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

## Documentation for package ‘CRISPRcleanR’ version 2.3.1

- DESCRIPTION file.

## Help Pages

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