Files in francescojm/CRISPRcleanR
Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting
.Rbuildignore
.gitignore
CRISPRcleanR.Rproj
DESCRIPTION
LICENSE
NAMESPACE
Quick_start.pdf
R/CRISPRcleanR.R
README.md
Reference_Manual.pdf
_vignettes/Demo-blx.bib
_vignettes/Demo-concordance.tex
_vignettes/Demo.Rnw
_vignettes/Demo.bbl
_vignettes/Demo.log
_vignettes/Demo.run.xml
_vignettes/Demo.synctex.gz
_vignettes/Demo.tex
_vignettes/references.bib
data/ADaM2021_essential.RData
data/AVANA_Library.RData
data/BAGEL_essential.RData
data/BAGEL_essential_curated.RData
data/BAGEL_essential_v2.RData
data/BAGEL_nonEssential.RData
data/BAGEL_nonEssential_curated.RData
data/Brunello_Library.RData
data/CCLE.gisticCNA.RData
data/CL.subset.RData
data/EPLC.272HcorrectedFCs.RData
data/EssGenes.DNA_REPLICATION_cons.RData
data/EssGenes.HISTONES.RData
data/EssGenes.KEGG_rna_polymerase.RData
data/EssGenes.PROTEASOME_cons.RData
data/EssGenes.SPLICEOSOME_cons.RData
data/EssGenes.ribosomalProteins.RData
data/GDSC.CL_annotation.RData
data/GDSC.geneLevCNA.RData
data/GeCKO_Library_v2.RData
data/HT.29correctedFCs.RData
data/KY_Library_v1.0.RData
data/KY_Library_v1.1.RData
data/MiniLibCas9_Library.RData
data/RNAseq.fpkms.RData
data/Whitehead_Library.RData
inst/extdata/A2058_counts.tsv
inst/extdata/EPLC-272H_counts.tsv
inst/extdata/HT-29-GeCKOv2_counts.tsv
inst/extdata/HT-29-Whitehead_counts.tsv
inst/extdata/HT-29_counts.tsv
inst/extdata/HT29-Brunello_counts.tsv
inst/extdata/HT29-MiniLibCas9_counts.tsv
inst/extdata/OUTPUT_README
inst/extdata/pipleline_main_v1.0.0.json
inst/extdata/pipleline_web_v1.0.0.json
inst/extdata/test_plasmid.fq.gz
inst/extdata/test_sample1.fq.gz
inst/extdata/test_sample2.fq.gz
man/AVANA_Library.Rd
man/BAGEL_essential.Rd
man/BAGEL_nonEssential.Rd
man/Brunello_Library.Rd
man/CCLE.gisticCNA.Rd
man/CL.subset.Rd
man/EPLC.272HcorrectedFCs.Rd
man/EssGenes.DNA_REPLICATION_cons.Rd
man/EssGenes.HISTONES.Rd
man/EssGenes.KEGG_rna_polymerase.Rd
man/EssGenes.PROTEASOME_cons.Rd
man/EssGenes.SPLICEOSOME_cons.Rd
man/EssGenes.ribosomalProteins.Rd
man/GDSC.CL_annotation.Rd
man/GDSC.geneLevCNA.Rd
man/GeCKO_Library_v2.Rd
man/HT.29correctedFCs.Rd
man/KY_Library_v1.0.Rd
man/KY_Library_v1.1.Rd
man/MiniLibCas9_Library.Rd
man/RNAseq.fpkms.Rd
man/Whitehead_Library.Rd
man/ccr.AnalysisPipeline.Rd
man/ccr.BAM2counts.Rd
man/ccr.CreateLibraryIndex.Rd
man/ccr.ExecuteMageck.Rd
man/ccr.FASTQ2counts.Rd
man/ccr.GWclean.Rd
man/ccr.NormfoldChanges.Rd
man/ccr.PlainTsvFile.Rd
man/ccr.PrRc_Curve.Rd
man/ccr.ROC_Curve.Rd
man/ccr.RecallCurves.Rd
man/ccr.RemoveExtraFiles.Rd
man/ccr.VisDepAndSig.Rd
man/ccr.checkCounts.Rd
man/ccr.cleanChrm.Rd
man/ccr.correctCounts.Rd
man/ccr.geneMeanFCs.Rd
man/ccr.geneSummary.Rd
man/ccr.genes2sgRNAs.Rd
man/ccr.get.CCLEgisticSets.Rd
man/ccr.get.gdsc1000.AMPgenes.Rd
man/ccr.get.nonExpGenes.Rd
man/ccr.getCounts.Rd
man/ccr.getLibrary.Rd
man/ccr.impactOnPhenotype.Rd
man/ccr.logFCs2chromPos.Rd
man/ccr.multDensPlot.Rd
man/ccr.perf_distributions.Rd
man/ccr.perf_statTests.Rd
man/ccr.sgRNAmeanFCs.Rd
web/CCRlogo.jpg
