samExploreR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 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: 3.13

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 "4.1") 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

Reference Manual PDF

Details

biocViews Alignment, ChIPSeq, DNASeq, GeneExpression, GeneRegulation, GeneTarget, GeneticVariability, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, SequenceMatching, Sequencing, Software, WholeGenome
Version 1.16.0
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
System Requirements
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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
Windows Binary
macOS 10.13 (High Sierra)
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/
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Old Source Packages for BioC 3.13 Source Archive