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caRpools (version 0.83)

CRISPR AnalyzeR for Pooled CRISPR Screens

Description

CRISPR-Analyzer for pooled CRISPR screens (caRpools) provides an end-to-end analysis of CRISPR screens including quality control, hit candidate analysis, visualization and automated report generation using R markdown. Needs MAGeCK (http://sourceforge.net/p/mageck/wiki/Home/), bowtie2 for all functions. CRISPR (clustered regularly interspaced short palindromic repeats) is a method to perform genome editing. See for more information on CRISPR.

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Install

install.packages('caRpools')

Monthly Downloads

83

Version

0.83

License

GPL

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Repository

https://github.com/boutroslab/caRpools

Homepage

http://www.crispr-analyzer.de

Maintainer

Jan Winter

Last Published

December 6th, 2015

Functions in caRpools (0.83)

Read-count data for treated sample, replicate 2

Read-count data for untreated sample, replicate 2

Calculating data set statistics

sgRNAs without reads

carpools.hit.scatter

Plot: Plotting Scatters for hit candidate genes for all provided sampled

carpools.waterfall.pval

Visualization of p-value distribution

Name of Read-count data for treated sample, replicate 2

Analysis: Analysis of pooled CRISPR screening data using a MAGeCK

Load sgRNA NGS Data especially for caRpools

aggregatetogenes

Aggregates pooled CRISPR screen sgRNA data to gene data

carpools.hit.overview

Analysis: Analysis of pooled CRISPR screening data using a Wilcoxon Test

Read-count data for untreated sample, replicate 1

Remove gene information from sgRNA data.frame

Name of Read-count data for untreated sample, replicate 1

Read-count data for untreated sample, replicate 1

Loading and Installing packages used for caRpools

CaRpools: Generating Table with Analysis Information from all Methods

carpools.sgrna.table

Table Output of sgRNA effect and Target Sequence

Test caRpools installation and dependent software

Name of fasta reference file without extension.

carpools.raw.genes

Plotting sgRNA phenotype effects of a given gene

Name of Read-count data for treated sample, replicate 1

compare.analysis

Exporting Hit Candidate Gene Information

Retrieving Gene Annotation and Gene Identifier Conversion from BiomaRt

CaRpools - CRISPR-AnalyzeR for pooled Screens

carpools.read.depth

QC: Plot Sequencing Read Depth

carpools.read.distribution

QC: Plot Readcount Distribution

Analysis: DESeq2 Analysis of pooled CRISPR NGS data

Starting caRpools eport generation from R console

carpools.reads.genedesigns

QC: Plot representation of sgRNAs per gene

Extracting sgRNA information from NGS FASTQ files to create read-count files for caRpools Analysis

Read-count data for treated sample, replicate 2

carpools.hitident

Visualization of hit analysis performed by Wilcox, DESeq2 and MAGeCK

FASTA file containing als sgRNA target sequences and identifiers. USed for mapping and sgRNA table.

carpools.hit.sgrna

Plotting sgRNA effects for all candidate genes or single genes

Name of Read-count data for untreated sample, replicate 2

Read-count data for treated sample, replicate 1

carpools.read.count.vs

QC: Scatterplots of Read-Counts

Read-count data for treated sample, replicate 1

Read-count data for untreated sample, replicate 2

Analysis: Analysis of pooled CRISPR screening data using a Wilcoxon Test

Retrieving overlapping hits from caRpools analysis