"GiRAFR improves gRNA detection and annotation in single cell CRISPR screens" source data

cellranger_output contains results generated by Cell Ranger feature barcoding analysis. See paper Table S2 for list of samples and citations.GiRAFR_output folder contain GiRAFR outputs using data from 12 studies.Explanation on the output file format: https://girafr.readthedocs.io/en/latest/output.htmlScripts using processed data to recreate figures can be found via: github.com/FunctionalEpigeneticsLab/GiRAFRfiltered_feature_bc_matrix contains Cell Ranger alignment results for our in-house CROP-seq, for which raw data can be downloaded from Gene Expression Omnibus (GEO) database under the accession number GSE216040.Figures and their corresponding scripts using source data:Figure 1a, b, g => Jupyter notebook Figure 1.ipynbFigure 1h, 1i => Source data.xsxFigure 2a => In_house data.ipynbFigure 2c => Jost_NatureBiotechnology.ipynbFigure 1e, f, 2b, d, e, S2b, 3c => Source data.xlsxFigure 3a, S2a, S3c => see individual notebooks with titles matching corresponding datasetFigure 3b, S3a, S3b => Inhouse downsample.ipynbFigure S4a => Mutant gRNA impact on TSO corrected studies.ipynbFigure S4b => scalability.xlsx