# CRISPR AnalyzeR for Pooled CRISPR Screens

## Documentation for package ‘caRpools’ version 0.83

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

CRISPR-AnalyzeR-package | CaRpools - CRISPR-AnalyzeR for pooled Screens
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
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 | CaRpools - CRISPR-AnalyzeR for pooled Screens
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
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
unmapped.genes | sgRNAs without reads
use.caRpools | Starting caRpools eport generation from R console