This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see samExploreR.
Bioconductor version: 3.8
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")
):
To install this package, start R (version "3.5") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("samExploreR")
R Script | samExploreR Vignette | |
Reference Manual |
biocViews | Alignment, ChIPSeq, DNASeq, GeneExpression, GeneRegulation, GeneTarget, GeneticVariability, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, SequenceMatching, Sequencing, Software, WholeGenome |
Version | 1.6.1 |
In Bioconductor since | BioC 3.5 (R-3.4) (2 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 |
Follow Installation instructions to use this package in your R session.
Source Package | samExploreR_1.6.1.tar.gz |
Windows Binary | |
Mac OS X 10.11 (El Capitan) | samExploreR_1.6.1.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 | http://bioconductor.org/packages/samExploreR/ |
Package Downloads Report | Download Stats |
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