DOI: 10.18129/B9.bioc.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>

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


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


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


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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) (4.5 years)
License GPL-3
Depends ggplot2, Rsubread, RNAseqData.HNRNPC.bam.chr14, edgeR, R (>= 3.4.0)
Imports grDevices, stats, graphics
Suggests BiocStyle, RUnit, BiocGenerics, Matrix
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