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.

Install the latest version of this package by entering the following in R:
install.packages("caRpools")
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

Functions

aggregatetogenes Man page
carpools.hitident Man page
carpools.hit.overview Man page
carpools.hit.scatter Man page
carpools.hit.sgrna Man page
carpools.raw.genes Man page
carpools.read.count.vs Man page
carpools.read.depth Man page
carpools.read.distribution Man page
carpools.reads.genedesigns Man page
carpools.sgrna.table Man page
carpools.waterfall.pval Man page
check.caRpools Man page
compare.analysis Man page
CONTROL1 Man page
CONTROL1.g Man page
CONTROL2 Man page
CONTROL2.g Man page
CRISPR-AnalyzeR Man page
CRISPR-AnalyzeR-package Man page
data.extract Man page
d.CONTROL1 Man page
d.CONTROL2 Man page
d.TREAT1 Man page
d.TREAT2 Man page
final.table Man page
generate.hits Man page
gene.remove Man page
get.gene.info Man page
libFILE Man page
load.file Man page
load.packages Man page
referencefile Man page
stat.DESeq Man page
stat.mageck Man page
stats.data Man page
stat.wilcox Man page
TREAT1 Man page
TREAT1.g Man page
TREAT2 Man page
TREAT2.g Man page
unmapped.genes Man page
use.caRpools Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.