caRpools: CRISPR AnalyzeR for Pooled CRISPR Screens

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 <https://en.wikipedia.org/wiki/CRISPR> for more information on CRISPR.

AuthorJan Winter, Florian Heigwer
Date of publication2015-12-06 13:31:59
MaintainerJan Winter <jan.winter@dkfz-heidelberg.de>
LicenseGPL
Version0.83
http://www.crispr-analyzer.de, https://github.com/boutroslab/caRpools

View on CRAN

Man pages

aggregatetogenes: Aggregates pooled CRISPR screen sgRNA data to gene data

caRpools: CaRpools - CRISPR-AnalyzeR for pooled Screens

carpools.hitident: Visualization of hit analysis performed by Wilcox, DESeq2 and...

carpools.hit.overview: Analysis: Analysis of pooled CRISPR screening data using a...

carpools.hit.scatter: Plot: Plotting Scatters for hit candidate genes for all...

carpools.hit.sgrna: Plotting sgRNA effects for all candidate genes or single...

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

data.extract: Extracting sgRNA information from NGS FASTQ files to create...

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

final.table: CaRpools: Generating Table with Analysis Information from all...

generate.hits: Retrieving overlapping hits from caRpools analysis

gene.remove: Remove gene information from sgRNA data.frame

get.gene.info: Retrieving Gene Annotation and Gene Identifier Conversion...

libFILE: FASTA file containing als sgRNA target sequences and...

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...

stats.data: Calculating data set statistics

stat.wilcox: Analysis: Analysis of pooled CRISPR screening data using a...

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

Files in this package

caRpools
caRpools/inst
caRpools/inst/doc
caRpools/inst/doc/CaRpools.R
caRpools/inst/doc/CaRpools.Rmd
caRpools/inst/doc/CaRpools.html
caRpools/NAMESPACE
caRpools/data
caRpools/data/caRpools.RData
caRpools/R
caRpools/R/load.packages.R caRpools/R/aggregatetogenes.R caRpools/R/venn.diagram.crispr.R caRpools/R/carpools.raw.genes.R caRpools/R/get.gene.info.R caRpools/R/check.caRpools.R caRpools/R/carpools.waterfall.pval.R caRpools/R/final.table.R caRpools/R/carpools.hitident.R caRpools/R/stat.mageck.R caRpools/R/carpools.read.count.vs.R caRpools/R/use.caRpools.R caRpools/R/carpools.read.count.vs_OLD.R caRpools/R/compare.analysis.R caRpools/R/carpools.read.ballmap.R caRpools/R/stat.wilcox.R caRpools/R/stats.data.R caRpools/R/carpools.read.depth.R caRpools/R/carpools.vioplot.R caRpools/R/carpools.read.distribution.R caRpools/R/carpools.hit.sgrna.R caRpools/R/unmapped.genes.R caRpools/R/carpools.sgrna.table.R caRpools/R/carpools.hit.scatter.R caRpools/R/data.extract.R caRpools/R/sgRNAs.compare.R caRpools/R/gene.remove.R caRpools/R/carpools.hit.overview.R caRpools/R/carpools.reads.genedesigns.R caRpools/R/generate.hits.R caRpools/R/stat.DESeq.R caRpools/R/load.file.R
caRpools/vignettes
caRpools/vignettes/pictures
caRpools/vignettes/pictures/start-symbol.png
caRpools/vignettes/pictures/rstudio-knit.png
caRpools/vignettes/pictures/fastq-format.png
caRpools/vignettes/pictures/workflow.png
caRpools/vignettes/pictures/rstudio.png
caRpools/vignettes/pictures/extract.png
caRpools/vignettes/pictures/extraction.png
caRpools/vignettes/pictures/ova-file.png
caRpools/vignettes/pictures/start-button.png
caRpools/vignettes/pictures/login.png
caRpools/vignettes/pictures/miaccs-fastq.png
caRpools/vignettes/pictures/CaRpools.png
caRpools/vignettes/pictures/configure-appliance.png
caRpools/vignettes/pictures/folder-sctructure-before.png
caRpools/vignettes/pictures/readcount.png
caRpools/vignettes/pictures/port-forward.png
caRpools/vignettes/pictures/alignment-match.png
caRpools/vignettes/pictures/folder-structure-before.png
caRpools/vignettes/pictures/folder-structure-FASTQ-before.png
caRpools/vignettes/pictures/folder-structure-FINAL.png
caRpools/vignettes/pictures/download.png
caRpools/vignettes/pictures/terminal.png
caRpools/vignettes/pictures/import-progress.png
caRpools/vignettes/pictures/miaccs-readcount.png
caRpools/vignettes/pictures/library-fasta.png
caRpools/vignettes/pictures/fastq-format-example.png
caRpools/vignettes/pictures/MIACCS1.png
caRpools/vignettes/pictures/miaccs-analysis.png
caRpools/vignettes/pictures/folder-structure-FASTQ-FINAL.png
caRpools/vignettes/CaRpools.Rmd
caRpools/MD5
caRpools/build
caRpools/build/vignette.rds
caRpools/DESCRIPTION
caRpools/man
caRpools/man/get.gene.info.Rd caRpools/man/data.extract.Rd caRpools/man/check.caRpools.Rd caRpools/man/TREAT2.Rd caRpools/man/CONTROL1.Rd caRpools/man/aggregatetogenes.Rd caRpools/man/CONTROL1.g.Rd caRpools/man/d.TREAT2.Rd caRpools/man/stat.wilcox.Rd caRpools/man/caRpools.Rd caRpools/man/carpools.reads.genedesigns.Rd caRpools/man/use.caRpools.Rd caRpools/man/stat.mageck.Rd caRpools/man/stats.data.Rd caRpools/man/d.TREAT1.Rd caRpools/man/compare.analysis.Rd caRpools/man/libFILE.Rd caRpools/man/TREAT1.Rd caRpools/man/carpools.hit.sgrna.Rd caRpools/man/carpools.hit.overview.Rd caRpools/man/d.CONTROL1.Rd caRpools/man/carpools.read.distribution.Rd caRpools/man/CONTROL2.g.Rd caRpools/man/carpools.waterfall.pval.Rd caRpools/man/load.packages.Rd caRpools/man/unmapped.genes.Rd caRpools/man/carpools.read.depth.Rd caRpools/man/carpools.sgrna.table.Rd caRpools/man/load.file.Rd caRpools/man/TREAT1.g.Rd caRpools/man/generate.hits.Rd caRpools/man/d.CONTROL2.Rd caRpools/man/referencefile.Rd caRpools/man/carpools.read.count.vs.Rd caRpools/man/gene.remove.Rd caRpools/man/final.table.Rd caRpools/man/stat.DESeq.Rd caRpools/man/carpools.hitident.Rd caRpools/man/carpools.hit.scatter.Rd caRpools/man/TREAT2.g.Rd caRpools/man/CONTROL2.Rd caRpools/man/carpools.raw.genes.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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