Man pages for francescojm/CRISPRcleanR
Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting
| 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.AnalysisPipeline | CRISPRcleanR analysis pipeline. |
| ccr.BAM2counts | Raw count file extraction from BAM file list. |
| ccr.checkCounts | Check consistency between library annotation and count files. |
| ccr.cleanChrm | Identification and correction of genomic regions of equal log... |
| ccr.correctCounts | Correction of sgRNA treatment counts for gene independent... |
| ccr.CreateLibraryIndex | Library index generation based on the sgRNA library to allow... |
| ccr.ExecuteMageck | Executing MAGeCK from R command line |
| ccr.FASTQ2counts | FASTQ files alignment and raw count file extraction. |
| 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.getCounts | Convert count inputs in a standard count matrix format. |
| ccr.get.gdsc1000.AMPgenes | Copy number amplified genes in a given cell line from the... |
| ccr.getLibrary | Convert library inputs in a standard library annotaion. |
| ccr.get.nonExpGenes | Non expressed genes in a given cell line |
| ccr.GWclean | Unsupervised identification and correction of gene... |
| ccr.impactOnPhenotype | Assessing the impact and potential distortion introduced by... |
| 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... |
| 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... |
| ccr.RecallCurves | CRISPRcleanR correction assessment: Recall curve inspection |
| ccr.RemoveExtraFiles | Clean intermediate files after pipeline execution. |
| ccr.ROC_Curve | Classification performances of reference sets of genes (or... |
| ccr.sgRNAmeanFCs | Extract corrected logFC in vectorial format. |
| ccr.VisDepAndSig | Depletion profile visualisation with genes signatures... |
| 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... |
| 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 |
| KY_Library_v1.1 | Genome-wide annotation for the Sanger sgRNA Library v1.1 |
| MiniLibCas9_Library | Genome-wide annotation for the MiniLibCas9 sgRNA library |
| RNAseq.fpkms | RNAseq derived genome-wide basal expression profiles for 15... |
| Whitehead_Library | Genome-wide annotation for the Whitehead sgRNA library |
