Package index • biopipen.utils

All functions

AddSeuratCommand(): AddSeuratCommand

LoadSeuratAndPerformQC(): Load samples into a Seurat object

PerformSeuratCellQC(): Perform cell QC

Reporter: Add and save report

RunEnrichment(): Run Enrichment Analysis (Over-representation Analysis)

RunSeuratDEAnalysis(): RunSeuratDEAnalysis

RunSeuratDoubletDetection(): Run doublet detection on a Seurat object

RunSeuratIntegration(): Run data integration on Seurat object

RunSeuratTransformation(): Run transformations on a Seurat object

VizDEGs(): Visualize DEGs

VizEnrich(): Visualize Enrichment

VizSeuratCellQC(): Visualize Cell QC metrics of Seurat object

VizSeuratDoublets(): Visualize detected doublets

VizSeuratGeneQC(): Visualize gene QC metrics of Seurat object

bQuote(): backtick quoting

case_info(): Create information for a casename

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

gene_name_conversion(): Convert gene names between different formats

get_cached(): Get signatures and cached data

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

list_rename(): Rename to names of a list

list_update(): Update the first list based on other lists

.size_compare() more_than() less_than() emerged() vanished(): Get more_than, less_than, emerged or vanished entities from a data frame.

paired(): Get paired entities from a data frame based on the other column

top(): Get top entities from a data frame based on the number of entities in each group

repr(): The string representation of an object

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

save_to_cache(): Save an object to cache

slugify(): Slugify strings