caRpools: CRISPR AnalyzeR for Pooled CRISPR Screens

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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.

Author
Jan Winter, Florian Heigwer
Date of publication
2015-12-06 13:31:59
Maintainer
Jan Winter <jan.winter@dkfz-heidelberg.de>
License
GPL
Version
0.83
URLs

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