CONTROL1                Read-count data for untreated sample, replicate
                        1
CONTROL1.g              Read-count data for untreated sample, replicate
                        1
CONTROL2                Read-count data for untreated sample, replicate
                        2
CONTROL2.g              Read-count data for untreated sample, replicate
                        2
CRISPR-AnalyzeR-package
                        CaRpools - CRISPR-AnalyzeR for pooled Screens
TREAT1                  Read-count data for treated sample, replicate 1
TREAT1.g                Read-count data for treated sample, replicate 1
TREAT2                  Read-count data for treated sample, replicate 2
TREAT2.g                Read-count data for treated sample, replicate 2
aggregatetogenes        Aggregates pooled CRISPR screen sgRNA data to
                        gene data
carpools.hit.overview   Analysis: Analysis of pooled CRISPR screening
                        data using a Wilcoxon Test
carpools.hit.scatter    Plot: Plotting Scatters for hit candidate genes
                        for all provided sampled
carpools.hit.sgrna      Plotting sgRNA effects for all candidate genes
                        or single genes
carpools.hitident       Visualization of hit analysis performed by
                        Wilcox, DESeq2 and MAGeCK
carpools.raw.genes      Plotting sgRNA phenotype effects of a given
                        gene
carpools.read.count.vs
                        QC: Scatterplots of Read-Counts
carpools.read.depth     QC: Plot Sequencing Read Depth
carpools.read.distribution
                        QC: Plot Readcount Distribution
carpools.reads.genedesigns
                        QC: Plot representation of sgRNAs per gene
carpools.sgrna.table    Table Output of sgRNA effect and Target
                        Sequence
carpools.waterfall.pval
                        Visualization of p-value distribution
check.caRpools          Test caRpools installation and dependent
                        software
compare.analysis        Exporting Hit Candidate Gene Information
d.CONTROL1              Name of Read-count data for untreated sample,
                        replicate 1
d.CONTROL2              Name of Read-count data for untreated sample,
                        replicate 2
d.TREAT1                Name of Read-count data for treated sample,
                        replicate 1
d.TREAT2                Name of Read-count data for treated sample,
                        replicate 2
data.extract            Extracting sgRNA information from NGS FASTQ
                        files to create read-count files for caRpools
                        Analysis
final.table             CaRpools: Generating Table with Analysis
                        Information from all Methods
gene.remove             Remove gene information from sgRNA data.frame
generate.hits           Retrieving overlapping hits from caRpools
                        analysis
get.gene.info           Retrieving Gene Annotation and Gene Identifier
                        Conversion from BiomaRt
libFILE                 FASTA file containing als sgRNA target
                        sequences and identifiers. USed for mapping and
                        sgRNA table.
load.file               Load sgRNA NGS Data especially for caRpools
load.packages           Loading and Installing packages used for
                        caRpools
referencefile           Name of fasta reference file without extension.
stat.DESeq              Analysis: DESeq2 Analysis of pooled CRISPR NGS
                        data
stat.mageck             Analysis: Analysis of pooled CRISPR screening
                        data using a MAGeCK
stat.wilcox             Analysis: Analysis of pooled CRISPR screening
                        data using a Wilcoxon Test
stats.data              Calculating data set statistics
unmapped.genes          sgRNAs without reads
use.caRpools            Starting caRpools eport generation from R
                        console
