samExploreR

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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>

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

Installation

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


if (!require("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")
samExploreR Vignette PDF R Script
Reference Manual PDF

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) (7 years)
License GPL-3
Depends ggplot2, Rsubread, RNAseqData.HNRNPC.bam.chr14, edgeR, R (>= 3.4.0)
Imports grDevices, stats, graphics
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Suggests BiocStyle, RUnit, BiocGenerics, Matrix
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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
Bioc Package Browser https://code.bioconductor.org/browse/samExploreR/
Package Short Url https://bioconductor.org/packages/samExploreR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive