Package index
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AddSeuratCommand() - Add a command to a Seurat object
@commandsslot
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AggregateExpressionPseudobulk() - Aggregate expression of single cells into psedobulk expression matrix
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Cache - Cache class for object, file or directory caching
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ConvertAnnDataToSeurat() - Convert an AnnData file (h5ad) to a Seurat object or an RDS/qs2 file
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ConvertSeuratToAnnData() - Convert a Seurat object (or RDS/H5Seurat/qs2 file) to an AnnData object file
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FinishSeuratQC() - Finish the QC process including the visualization
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GetIdentityColumn() - Get the column name in meta.data that works as identity
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LoadSeuratAndPerformQC() - Load samples into a Seurat object
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PerformGeneQC() - Perform gene QC
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PerformSeuratCellQC() - Perform cell QC
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Reporter - Add and save report
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RunDEGAnalysis() - Run differential gene expression analysis
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RunGSEA() - Run GSEA using fgsea
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RunGSEAPreRank() - Pre-rank genes based on expression data
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RunSeuratClustering() - Run seurat unsupervised clustering
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RunSeuratDEAnalysis() - RunSeuratDEAnalysis
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RunSeuratDoubletDetection() - Run doublet detection on a Seurat object
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RunSeuratIntegration() - Run data integration on Seurat object
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RunSeuratMap2Ref() - Run Seurat MapQuery to reference
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RunSeuratSubClustering() - Run subset clustering on a Seurat object
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RunSeuratTransformation() - Run transformations on a Seurat object
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RunSeuratUMAP() - Run seurat UMAP
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ScRepMutate() - Mutate scRepertorie object
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ScRepSubset() - Subset scRepertorie object
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VizBulkDEGs() - Visualize DEGs
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VizDEGs() - Visualize DEGs
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VizGSEA() - Visualize GSEA results
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VizSeuratCellQC() - Visualize Cell QC metrics of Seurat object
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VizSeuratDoublets() - Visualize detected doublets
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VizSeuratGeneQC() - Visualize gene QC metrics of Seurat object
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VizSeuratMap2Ref() - Visualize features between the query and reference Seurat objects by
RunSeuratMap2Ref()
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bQuote() - backtick quoting
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case_info() - Create information for a casename
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do_call() - Call a function with a list of arguments
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expand_cases() - Expand the cases with default values
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extract_vars() - Extract variables from a named list
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gene_name_conversion() - Convert gene names between different formats
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get_biopipen_dir() - Get the path where biopipen is installed
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get_logger() - Setup and return the logger
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get_reporter() - Get a reporter object
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gettempdir() - Get the temporary directory, without suffix. It works like
tempfile.gettempdir()in Python.
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html_escape() - Escape HTML entities
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list_rename() - Rename to names of a list
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list_update() - Update the first list based on other lists
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RunEnrichment()ParseGMT()VizEnrichment() - Re-exported functions from other packages
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read_obj()load_obj()save_obj()write_obj() - Read and write objects to/from files
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repr() - The string representation of an object
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run_command() - Run a command
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save_plot() - Save the plot into multiple formats
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save_plotcode() - Save the plot code and data to reproduce the plot
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slugify() - Slugify strings