A unified language for interacting with Seurat and SingleCellExperiment

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Documentation for package ‘scLang’ version 0.99.3

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

dimPlot	Creates a dimensionality reduction plot
dimredNames	Extract the names of available dimensionality reductions from object
dimredNames.default	Extract the names of available dimensionality reductions from object
dimredNames.Seurat	Extract the names of available dimensionality reductions from object
dimredNames.SingleCellExperiment	Extract the names of available dimensionality reductions from object
featurePlot	Create a dimensionality reduction plot to represent a feature
metadataDF	Extract metadata from object as a data frame
metadataDF.default	Extract metadata from object as a data frame
metadataDF.Seurat	Extract metadata from object as a data frame
metadataDF.SingleCellExperiment	Extract metadata from object as a data frame
metadataNames	Return metadata names
scCol	Extract a metadata/coldata column from object.
scCol.default	Extract a metadata/coldata column from object.
scCol.Seurat	Extract a metadata/coldata column from object.
scCol.SingleCellExperiment	Extract a metadata/coldata column from object.
scCol<-	Extract a metadata/coldata column from object.
scCol<-.default	Extract a metadata/coldata column from object.
scCol<-.Seurat	Extract a metadata/coldata column from object.
scCol<-.SingleCellExperiment	Extract a metadata/coldata column from object.
scColCounts	Extract per-group counts from the column of a single-cell expression object
scColPairCounts	Extract counts from two columns of a single-cell expression object
scColPairPercs	Extract percentages from two columns of a single-cell expression object
scDimredMat	Extracts a dimensionality reduction matrix from object.
scDimredMat.default	Extracts a dimensionality reduction matrix from object.
scDimredMat.Seurat	Extracts a dimensionality reduction matrix from object.
scDimredMat.SingleCellExperiment	Extracts a dimensionality reduction matrix from object.
scExpMat	Extracts the expression matrix from object.
scExpMat.default	Extracts the expression matrix from object.
scExpMat.dgCMatrix	Extracts the expression matrix from object.
scExpMat.matrix	Extracts the expression matrix from object.
scExpMat.Seurat	Extracts the expression matrix from object.
scExpMat.SingleCellExperiment	Extracts the expression matrix from object.
scGeneExp	Extracts the expression of a single gene
scGeneExp.default	Extracts the expression of a single gene
scGeneExp.dgCMatrix	Extracts the expression of a single gene
scGeneExp.matrix	Extracts the expression of a single gene
scGeneExp.Seurat	Extracts the expression of a single gene
scGeneExp.SingleCellExperiment	Extracts the expression of a single gene
scPCAMat	Extracts the PCA matrix from object.
scUMAPMat	Extracts the UMAP matrix from object.
violinPlot	Create a violin plot to represent a feature