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("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 | R Script | |
| 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) (7 years) |
| License | GPL-3 |
| Depends | ggplot2, Rsubread, RNAseqData.HNRNPC.bam.chr14, edgeR, R (>= 3.4.0) |
| Imports | grDevices, stats, graphics |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, RUnit, BiocGenerics, Matrix |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 [email protected]: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 |