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caRpools  

CRISPR AnalyzeR for Pooled CRISPR Screens
View on CRAN: Click here


Download and install caRpools package within the R console
Install from CRAN:
install.packages("caRpools")

Install from Github:
library("remotes")
install_github("cran/caRpools")

Install by package version:
library("remotes")
install_version("caRpools", "0.83")



Attach the package and use:
library("caRpools")
Maintained by
Jan Winter
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-08-10
Latest Update: 2023-08-18
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.
How to cite:
Jan Winter (2015). caRpools: CRISPR AnalyzeR for Pooled CRISPR Screens. R package version 0.83, https://cran.r-project.org/web/packages/caRpools. Accessed 21 Dec. 2024.
Previous versions and publish date:
0.82.3 (2015-08-14 08:27), 0.82.5 (2015-11-04 19:47), 0.82 (2015-08-10 18:31), 0.83 (2015-12-06 13:32)
Other packages that cited caRpools R package
View caRpools citation profile
Other R packages that caRpools depends, imports, suggests or enhances
Functions, R codes and Examples using the caRpools R package
Some associated functions: CONTROL1.g . CONTROL1 . CONTROL2.g . CONTROL2 . TREAT1.g . TREAT1 . TREAT2.g . TREAT2 . aggregatetogenes . caRpools . carpools.hit.overview . carpools.hit.scatter . carpools.hit.sgrna . carpools.hitident . carpools.raw.genes . carpools.read.count.vs . carpools.read.depth . carpools.read.distribution . carpools.reads.genedesigns . carpools.sgrna.table . carpools.waterfall.pval . check.caRpools . compare.analysis . d.CONTROL1 . d.CONTROL2 . d.TREAT1 . d.TREAT2 . data.extract . final.table . gene.remove . generate.hits . get.gene.info . libFILE . load.file . load.packages . referencefile . stat.DESeq . stat.mageck . stat.wilcox . stats.data . unmapped.genes . use.caRpools . 
Some associated R codes: aggregatetogenes.R . carpools.hit.overview.R . carpools.hit.scatter.R . carpools.hit.sgrna.R . carpools.hitident.R . carpools.raw.genes.R . carpools.read.ballmap.R . carpools.read.count.vs.R . carpools.read.count.vs_OLD.R . carpools.read.depth.R . carpools.read.distribution.R . carpools.reads.genedesigns.R . carpools.sgrna.table.R . carpools.vioplot.R . carpools.waterfall.pval.R . check.caRpools.R . compare.analysis.R . data.extract.R . final.table.R . gene.remove.R . generate.hits.R . get.gene.info.R . load.file.R . load.packages.R . sgRNAs.compare.R . stat.DESeq.R . stat.mageck.R . stat.wilcox.R . stats.data.R . unmapped.genes.R . use.caRpools.R . venn.diagram.crispr.R .  Full caRpools package functions and examples
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