sgRSEA: Enrichment Analysis of CRISPR/Cas9 Knockout Screen Data
Version 0.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorJungsik Noh, Beibei Chen
Date of publication2015-06-15 17:08:25
MaintainerJungsik Noh <Jungsik.Noh@UTSouthwestern.edu>
LicenseGPL-2
Version0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sgRSEA")

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...

Functions

PermPval Source code
TCnormalize Man page Source code
TCnormalize.count Source code
Tmaxmean.Null.Tss2 Source code
Tmean.Null.Tss2 Source code
UQnormalize Man page Source code
UQnormalize.count Source code
Zfit Source code
Zstat Source code
maxmean Source code
maxmean.op Source code
mean Source code
melanoma808 Man page
outdatZ Source code
pMME Source code
plotNScores Man page Source code
plotScores Man page Source code
sgCount Man page Source code
sgRSEA Man page Source code
sgRSEA.mean Man page Source code
stdofT Source code

Files

inst
inst/sgCount_R.py
inst/extdata
inst/extdata/library2.txt
inst/extdata/fqInfo.txt
inst/extdata/test1.fastq
inst/extdata/test2.fastq
NAMESPACE
data
data/melanoma808.rda
R
R/sgCount.R
R/TCnormalize.R
R/Tmean.Null.Tss2.R
R/UQnormalize.count.R
R/plotNScores.R
R/stdofT.R
R/outdatZ.R
R/PermPval.R
R/plotScores.R
R/Tmaxmean.Null.Tss2.R
R/maxmean.op.R
R/T.mean.R
R/Zstat.R
R/UQnormalize.R
R/sgRSEA.R
R/sgRSEA.mean.R
R/pMME.R
R/TCnormalize.count.R
R/Zfit.R
R/T.maxmean.R
MD5
DESCRIPTION
man
man/plotNScores.Rd
man/UQnormalize.Rd
man/sgRSEA.Rd
man/melanoma808.Rd
man/sgRSEA.mean.Rd
man/sgCount.Rd
man/plotScores.Rd
sgRSEA documentation built on May 20, 2017, 3:46 a.m.