring a given cell.CalcDispersion to calculate the dispersion of
features.CCAIntegration to perform Seurat-CCA
Integration.CountSketch to generate a CountSketch random
matrix.CreateCategoryMatrix to create a one-hot matrix for
a given label.DISP to find variable features based on
dispersion.FastRPCAIntegration as a convenience wrapper
function around the following three functions that are often run
together when performing integration.FetchResiduals_reference as a temporary function to
get residuals from the reference.FetchResiduals to call
sctransform::get_residuals.FetchResidualSCTModel to calculate Pearson
residuals of features not in the scale.data.FindBridgeAnchor to find bridge anchors between two
unimodal datasets.FindBridgeIntegrationAnchors to find a set of
anchors for integration between unimodal query and the other unimodal
reference using a pre-computed BridgeReferenceSet.FindBridgeTransferAnchors to find a set of anchors
for label transfer between unimodal query and the other unimodal
reference using a pre-computed BridgeReferenceSet.GaussianSketch to perform Gaussian sketching.HarmonyIntegration to perform Harmony
integration.IntegrateLayers to integrate layers in an assay
object.JointPCAIntegration to perform Seurat-Joint PCA
Integration.LeverageScore to compute the leverage scores for a
given object.LoadCurioSeeker to load Curio Seeker data.MVP to find variable features based on
mean.var.plot.NNtoGraph to convert the Neighbor class to an
asymmetrical Graph class.PrepareBridgeReference to preprocess the multi-omic
bridge and unimodal reference datasets into an extended reference.ProjectCellEmbeddings to project query data onto
the reference dimensional reduction.ProjectData to project high-dimensional single-cell
RNA expression data from a full dataset onto the lower-dimensional
embedding of the sketch of the dataset.ProjectDimReduc to project query data to reference
dimensional reduction.ProjectIntegration to integrate embeddings from the
integrated sketched.assay.PseudobulkExpression to normalize the count data
present in a given assay.Read10X_probe_metadata to read the probe metadata
from a 10x Genomics probe barcode matrix file in HDF5 format.RPCAIntegration to perform Seurat-RPCA
Integration.RunGraphLaplacian to run a graph Laplacian
dimensionality reduction.SelectIntegrationFeatures5 to select integration
features for v5 assays.SelectSCTIntegrationFeatures to select SCT
integration features.SketchData to use sketching methods to downsample
high-dimensional single-cell RNA expression data for help with
scalability for large datasets.TransferSketchLabels to transfer cell type labels
from a sketched dataset to a full dataset based on the similarities in
the lower-dimensional space.UnSketchEmbeddings to transfer embeddings from
sketched cells to the full data.VST to apply a variance stabilizing transformation
for selection of variable features.FindTransferAnchors so that anchor filtering is
not performed by defaultmerge so that layers will be added to a single
Seurat object instead of combining raw count matricesslot parameter in favor of
layers in accessor and set methodsPrepSCTFindMarkersLoadNanostring(#7566)as.Seurat.SingleCellExperiment() (#6692)LoadCurioSeeker to load sequencing-based spatial
datasets generated using the Curio Seekerpt.size bug when rasterization is set to true (#7379)FoldChange and FindMarkers to support
all normalization approaches (#7115,#7110,#7095,#6976,#6654,#6701,#6773, #7107)ReadParseBio
(#7565)ReadMtx() to add back missing
parametersSCTransform() for V5 assays to retain gene
attributes (#7557)LeverageScore() for objects with few features (#7650FindMarkers() when run post
Integration/Transfer (#6856)spatstat.core with
spatstat.exploreFindMarkers() when using SCT
assay (#6856)DoHeatmap() (#5783)ScaleData() when regressing out one gene (#5970)PlotPerturbScore() (#6081)SpatialDimPlot() when using
group.by (#6179)add.noise parameter in VlnPlot() (#5756)pseudocount.use in differential expression
functions to be set at the Assay levelgiveCsparse related warnings in
Read10X_h5SpatialPlot (#5774)ReadMtx on Windows (#5687)VlnPlot to switch on rasterization only when
required (#5846)ncol behavior in SpatialPlot (#5774)jitter to FALSE in FeatureScatter (#5876)Cells methods to new signature
(x, ...)default.stringsAsFactors() with
getOption("stringsAsFactors")raster.dpi parameter to
DimPlot/FeaturePlot to optionally rasterize individual
points (#5392)ReadParseBio to support split-pipe 0.9.6p (#5446)split.by in
FeaturePlot() (#5243)raster parameter to VlnPlot to
optionally rasterize individual points (#5076)min.cells.group parameter to
FindConservedMarkers (#5079)do.center to FALSE for lsiproject in
FindTransferAnchorsReadMtx() (#5158)label.color parameter to FeaturePlot
(#5314)ProjectUMAP (#5257, #5104, #5373)to.upper parameter in
Load10X_Spatial() (#4576)RunSPCA() (#4978)RunUMAP() when using the
umap-learn method (#5194)reduction parameter to
BuildClusterTree() (#4598)RunUMAP() (#4630)image parameter to Load10X_Spatial()
and image.name parameter to Read10X_Image()
(#4641)ReadSTARsolo() function to read output from
STARsolodensify parameter to
FindMarkers()ReadParsebio() function to read output from Parse
Biosciencesimage.alpha parameter to
SpatialDimPlot() and SpatialFeaturePlot()RunUMAP (#4972)FindSpatiallyVariableFeatures() (#4611)FindVariableFeatures() when using
selection.method = "mvp" and
binning.method = "equal_frequency" (#4712)DoHeatmap() to remove random characters from
plot legend(#4660)RunCCA()VariableFeaturePlot()jitter parameter to
FeatureScatter()as.SingleCellExperiment.Seurat() for
the latest verion of SingleCellExperiment (#4532)MapQuery()UpdateSymbolList(), no longer searches aliases
and exposes the search.types parameter in
GeneSymbolThesarus() (#4545)scale.data slot as well when converting with
as.SingleCellExperiment.Seurat()alpha parameter for
SpatialDimPlot()as.SingleCellExperiment.Seurat() conversion for
atypical reducedDim componentsAddAzimuthScores() and
AddAzimuthResults() functionsshuffle parameter to FeatureScatter()
(#4280)lsiproject and rpca options for
FindTransferAnchors()rlsi option for
FindIntegrationAnchors()SingleCellExperiment to SeuratObject class (#4205)SingleCellExperiment to SeuratObject class (#3764)score.thresh parameter in
ScoreJackStraw() (#4268)FindMarkers() non-log transformed
data.RunUMAP()DotPlot to use log1p when
scale=False (#4298)DimPlotident.1 in
FindMarkers()FindIntegrationAnchors()fc.name parameter in FindMarkers() (#4474)group.by parameter in
PlotPerturbScore() in favor of
mixscape.class.PlotClusterTree()cols parameter to JackStrawPlot()ReadMtx() to read local and remote mtx files with
associated cell and feature name filesFindMarkers (e.g, >= logfc.threshold rather than
>)Read10X() now prepends dataset number for first dataset
when reading multiple datasetssubset.AnchorSet()FindMarkers() when
setting a different pseudocount (#4111)RunLDA() related to proper passing of assay
parameter.order=TRUE in SingleDimPlot(),
print NA points under all others.data.dir in
Read10X()RunUMAP now checks for graph/neighbor consistencyFoldChange() component in
FindMarkers().merge.DimReduc methodIntegrateEmbeddings() to correct embeddings of
DimReducsProjectUMAP() to project query cells into a
reference UMAP spaceMapQuery() as a wrapper around
IntegrateData(), IntegrateEmbeddings(), and
ProjectUMAP()MappingScore to compute a per-cell mapping score
used in AzimuthAggregateExpression() for summation based
pseudobulk calculationsCalcPerturbSig(),
PrepLDA(), RunLDA(),
DEenrichRPlot(), MixscapeHeatmap(),
MixscapeLDA(), PlotPerturbScore(),
RunMixscape()FindSubCluster() to further cluster existing
clustersRunSPCA()FindMultiModalNeighbors()NNPlot().PredictAssay() to impute expression or embeddings
from nearest neighborsGraphs() function to access the names of the stored
Graph objects or pull a specific oneAnnotateAnchors() to aid in AnchorSet
interpretation as well as subset.AnchorSet()Read10X()FeatureScatter() and
VariableFeaturePlot()PrepVSTResults()ncells parameter in SCTransform()
changed to 5000FindMarkers() changed from ln to
log2AverageExpression()AnchorSet class re-implemented as a virtual class from
which IntegrationAnchorSet and
TransferAnchorSet now inherit.VlnPlot() now set automatically if not
specifiedas.character.quosure usage with
as_label due to deprecationDimPlot() and
FeaturePlot() changed from 50,000 to 100,000SCTransform() now returns a formalized
Assay subclass SCTAssay()normalization.method='SCT' in
FindTransferAnchors(), normalize query using reference SCT
model when possible.FindNeighbors to
Assay.nnCreateGeneActivityMatrix replaced by
Signac::GeneActivity()RunLSI replaced by by Signac::RunTFIDF()
and Signac::RunSVD()ReadAlevin and ReadAlevinCsv moved to
SeuratWrappersExportToCellbrowser and StopCellbrowser
moved to SeuratWrappersDimPlot when specifying
group.by parameterkeep.scale parameter added to FeaturePlot
to control scaling across multiple features and/or splits.Same deprecated in favor of
base::identityDietSeurat to work with specialized
Assay objectsape implementation of
Moran’s IKey<-.DimReduc that allow handling of
empty reduction column namesctrl in
CellCycleScoringexport(rng=FALSE) to avoid
potential future warningsSetHighlight in plotsdo.cpp deprecated and will default to trueWhichCells regardless of whether or not
idents is passedCreateAssayObject() when
data.frame has no rownames.return.model parameter in RunUMAP()DoHeatmap()label.color and label.box parameters
to DimPlotshuffle and seed parameters to
DimPlot() to help with overplottingslot parameter in
RunUMAPSpatial*Plot when running with
interactive=TRUETop and remove
duplicate items when balanced=TRUEdo.call()RunPCA()CellSelectorCreateActivityMatrix deprecated in favor of
Signac::GeneActivityReadAlevin and ReadAlevinCsv deprecated in
favor of SeuratWrappers::ReadAlevinExportToCellbrowser and StopCellbrowser
deprecated in favor of SeuratWrappers::ExportToCellbrowser
and SeuratWrappers::StopCellbrowserReadH5AD and WriteH5AD deprecated in favor
of h5Seurat/H5AD functionality found in SeuratDiskas.loom and as.Seurat.loom deprecated in
favor of functionality found in SeuratDiskDotPlotDotPlotsadd.iter parameter from RunTSNE
functionDoHeatmap group bar + labelsScoreAnchors)FindClusters() when the last node has no
edgesRunLeiden. Remove corresponding weights parameter from
FindClusters().FeatureScatter()CellSelector to use Shiny gadgets instead of
SDMToolsPointLocator as defunctSDMToolsAverageExpression when
subsetting features and returning a Seurat objectscale parameter in DotPlotkeep.sparse parameter inCreateGeneActivityMatrix`
for a more memory efficient optionstrip.suffix option in Read10X.
This changes the default behavior of
Read10X. A trailing -1 present in all
cell names will not be removed by default.group.by parameter to
FeatureScatterVlnPlots when using the
split.by optionsort.cell parameter in
FeaturePlotDotPlotSampleUMIsubset and
WhichCellsFeaturePlot when using
blendassay.used slot for DimReducs when
Assay is renamedDoHeatmap to remain compatible with ggplot2
v3.3patchwork framework to replace
CombinePlotsWhich function to address problems
with FItSNE on WindowsCellsByIdentities and
RowMergeSparseMatrices functionsUpdateSeuratObjectFindClustersRunCCA,
RunTSNE, WhichCells, HTODemux,
AddModuleScore, VlnPlot, and
RidgePlotAssay-derived
objectsCalcN (generates nFeatures and nCounts) when
counts changesinherits or
is.* for R 4.0 compatabilityRegroupIdents function to reassign idents based on
metadata column majorityUpdateSymbolList function to pull new gene names from
HGNCSeurat objectobsm and varm
stuctureAddModuleScoreMapQuery)PrepSCTIntegration function to facilitate
integration after SCTransformreference
parameter in FindIntegrationAnchorsreduction option in
FindIntegrationAnchorsCollapseEmbeddingOutliers functionFindTransferAnchors after
SCTransformColorDimSplit functionalityCheckDots to catch unused parameters and suggest
updated namesReductions and Assays assays functions to
list stored DimReducs and AssaysLogSeuratCommandRead10XReadH5AD to distinguish FVF methodsAssay specification in
BuildClusterTreeFeaturePlot when using both blend and
split.byWhichCells when passing cells and
invertHoverLocator labels and title|)RunLSI and RunALRAExIPlotFindClustersFeaturePlotsGetResidual functionSeurat objectDimReduc object
column namesDoHeatmapFeaturePlotSingleDimPlotFindClustersDimPlotlevels<-.SeuratBuildClusterTreeScaleDatapbmc_small and
cc.genesThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.