Unsupervised Correction of Gene Independent Cell Responses to CRISPR-Cas9 Targeting

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Documentation for package ‘CRISPRcleanR’ version 2.3.1

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AVANA_Library Genome-wide annotation for the AVANA sgRNA library
BAGEL_essential Reference Core fitness essential genes
BAGEL_nonEssential Reference set of non essential genes
Brunello_Library Genome-wide annotation for the Brunello sgRNA library
CCLE.gisticCNA Genome-wide copy number data for 13 human cancer cell lines.
ccr.cleanChrm Identification and correction of genomic regions of equal log fold changes involving sgRNAs targeting a minimal number of genes within a given chromosome.
ccr.correctCounts Correction of sgRNA treatment counts for gene independent responses to CRISPR-Cas9 targeting
ccr.ExecuteMageck Executing MAGeCK from R command line
ccr.geneMeanFCs Gene level log fold changes
ccr.genes2sgRNAs Targeting sgRNAs
ccr.geneSummary Gene level depletion summary
ccr.get.CCLEgisticSets CCLE gistic score gene sets
ccr.get.gdsc1000.AMPgenes Copy number amplified genes in a given cell line from the GDSC1000
ccr.get.nonExpGenes Non expressed genes in a given cell line
ccr.GWclean Unsupervised identification and correction of gene independent cell responses to CRISPR-Cas9 targeting.
ccr.impactOnPhenotype Assessing the impact and potential distortion introduced by the CRISPRcleanR correction on the genes showing loss/gain-of-fitness effect.
ccr.logFCs2chromPos Genomic sorting of sgRNAs' log fold changes.
ccr.multDensPlot Mutiple shaded density plot
ccr.NormfoldChanges Normalisation of sgRNA counts and fold change computation
ccr.perf_distributions CRISPRcleanR correction assessment: inspection of sgRNA log fold changes distributions
ccr.perf_statTests CRISPRcleanR correction assessment: Statistical tests
ccr.PlainTsvFile Saving a sgRNA counts' object in plain tsv file
ccr.PrRc_Curve Classification performances of reference sets of genes (or sgRNAs) based on depletion log fold-changes
ccr.RecallCurves CRISPRcleanR correction assessment: Recall curve inspection
ccr.ROC_Curve Classification performances of reference sets of genes (or sgRNAs) based on depletion log fold-changes
ccr.VisDepAndSig Depletion profile visualisation with genes signatures superimposed and recall
CL.subset COSMIC identifiers of 15 immortalised human cancer cell lines
EPLC.272HcorrectedFCs CRISPRcleanR corrected data for an example cell line
EssGenes.DNA_REPLICATION_cons Core Fitness essential genes involved in DNA replication
EssGenes.HISTONES Core Fitness essential histone genes
EssGenes.KEGG_rna_polymerase Core Fitness essential rna polymerase genes
EssGenes.PROTEASOME_cons Core Fitness essential proteasome genes
EssGenes.ribosomalProteins Core Fitness essential genes coding for ribosomal proteins
EssGenes.SPLICEOSOME_cons Core Fitness essential spliceosome genes
GDSC.CL_annotation Tissue type and other annotations for 1,001 human cancer cell lines
GDSC.geneLevCNA Genome-wide copy number data for 15 human cancer cell lines.
GeCKO_Library_v2 Genome-wide annotation for the GeCKO (v2) sgRNA library
HT.29correctedFCs CRISPRcleanR corrected data for an example cell line
KY_Library_v1.0 Genome-wide annotation for the Sanger sgRNA Library v1.0
MiniLibCas9_Library Genome-wide annotation for the MiniLibCas9 sgRNA library
RNAseq.fpkms RNAseq derived genome-wide basal expression profiles for 15 cell lines.
Whitehead_Library Genome-wide annotation for the Whitehead sgRNA library