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Recent Releases of Seurat

Seurat - Version 5.3.0

Bug releases and performance improvements, including: * Refactoring and speed-up of sctransform * Refactroring and speed-up of leverage score calcluation * Fixes to variable feature selection, module score calculation, PseudobulkExpression, and other bugs that could cause errors in edge cases * Improved testing, CI

- R
Published by rsatija about 1 year ago

Seurat - Version 5.2.1

Changes

  • Fixed test_find_clusters.R to accommodate variability in label assignments given by FindClusters across different systems (#9641)

- R
Published by dcollins15 over 1 year ago

Seurat - Version 5.2.0

Changes

  • Added group.by parameter to FindAllMarkers, allowing users to regroup their data using a non-default identity class prior to performing differential expression (#9550)
  • Added image.type parameter to Read10X_Image enabling VisiumV1 instances to be populated instead of instances of the default VisiumV2 class (#9556)
  • Fixed IntegrateLayers to respect the dims.to.integrate parameter
  • Added stroke.size parameter to DimPlot (#8180)
  • Updated 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)
  • Updated RunPCA to use the BPCells-provided SVD solver on BPCells matrices; updated JackStraw to support BPCells matrices (#8271)
  • Fixed RunPCA to avoid converting BPCells matrices into dense matrices - significantly reduces the function's memory usage when running on BPCells matrices (#8966)
  • Updated RunSLSI to support BPCells matrices
  • Fixed DietSeurat so that the layers parameter is respected (#8197)
  • Updated RunUMAP to support umap-learn version >= 0.5.0 (#9559)
  • Updated 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 cellfeaturematrix.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)
  • Fixed LoadXenium to accommodate datasets without "Blank Codeword" or "Unassigned Codeword" matrices(#9135)
  • Fixed ReadXenium to properly parse multiple molecular outputs at once (#8265)
  • Added features parameter to LeverageScore and SketchData
  • Updated SketchData's ncells parameter to accept integer vector

- R
Published by dcollins15 over 1 year ago

Seurat - Version 5.1.0

Changes

  • Updated interactive SpatialDimPlots to display spatial coordinates
  • Updated BuildClusterTree to PseudobulkExpression(..., method = "aggregate") instead of AverageExpression
  • Fixed SpatialPlot to properly handle images with shared cells
  • Added cluster.name parameter to BuildNicheAssay
  • Added VisiumV2 class, inherits SeuratObject::FOV, returned by Load10X_Spatial
  • Updated Load10X_Spatial to support loading Visium HD datasets - added bin.size parameter
  • Updated Read10X_Coordinates to handle new tissue_coordinates.parquet files
  • Added shape parameter to SpatialPlot and wrappers: SpatialFeaturePlot and SpatialDimPlot
  • Added image.scale parameter to SpatialPlot and related functions: SpatialFeaturePlot/ISpatialFeaturePlot and SpatialDimPlot/ISpatialDimPlot
  • Restored image.name parameter to Read10X_Image
  • Added scale parameter to Radius.VisiumV1
  • Fixed calculation of spot.radius attribute for VisiumV1 instance returned by Read10X_Image — replace scale.factors$fiducial with scale.factors$spot
  • Added Read10X_Coordinates and Read10X_ScaleFactors
  • Fixed SpatialPlot to properly handle mutli-assay Seurat instances

- R
Published by dcollins15 about 2 years ago

Seurat - Version 5.0.3

Changes

  • Fixed PercentAbove to discount null values (#8412)
  • Added log parameter to FeatureScatter
  • Fixed handling of clip.range for SCTransform when ncells is less than the size of the passed dataset

- R
Published by dcollins15 over 2 years ago

Seurat - Version 5.0.2

Changes

  • Fixed AverageExpression to handle features vector when layer="scale.data" and return.seurat=TRUE
  • Added fc.slot parameter to FindMarkers
  • Fixed SCTransform to handle vars.to.regress (#8148) and (#8349)
  • Fixed SCTransform to handle fetching residuals (#8185)

- R
Published by dcollins15 over 2 years ago

Seurat - Version 5.0.1

Changes

  • Fixed SCTransform.StdAssay to pass extra arguments to sctransform::vst(). Fixes https://github.com/satijalab/seurat/issues/7998
  • Fixed PercentageFeatureSet Layer calling https://github.com/satijalab/seurat/issues/8009
  • Fixed cell highlighting https://github.com/satijalab/seurat/pull/7914
  • Updated marker sorting to be by p-value with ties broken by absolute difference in percent expression
  • Fixed issue with replicated barcodes in MappingScore https://github.com/satijalab/seurat/issues/7922
  • Improved PseudobulkExpression by adding 'g' to cell names that started with numeric values
  • Improved PseudobulkExpression by adding each variable specified in group.by as columns in the object metadata when return.seurat=TRUE
  • Fixed DimPlot and FeatureScatter which were breaking when using the split.by argument with a variable that contained NAs

- R
Published by dcollins15 over 2 years ago

Seurat - v5.0.0

Added

  • Add BridgeCellsRepresentation to construct a dictionary representation for each unimodal dataset.
  • Add 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.
  • Add CalcDispersion to calculate the dispersion of features.
  • Add CCAIntegration to perform Seurat-CCA Integration.
  • Add CountSketch to generate a CountSketch random matrix.
  • Add CreateCategoryMatrix to create a one-hot matrix for a given label.
  • Add DISP to find variable features based on dispersion.
  • Add FastRPCAIntegration as a convenience wrapper function around the following three functions that are often run together when performing integration.
  • Add FetchResiduals_reference as a temporary function to get residuals from the reference.
  • Add FetchResiduals to call sctransform::get_residuals.
  • Add FetchResidualSCTModel to calculate Pearson residuals of features not in the scale.data.
  • Add FindBridgeAnchor to find bridge anchors between two unimodal datasets.
  • Add FindBridgeIntegrationAnchors to find a set of anchors for integration between unimodal query and the other unimodal reference using a pre-computed BridgeReferenceSet.
  • Add FindBridgeTransferAnchors to find a set of anchors for label transfer between unimodal query and the other unimodal reference using a pre-computed BridgeReferenceSet.
  • Add GaussianSketch to perform Gaussian sketching.
  • Add HarmonyIntegration to perform Harmony integration.
  • Add IntegrateLayers to integrate layers in an assay object.
  • Add JointPCAIntegration to perform Seurat-Joint PCA Integration.
  • Add LeverageScore to compute the leverage scores for a given object.
  • Add LoadCurioSeeker to load Curio Seeker data.
  • Add MVP to find variable features based on mean.var.plot.
  • Add NNtoGraph to convert the Neighbor class to an asymmetrical Graph class.
  • Add PrepareBridgeReference to preprocess the multi-omic bridge and unimodal reference datasets into an extended reference.
  • Add ProjectCellEmbeddings to project query data onto the reference dimensional reduction.
  • Add 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.
  • Add ProjectDimReduc to project query data to reference dimensional reduction.
  • Add ProjectIntegration to integrate embeddings from the integrated sketched.assay.
  • Add PseudobulkExpression to normalize the count data present in a given assay.
  • Add Read10X_probe_metadata to read the probe metadata from a 10x Genomics probe barcode matrix file in HDF5 format.
  • Add RPCAIntegration to perform Seurat-RPCA Integration.
  • Add RunGraphLaplacian to run a graph Laplacian dimensionality reduction.
  • Add SelectIntegrationFeatures5 to select integration features for v5 assays.
  • Add SelectSCTIntegrationFeatures to select SCT integration features.
  • Add SketchData to use sketching methods to downsample high-dimensional single-cell RNA expression data for help with scalability for large datasets.
  • Add TransferSketchLabels to transfer cell type labels from a sketched dataset to a full dataset based on the similarities in the lower-dimensional space.
  • Add UnSketchEmbeddings to transfer embeddings from sketched cells to the full data.
  • Add VST to apply a variance stabilizing transformation for selection of variable features.

Changes

  • Change FindTransferAnchors so that anchor filtering is not performed by default
  • Change merge so that layers will be added to a single Seurat object instead of combining raw count matrices
  • Deprecate slot parameter in favor of layers in accessor and set methods

Full Changelog: https://github.com/satijalab/seurat/compare/v4.4.0...v5.0.0

- R
Published by saketkc over 2 years ago

Seurat - Version 4.4.0

Added

  • Added parallelization support with speed improvements for PrepSCTFindMarkers
  • Fix bug in LoadNanostring(#7566)

Changes

  • Fix bug in as.Seurat.SingleCellExperiment() (#6692)
  • Support for Visium probe information introduced in Spaceranger 2.1 (#7141)
  • Add LoadCurioSeeker to load sequencing-based spatial datasets generated using the Curio Seeker
  • Fix fold change calculation for assays (#7095)
  • Fix pt.size bug when rasterization is set to true (#7379)
  • Fix FoldChange and FindMarkers to support all normalization approaches (#7115,#7110,#7095,#6976,#6654,#6701,#6773, #7107)
  • Fix for handling newer ParseBio formats in ReadParseBio (#7565)
  • Fix for handling rasterization by default (#7842)
  • Fix sce object conversion by @timoast in https://github.com/satijalab/seurat/pull/6771
  • Fix(Xenium): load renamed feature by @jsicherman in https://github.com/satijalab/seurat/pull/6986
  • keep.scale for SpatialPlot/SpatialFeaturePlot by @samuel-marsh in https://github.com/satijalab/seurat/pull/6905
  • spaceranger 2.1 update by @stephenwilliams22 in https://github.com/satijalab/seurat/pull/7141
  • update ReadParseBio to be compatible with latest split-pipe v1.1.0 by @epapalexi in https://github.com/satijalab/seurat/pull/7565
  • Correct lost gene expression column when loading NanoString CosMx data by @mtgregory in https://github.com/satijalab/seurat/pull/7566

New Contributors

  • @jsicherman made their first contribution in https://github.com/satijalab/seurat/pull/6986
  • @mtgregory made their first contribution in https://github.com/satijalab/seurat/pull/7566

Full Changelog: https://github.com/satijalab/seurat/compare/v4.3.0...v4.4.0

- R
Published by saketkc almost 3 years ago

Seurat - Version 4.3.0

Added

  • Add support for imaging-based spatial datasets

Changes

  • Fix bug in FindMarkers() when run post Integration/Transfer (#6856)

- R
Published by AustinHartman over 3 years ago

Seurat - Version 4.2.0

Changes

  • Fix legend color in DoHeatmap() (#5783)
  • Fix bug in ScaleData() when regressing out one gene (#5970)
  • Fix name pulling in PlotPerturbScore() (#6081)
  • Support spaceranger 2.0 (#6208)
  • Fix bug in SpatialDimPlot() when using group.by (#6179)
  • Add add.noise parameter in VlnPlot() (#5756)
  • Fix uwot model backwards compatibility (#6345)
  • Allow pseudocount.use in differential expression functions to be set at the Assay level

- R
Published by mojaveazure over 3 years ago

Seurat - Version 4.1.1

Changes

  • Fix giveCsparse related warnings in Read10X_h5
  • Fix ident labeling for SpatialPlot (#5774)
  • Fix ReadMtx on Windows (#5687)
  • Fix VlnPlot to switch on rasterization only when required (#5846)
  • Fix ncol behavior in SpatialPlot (#5774)
  • Set jitter to FALSE in FeatureScatter (#5876)
  • Update Cells methods to new signature (x, ...)
  • Replace use of default.stringsAsFactors() with getOption("stringsAsFactors")

- R
Published by mojaveazure about 4 years ago

Seurat - Version 4.1.0

Changes - Update ReadParseBio to support split-pipe 0.9.6p (#5446) - Fixes for MAST differential expression (#5441) - Fix scaling options when using split.by in FeaturePlot() (#5243)

Additions - Add raster.dpi parameter to DimPlot/FeaturePlot to optionally rasterize individual points (#5392) - Add support for sctransform v2, differential expression on with SCT

- R
Published by mojaveazure over 4 years ago

Seurat - Version 4.0.6

Changes - Add raster parameter to VlnPlot to optionally rasterize individual points (#5076) - Add min.cells.group parameter to FindConservedMarkers (#5079) - Set do.center to FALSE for lsiproject in FindTransferAnchors - Fix error message in ReadMtx() (#5158) - Add label.color parameter to FeaturePlot (#5314) - Fix issues in ProjectUMAP (#5257, #5104, #5373)

Additions - Implement supervised LSI

- R
Published by mojaveazure over 4 years ago

Seurat - Version 4.0.5

Changes - Update documentation for to.upper parameter in Load10X_Spatial() (#4576) - Update concept tags for RunSPCA() (#4978) - Conditionally run tests/packages that use suggested packages (#5160)

- R
Published by mojaveazure over 4 years ago

Seurat - Version 4.0.4

Changes - Warn and continue rather than erroring if not all features are available in FindSpatiallyVariableFeatures() (#4611) - Bug fix for SCT-based integration in selecting proper reference model (#4355) - Bug fix for reading from absolute paths in ReadMtx (#4723) - Bug fix in SingleCellExperiment conversion (#4633) - Bug fix in FindVariableFeatures() when using selection.method = "mvp" and binning.method = "equal_frequency" (#4712) - Bug fix in DoHeatmap() to remove random characters from plot legend(#4660) - Fix cell renaming in RunCCA() - Fix issue in SingleCellExperiment conversion where the mainExp would not be set properly - Fix for default dispersion info displayed in VariableFeaturePlot()

Additions - Add reduction parameter to BuildClusterTree() (#4598) - Add DensMAP option to RunUMAP() (#4630) - Add image parameter to Load10X_Spatial() and image.name parameter to Read10X_Image() (#4641) - Add ReadSTARsolo() function to read output from STARsolo - Add densify parameter to FindMarkers() - Add ReadParsebio() function to read output from Parse Biosciences - Add the image.alpha parameter to SpatialDimPlot() and SpatialFeaturePlot()

- R
Published by mojaveazure almost 5 years ago

Seurat - Version 4.0.3

Changes - Fix issues with as.SingleCellExperiment.Seurat() for the latest verion of SingleCellExperiment (#4532) - Ensure proper reference.reduction is used in MapQuery() - Fix to UpdateSymbolList(), no longer searches aliases and exposes the search.types parameter in GeneSymbolThesarus() (#4545) - Transfer scale.data slot as well when converting with as.SingleCellExperiment.Seurat() - Enable alpha parameter for SpatialDimPlot() - Fix as.SingleCellExperiment.Seurat() conversion for atypical reducedDim components

Additions - Add jitter parameter to FeatureScatter()

- R
Published by mojaveazure about 5 years ago

Seurat - Version 4.0.2

Changes - Preserve feature metadata when converting from SingleCellExperiment to SeuratObject class (#4205) - Preserve multiple assays when converting from SingleCellExperiment to SeuratObject class (#3764) - Fix passing of score.thresh parameter in ScoreJackStraw() (#4268) - Fix FC calculation in FindMarkers() non-log transformed data. - Add umap-learn version >= 0.5.0 compatibility for RunUMAP() - Fix DotPlot to use log1p when scale=False (#4298) - Fix split and shuffled DimPlot - Disallow NULL or another length 0 vector for ident.1 in FindMarkers() - Fix range shift when labeling clusters on a GeomSpatial plot - Fix SpatialPlot distortion for non-square images. - Fix future-related warnings in FindIntegrationAnchors() - Fix fc.name parameter in FindMarkers() (#4474) - Deprecate group.by parameter in PlotPerturbScore() in favor of mixscape.class.

Additions - New AddAzimuthScores() and AddAzimuthResults() functions - Add shuffle parameter to FeatureScatter() (#4280) - Add lsiproject and rpca options for FindTransferAnchors() - Add rlsi option for FindIntegrationAnchors()

- R
Published by mojaveazure about 5 years ago

Seurat - Version 4.0.1

Changes - Equality added to differential expression thresholds in FindMarkers (e.g, >= logfc.threshold rather than >) - Read10X() now prepends dataset number for first dataset when reading multiple datasets - Bug fix for subset.AnchorSet() - Bug fix for fold change values in FindMarkers() when setting a different pseudocount (#4111) - Bug fix for RunLDA() related to proper passing of assay parameter. - When using order=TRUE in SingleDimPlot(), print NA points under all others. - Remove default parameter value for data.dir in Read10X() - Import spatstat fxns from subpackages (spatstat.core, spatstat.geom) - RunUMAP now checks for graph/neighbor consistency

Additions - Add direction option to PlotClusterTree() - Add cols parameter to JackStrawPlot() - Add ReadMtx() to read local and remote mtx files with associated cell and feature name files

- R
Published by mojaveazure over 5 years ago

Seurat - Version 4.0.0

Changes - Removed old, deprecated code - Utilize SeuratObject as base of object code - Default neighbor finding algorithm changed from "rann" to "annoy" - Default ncells parameter in SCTransform() changed to 5000 - Default fold change in FindMarkers() changed from ln to log2 - Implementation improvements to AverageExpression() - AnchorSet class re-implemented as a virtual class from which IntegrationAnchorSet and TransferAnchorSet now inherit. - Point size in VlnPlot() now set automatically if not specified - Return the sample.tree properly when integrating with a single reference dataset - Replace as.character.quosure usage with as_label due to deprecation - Minor changes to the exact calculation of the anchor weight matrix - Default rasterization limit in DimPlot() and FeaturePlot() changed from 50,000 to 100,000 - SCTransform() now returns a formalized Assay subclass SCTAssay() - When using normalization.method='SCT' in FindTransferAnchors(), normalize query using reference SCT model when possible.

Additions - Expose FoldChange() component in FindMarkers() - Add IntegrateEmbeddings() to correct embeddings of DimReducs - Add ProjectUMAP() to project query cells into a reference UMAP space - Add MapQuery() as a wrapper around IntegrateData(), IntegrateEmbeddings(), and ProjectUMAP() - Add MappingScore to compute a per-cell mapping score used in Azimuth - Add AggregateExpression() for summation based pseudobulk calculations - Add mixscape functionality via CalcPerturbSig(), PrepLDA(), RunLDA(), DEenrichRPlot(), MixscapeHeatmap(), MixscapeLDA(), PlotPerturbScore(), RunMixscape() - Add FindSubCluster() to further cluster existing clusters - Add supervised PCA functionality via RunSPCA() - Add functionality to enable weighted nearest neighbor analyses via FindMultiModalNeighbors() - Add neighbor visualization plot via NNPlot(). - Add PredictAssay() to impute expression or embeddings from nearest neighbors - Add AnnotateAnchors() to aid in AnchorSet interpretation as well as subset.AnchorSet() - Add flexibility of choice for cell column in Read10X() - Add rasterization option to FeatureScatter() and VariableFeaturePlot()

- R
Published by mojaveazure over 5 years ago

Seurat - Version 3.2.3

Deprecations - do.cpp parameter in IntegrateData and TransferData deprecated and will default to true

Changes - Same deprecated in favor of base::identity - Fix in DietSeurat to work with specialized Assay objects - Fix p-value return when using the ape implementation of Moran's I - Fix bug in FindMarkers when using MAST with a latent variable - Updates to Key<-.DimReduc that allow handling of empty reduction column names - Allow setting ctrl in CellCycleScoring - Modify subset.Seurat to allow specialized Assay subsetting methods - Fix image selection in interactive spatial plots - Update Rcpp functions with export(rng=FALSE) to avoid potential future warnings - Fix RenameCells bug for integrated SCT assays - Fix highlight order with proper factor levels when using SetHighlight in plots - Small change in CellRanger version detection logic of h5 file to improve robustness to outside tools.

Additions - Titles added to DimPlot when specifying group.by parameter - keep.scale parameter added to FeaturePlot to control scaling across multiple features and/or splits. - raster parameter in various scatter plots (eg. DimPlot, FeaturePlot, CellScatter) for plot-native rasterization instead of using AugmentPlot

- R
Published by mojaveazure over 5 years ago

Seurat - Version 3.2.2

Changes - Set the seed in WhichCells regardless of whether or not idents is passed - Retain Graph and Neighbor objects when subsetting only on features - Fix data.frame input to CreateAssayObject() when data.frame has no rownames. - Default annoy search to sequential if not using multicore future plans. - Require sctransform >= 0.3.0

- R
Published by mojaveazure almost 6 years ago

Seurat - Version 3.2.1

Deprecations - CreateActivityMatrix deprecated in favor of Signac::GeneActivity - ReadAlevin and ReadAlevinCsv deprecated in favor of SeuratWrappers::ReadAlevin - ExportToCellbrowser and StopCellbrowser deprecated in favor of SeuratWrappers::ExportToCellbrowser and SeuratWrappers::StopCellbrowser - ReadH5AD and WriteH5AD deprecated in favor of h5Seurat/H5AD functionality found in SeuratDisk - as.loom and as.Seurat.loom deprecated in favor of functionality found in SeuratDisk

Changes - Allow setting slot parameter in RunUMAP - Added support for FIt-SNE v1.2+ - Fix for Spatial*Plot when running with interactive=TRUE - Set max for number of items returned by Top and remove duplicate items when balanced=TRUE - Fix logging bug when functions were run via do.call() - Fix handling of weight.by.var parameter when approx=FALSE in RunPCA() - Fix issue where feature names with dashes crashed CellSelector - Fix issue where errors in subsetting were being swallowed - Fix issue where labeling uncropped spatial plots was broken

Additions - Added support for nearest neighbor input and return.model parameter in RunUMAP() - Enable named color vectors in DoHeatmap() - Add label.color and label.box parameters to DimPlot - Added shuffle and seed parameters to DimPlot() to help with overplotting - Added new stacked violin plot functionality

- R
Published by mojaveazure almost 6 years ago

Seurat - Version 3.2.0

Changes:

  • Removed add.iter parameter from RunTSNE function
  • Fixed integer overflow error in the WilcoxDETest function
  • Minor visual fixes in DoHeatmap group bar + labels
  • Efficiency improvements in anchor scoring (ScoreAnchors)
  • Fix bug in FindClusters() when the last node has no edges
  • Default to weighted = TRUE when constructing igraph objects in RunLeiden. Remove corresponding weights parameter from FindClusters().
  • Fix handling of keys in FeatureScatter()
  • Change CellSelector to use Shiny gadgets instead of SDMTools
  • Mark PointLocator as defunct
  • Remove SDMTools
  • Fixed data slot return in AverageExpression when subsetting features and returning a Seurat object

Additions

  • Added ability to create a Seurat object from an existing Assay object, or any object inheriting from the Assay class
  • Added ability to cluster idents and group features in DotPlot
  • Added ability to use RColorBrewer plaettes for split DotPlots
  • Added visualization and analysis functionality for spatially resolved datasets (Visium, Slide-seq).

- R
Published by mojaveazure almost 6 years ago

Seurat - Version 3.1.5

Changes - Replace wilcox.test with limma implementation for a faster FindMarkers default method - Better point separation for VlnPlots when using the split.by option - Efficiency improvements for anchor pairing - Deprecate redundant sort.cell parameter in FeaturePlot - Fixes to ensure correct class of Matrix passed to c++ functions - Fixes for underscores in ident labels for DotPlot - Ensure preservation of matrix dimnames in SampleUMI - Fix non-standard evaluation problems in subset and WhichCells - Default split violin option is now a multi group option - Preserve alpha in FeaturePlot when using blend - Update assay.used slot for DimReducs when Assay is renamed

Additions: - New scale parameter in DotPlot - New keep.sparse parameter in CreateGeneActivityMatrix for a more memory efficient option - Added ability to store model learned by UMAP and project new data - New stip.suffix option in Read10X - Added group.by parameter to FeatureScatter

- R
Published by mojaveazure about 6 years ago

Seurat - Version 3.1.4

Changes: - Fixes to DoHeatmap to remain compatible with ggplot2 v3.3 - Adoption of patchwork framework to replace CombinePlots

- R
Published by mojaveazure over 6 years ago

Seurat - Version 3.1.3

Changes: - Export CellsByIdentites and RowMergeSparseMatrices - nCount and nFeature metadata variables retained after subset and updated properly with UpdateSeuratObject - Fix uwot support for running directly on feature matrices - Fixes for keys with underscores - Fix issue with leiden option for FindClusters - Fix for data transfer when using sctransform - SDMTools moved to Suggests as package is orphaned

Additions: - New system-agnostic executable locator to fix FIt-SNE problem on Windows

- R
Published by mojaveazure over 6 years ago

Seurat - Version 3.1.2

Changes: - Only run CalcN (generates nFeatures and nCounts) when counts changes - Fix issue regarding colons in feature names - Change object class testing to use inherits or is.* for R 4.0 compatability

Additions: - New RegroupIdents function to reassign idents based on metadata column majority - UpdateSymbolList function to pull new gene names from HGNC - Added support for H5AD layers as additional assays in a Seurat object

- R
Published by mojaveazure over 6 years ago

Seurat - Version 3.1.1

Changes: - Fix rownames issue when running UMAP on dist object - Add support for new H5AD obsm and varm stucture - Fix issue when trying to read non-existent feature-level metadata from an H5AD file - Fix in integration workflow when using SCTransform - Improved error checking for AddModuleScore - cbind fix in reference-based integration (MapQuery) - Fix for convenience plots error hanging - Ensure Seurat objects aren't stored in the command logs

Additions: - New RegroupIdents function to reassign idents based on metadata column majority - UpdateSymbolList function to pull new gene names from HGNC - Added support for H5AD layers as additional assays in a Seurat object

- R
Published by mojaveazure over 6 years ago

Seurat - Version 3.1.0

Changes: - Bug fixes in LogSeuratCommand, Read10X, UpdateSeuratObject, FeaturePlot, WhichCells, and HoverLocator - Prevent dimnames for counts/data/scale.data matrices from being arrays - Updates ReadH5AD to distinguish FVF methods - Sink all output from stdout to stderr - Fix to scale.data cell ordering after subsetting - Enable Assay specification in BuildClusterTree - Ensure features names don't contain pipes (|) - Deprecation of RunLSI and RunALRA - Fix legend bug when sorting in ExIPlot

Additions: - New PrepSCTIntegration function to facilitate integration after SCTransform - Reference-based integration with the reference parameter in FindIntegrationAnchors - Reciprocal PCA as a reduction option in FindIntegrationAnchors - New CollapseEmbeddingOutliers function - Enable FindTransferAnchors after SCTransform - Added back ColorDimSplit functionality - Include a code of conduct - Added uwot support as new default UMAP method - Added CheckDots to catch unused parameters and suggest updated names - Reductions and Assays assays functions to list stored DimReducs and Assays

- R
Published by mojaveazure almost 7 years ago

Seurat - Version 3.0.2

Changes: - Improvements to visualization functions - Improvements to identity assignment in FindClusters

Additions: - New Seurat ↔ Monocle converters - New GetResidual function - Custom colors for blended FeaturePlot

- R
Published by mojaveazure about 7 years ago

Seurat - Version 3.0.1

Changes: - Improvements to conversion functions - Fixes to various plotting functions - Export new functions to the benefit of external packages

Additions: - New global options using R's options manager - New split.by parameter to ScaleData

- R
Published by mojaveazure about 7 years ago

Seurat - Version 3.0.0

Changes: * Significant code restructuring * Most occurances of "gene(s)" in function names/arguments renamed to "feature(s)" * Changes to the Seurat object class to facilitate multimodal data * New BlendPlot implementation

Additions: * New method for identifying anchors across single-cell datasets * Parallelization support via future * Additional method for demultiplexing with MULTIseqDemux * Support normalization via sctransform * New option for clustering with the Leiden algorithm * Support for reading 10X v3 files * New function to export Seurat objects for the UCSC cell browser * Support for data import from Alevin outputs * Imputation of dropped out values via ALRA

- R
Published by andrewwbutler about 7 years ago

Seurat - Version 2.3.3

Changes: - New HTOHeatmap function - Removed unused compiler flags - Support for custom PNG arguments for vector-friendly plotting - Fix for 'NA'-labeled cells disappearing with custom color scales - Moved several lightly-used packages from 'imports' to 'suggests'

- R
Published by mojaveazure almost 8 years ago

Seurat - Version 2.3.2

  • New functions for reading in and manipulating data
  • Better support for and validation of assay data
  • Compatability updates for ggplot2 v2.3.0

- R
Published by mojaveazure about 8 years ago

Seurat - Version 2.3.1

Changes: - Support for UMAP dimensional reduction technique - New conversion functions - Dependency update: requires R 3.4.0 or higher and Matrix 1.2-14 or higher - Bug fixes, including memory enhancements to FetchData and AddModuleScore, as well as improvments to visualization functions

- R
Published by mojaveazure about 8 years ago

Seurat - Version 2.3.0

Changes: - Support for HTO demultiplexing - Utility functions: TransferIdent, CombineIdent, SplitObject, vector.friendly - C++ implementation for parts of BuildSNN - Preliminary parallelization support (regression and JackStraw) - Support for FItSNE - MetaDE replaced with metap for combining p-values (MetaDE was removed from CRAN) - NMF heatmaps replaced (NMF to be archived by CRAN)

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Published by mojaveazure about 8 years ago

Seurat - Version 2.2.1

Changes: - Support for multiple-dataset alignment with RunMultiCCA and AlignSubspace - New methods for evaluating alignment performance - MetaDE replaced with metap for combining p-values (MetaDE was removed from CRAN) - NMF heatmaps replaced (NMF to be archived by CRAN)

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Published by mojaveazure over 8 years ago

Seurat - Version 2.1.0

Version 2.1 Changes: * Support for using MAST and DESeq2 packages for differential expression testing in FindMarkers * Support for multi-modal single-cell data via @assay slot

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Published by andrewwbutler over 8 years ago

Seurat - Version 2.0.1

Version 2.0.1 -- CRAN Release

Seurat is now available on CRAN. This version on Seurat is compatible with 2.0.0, but includes updated documentation, example data sets, and minor bug fixes. Installation can now be done with install.packages(). Binaries are no longer provided as they are built by CRAN. See the CRAN package page for Seurat here.

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Published by mojaveazure almost 9 years ago

Seurat - Version 2.0.0

Version 2.0 Changes: * Preprint released for integrated analysis of scRNA-seq across conditions, technologies and species * Significant restructuring of code to support clarity and dataset exploration * Methods for scoring gene expression and cell-cycle phase

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Published by andrewwbutler almost 9 years ago

Seurat - Pre-release v2.0

Pre-release version of Seurat v2.0.

Additional documentation and vignettes for all new features in Seurat v2.0 will accompany a full release in the near future

Changes: * Preprint released for integrated analysis of scRNA-seq across conditions, technologies and species * Significant restructuring of code to support clarity and dataset exploration

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Published by satijalab almost 9 years ago

Seurat - Release Version 1.4.0

Major Changes: - Added methods for negative binomial regression and differential expression testing for UMI count data - New ways to merge and downsample Seurat objects

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Published by andrewwbutler over 9 years ago

Seurat - Version 1.3.0

Major Changes : - Improved clustering approach - All functions support sparse matrices - Methods for removing unwanted sources of variation - Consistent function names - Updated visualizations

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Published by satijalab almost 10 years ago