Man pages for caRpools
CRISPR AnalyzeR for Pooled CRISPR Screens

aggregatetogenesAggregates pooled CRISPR screen sgRNA data to gene data
caRpoolsCaRpools - CRISPR-AnalyzeR for pooled Screens
carpools.hitidentVisualization of hit analysis performed by Wilcox, DESeq2 and...
carpools.hit.overviewAnalysis: Analysis of pooled CRISPR screening data using a...
carpools.hit.scatterPlot: Plotting Scatters for hit candidate genes for all...
carpools.hit.sgrnaPlotting sgRNA effects for all candidate genes or single...
carpools.raw.genesPlotting sgRNA phenotype effects of a given gene
carpools.read.count.vsQC: Scatterplots of Read-Counts
carpools.read.depthQC: Plot Sequencing Read Depth
carpools.read.distributionQC: Plot Readcount Distribution
carpools.reads.genedesignsQC: Plot representation of sgRNAs per gene
carpools.sgrna.tableTable Output of sgRNA effect and Target Sequence
carpools.waterfall.pvalVisualization of p-value distribution
check.caRpoolsTest caRpools installation and dependent software
compare.analysisExporting Hit Candidate Gene Information
CONTROL1Read-count data for untreated sample, replicate 1
CONTROL1.gRead-count data for untreated sample, replicate 1
CONTROL2Read-count data for untreated sample, replicate 2
CONTROL2.gRead-count data for untreated sample, replicate 2
data.extractExtracting sgRNA information from NGS FASTQ files to create...
d.CONTROL1Name of Read-count data for untreated sample, replicate 1
d.CONTROL2Name of Read-count data for untreated sample, replicate 2
d.TREAT1Name of Read-count data for treated sample, replicate 1
d.TREAT2Name of Read-count data for treated sample, replicate 2
final.tableCaRpools: Generating Table with Analysis Information from all...
generate.hitsRetrieving overlapping hits from caRpools analysis
gene.removeRemove gene information from sgRNA data.frame
get.gene.infoRetrieving Gene Annotation and Gene Identifier Conversion...
libFILEFASTA file containing als sgRNA target sequences and...
load.fileLoad sgRNA NGS Data especially for caRpools
load.packagesLoading and Installing packages used for caRpools
referencefileName of fasta reference file without extension.
stat.DESeqAnalysis: DESeq2 Analysis of pooled CRISPR NGS data
stat.mageckAnalysis: Analysis of pooled CRISPR screening data using a...
stats.dataCalculating data set statistics
stat.wilcoxAnalysis: Analysis of pooled CRISPR screening data using a...
TREAT1Read-count data for treated sample, replicate 1
TREAT1.gRead-count data for treated sample, replicate 1
TREAT2Read-count data for treated sample, replicate 2
TREAT2.gRead-count data for treated sample, replicate 2
unmapped.genessgRNAs without reads
use.caRpoolsStarting caRpools eport generation from R console
caRpools documentation built on May 30, 2017, 2:52 a.m.