sgRSEA: Enrichment Analysis of CRISPR/Cas9 Knockout Screen Data

Provides functions to implement sgRSEA (single-guide RNA Set Enrichment Analysis), which is a robust test for identification of essential genes from genetic screening data using CRISPR (clustered regularly interspaced short palindromic repeats) and Cas9 (CRISPR-associated nuclease 9) system.

Author
Jungsik Noh, Beibei Chen
Date of publication
2015-06-15 17:08:25
Maintainer
Jungsik Noh <Jungsik.Noh@UTSouthwestern.edu>
License
GPL-2
Version
0.1

View on CRAN

Man pages

melanoma808
A subset of CRISPR/Cas9 knockout screening data on melanoma...
plotNScores
Plot histograms of normalized gene scores
plotScores
Plot histograms of gene scores
sgCount
Generate a raw sgRNA read count table from fastq files
sgRSEA
Perform a permutation test which computes gene scores and...
sgRSEA.mean
Perform a permutation test similar to sgRSEA
UQnormalize
Upper-quartile/total-count normalization of raw sgRNA read...

Files in this package

sgRSEA
sgRSEA/inst
sgRSEA/inst/sgCount_R.py
sgRSEA/inst/extdata
sgRSEA/inst/extdata/library2.txt
sgRSEA/inst/extdata/fqInfo.txt
sgRSEA/inst/extdata/test1.fastq
sgRSEA/inst/extdata/test2.fastq
sgRSEA/NAMESPACE
sgRSEA/data
sgRSEA/data/melanoma808.rda
sgRSEA/R
sgRSEA/R/sgCount.R
sgRSEA/R/TCnormalize.R
sgRSEA/R/Tmean.Null.Tss2.R
sgRSEA/R/UQnormalize.count.R
sgRSEA/R/plotNScores.R
sgRSEA/R/stdofT.R
sgRSEA/R/outdatZ.R
sgRSEA/R/PermPval.R
sgRSEA/R/plotScores.R
sgRSEA/R/Tmaxmean.Null.Tss2.R
sgRSEA/R/maxmean.op.R
sgRSEA/R/T.mean.R
sgRSEA/R/Zstat.R
sgRSEA/R/UQnormalize.R
sgRSEA/R/sgRSEA.R
sgRSEA/R/sgRSEA.mean.R
sgRSEA/R/pMME.R
sgRSEA/R/TCnormalize.count.R
sgRSEA/R/Zfit.R
sgRSEA/R/T.maxmean.R
sgRSEA/MD5
sgRSEA/DESCRIPTION
sgRSEA/man
sgRSEA/man/plotNScores.Rd
sgRSEA/man/UQnormalize.Rd
sgRSEA/man/sgRSEA.Rd
sgRSEA/man/melanoma808.Rd
sgRSEA/man/sgRSEA.mean.Rd
sgRSEA/man/sgCount.Rd
sgRSEA/man/plotScores.Rd