samExploreR

DOI: 10.18129/B9.bioc.samExploreR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see samExploreR.

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

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("samExploreR")

For older versions of R, please refer to the appropriate Bioconductor release.

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, ImmunoOncology, Preprocessing, RNASeq, SequenceMatching, Sequencing, Software, WholeGenome
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
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
Links To Me
Build Report

Package Archives

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

Source Package	samExploreR_1.8.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	samExploreR_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/samExploreR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/samExploreR
Package Short Url	https://bioconductor.org/packages/samExploreR/
Package Downloads Report	Download Stats