Package index • biopipen.utils

All functions

AddSeuratCommand(): Add a command to a Seurat object @commands slot
AggregateExpressionPseudobulk(): Aggregate expression of single cells into psedobulk expression matrix
Cache: Cache class for object, file or directory caching
ConvertAnnDataToSeurat(): Convert an AnnData file (h5ad) to a Seurat object or an RDS/qs2 file
ConvertSeuratToAnnData(): Convert a Seurat object (or RDS/H5Seurat/qs2 file) to an AnnData object file
EnsureSeuratScaleData(): Ensure marker genes are in the scale.data layer of an assay of the Seurat object
FinishSeuratQC(): Finish the QC process including the visualization
GetIdentityColumn(): Get the column name in meta.data that works as identity
LoadSeuratAndPerformQC(): Load samples into a Seurat object
LoadSeuratSamples(): Load samples into a list of Seurat objects
MutateScRep() ScRepMutate(): Mutate scRepertorie object
MutateSeuratMeta(): Mutater the Seurat metadata
PerformGeneQC(): Perform gene QC
PerformSeuratCellQC(): Perform cell QC
PerformSeuratQC(): Perform cell and gene QC on a Seurat object
RenameSeuratIdents(): Rename cluster names
Reporter: Add and save report
RunCellTypeAnnotation(): Run a cell type annotation tool
RunContamCorrection(): Run contaminant RNA correction on a Seurat object
RunDEGAnalysis(): Run differential gene expression analysis
RunGSEA(): Run GSEA using fgsea
RunGSEAPreRank(): Pre-rank genes based on expression data
RunModuleScoring(): Run module scoring for expression programs on a Seurat object
RunSeuratClustering(): Run seurat unsupervised clustering
RunSeuratDEAnalysis(): RunSeuratDEAnalysis
RunSeuratDoubletDetection(): Run doublet detection on a Seurat object
RunSeuratIntegration(): Run data integration on Seurat object
RunSeuratMap2Ref(): Run Seurat MapQuery to reference
RunSeuratSubClustering(): Run subset clustering on a Seurat object
RunSeuratTransformation(): Run transformations on a Seurat object
RunSeuratUMAP(): Run seurat UMAP
ScRepSubset(): Subset scRepertorie object
VizBulkDEGs(): Visualize DEGs
VizDEGs(): Visualize DEGs
VizGSEA(): Visualize GSEA results
VizSeuratCellQC(): Visualize Cell QC metrics of Seurat object
VizSeuratContamination(): Visualize contamination correction results of Seurat object
VizSeuratDoublets(): Visualize detected doublets
VizSeuratGeneQC(): Visualize gene QC metrics of Seurat object
VizSeuratMap2Ref(): Visualize features between the query and reference Seurat objects by RunSeuratMap2Ref()
apply_marker_cols(): Canonicalize the marker table columns and select a subset of them
apply_marker_filters(): Filter a marker table by tissue/cancer/species
bQuote(): backtick quoting
canonicalize_marker_cols(): Canonicalize the marker table column names
case_info(): Create information for a casename
celltype_annotation_tools(): List the cell type annotation tools supported by RunCellTypeAnnotation()
do_call(): Call a function with a list of arguments
expand_cases(): Expand the cases with default values
extract_vars(): Extract variables from a named list
filter_positive_markers(): Keep only the positive markers of a marker table
gene_name_conversion(): Convert gene names between different formats
get_biopipen_dir(): Get the path where biopipen is installed
get_logger(): Setup and return the logger
get_reporter(): Get a reporter object
gettempdir(): Get the temporary directory, without suffix. It works like tempfile.gettempdir() in Python.
html_escape(): Escape HTML entities
is_garnett_native_marker(): Detect a garnett-native marker file
is_marker_canonical(): Check whether a marker table has the canonical columns
list_rename(): Rename to names of a list
list_update(): Update the first list based on other lists
load_marker_table(): Load a marker table
majority_vote(): Majority vote the labels of each cluster
markers_to_garnett_file(): Convert a marker table to a garnett-native marker file
markers_to_named_list(): Convert a marker table to a named list
markers_to_sccatch_df(): Convert a marker table to the scCATCH format
markers_to_scsa_df(): Convert a marker table to the python wrappers' marker file format
markers_to_scsorter_df(): Convert a marker table to the scSorter format
markers_to_sctype_df(): Convert a marker table to the ScType format
markers_to_singscore_list(): Convert a marker table to the singscore format
markers_to_ucell_list(): Convert a marker table to the UCell signature format
normalize_marker_direction(): Normalize the marker directions
patch_garnett_make_predictions(): Patch garnett's make_predictions for glmnet >= 4.0 multinomial fits
RunEnrichment() ParseGMT() VizEnrichment(): Re-exported functions from other packages
read_obj() load_obj() save_obj() write_obj(): Read and write objects to/from files
read_table() load_table() write_table() save_table(): Read a table, like read.delim, but with annotated factor levels
repr(): The string representation of an object
require_package(): Require a package to be installed with optional version check
run_command(): Run a command
save_plot(): Save the plot into multiple formats
save_plotcode(): Save the plot code and data to reproduce the plot
slugify(): Slugify strings
stop_on_filtering_native_db(): Stop on filtering a native (non-universal) marker database