To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("samExploreR")

In most cases, you don't need to download the package archive at all.

samExploreR

 

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Bioconductor version: Release (3.5)

This R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread.

Author: Alexey Stupnikov, Shailesh Tripathi and Frank Emmert-Streib

Maintainer: shailesh tripathi <shailesh.tripathy at gmail.com>

Citation (from within R, enter citation("samExploreR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("samExploreR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("samExploreR")

 

PDF R Script samExploreR Vignette
PDF   Reference Manual

Details

biocViews Alignment, ChIPSeq, DNASeq, GeneExpression, GeneRegulation, GeneTarget, GeneticVariability, GenomeAnnotation, Preprocessing, RNASeq, SequenceMatching, Sequencing, Software, WholeGenome
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL-3
Depends ggplot2, Rsubread, RNAseqData.HNRNPC.bam.chr14, edgeR, R (>= 3.4.0)
Imports grDevices, stats, graphics
LinkingTo
Suggests BiocStyle, RUnit, BiocGenerics, Matrix
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source samExploreR_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) samExploreR_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/samExploreR/tree/release-3.5
Package Short Url http://bioconductor.org/packages/samExploreR/
Package Downloads Report Download Stats

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