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htSeqTools

htSeqTools

htSeqTools is an R package to process, quality control, and visualize RNA-seq and ChIP-seq datasets. The package includes MDS plots, detection of amplification artifacts, functions for the identification of high coverage genomic regions, and visualization of coverage profiles.

Topic

Sequencing; ChIP-seq; RNA-seq

Details

  • Operation: Sequence analysis
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v>=2
  • Cost: Free
  • Version name: 1.30.0
  • Maturity: Stable
  • Credit: -
  • Contact: Oscar Reina oscar.reina _at_ irbbarcelona.org
  • Collection: Bioconductor

Publications

Planet E, Attolini CS, Reina O, Flores O, Rossell D "htSeqTools: high-throughput sequencing quality control, processing and visualization in R." Bioinformatics. 2012 Feb 15;28(4):589-90. https://doi.org/10.1093/bioinformatics/btr700
PMID: 22199381


Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590


Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


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