Data loading module

Set of python functions to read, write, and integrate CRISPR screening resources (e.g. guide RNA libraries) and datasets from different platforms and analysis tools.

Load module

Functions to load screen datasets and sgRNA library tables.

screenpro.load.loadScreenProcessingData(experimentName, collapsedToTranscripts=True, premergedCounts=False)[source]

Load ScreenProcessing outputs (see original code here) Input files:

  • *_librarytable.txt => library table

  • *_mergedcountstable.txt => merged counts table

  • *_phenotypetable.txt => phenotype table

Parameters

  • experimentName (str) – name of the experiment

  • collapsedToTranscripts (bool) – whether the gene scores are collapsed to transcripts

  • premergedCounts (bool) – whether the counts are premerged

Returns

dictionary of dataframes

Return type

dict

screenpro.load.load_cas9_sgRNA_library(library_path, library_type, sep='\t', index_col=0, protospacer_length=19, verbose=True, **args)[source]

Load Cas9 sgRNA library table for single or dual guide design.