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bcSeq (Duke)

bcSeq (Duke)

bcSeq is an R tool to map short hairpin RNA ( shRNA) and CRISPR screens reference barcode library. The bcSeq parallelized algorithm uses the Trie data structure and resolves sequencing errors using Phred quality scores. It also uses a Baye's method to classify read barcode origins. It also supports user-defined probability models and supports multi-threading.

Topic

Compound libraries and screening; Gene regulation; Sequencing; Mapping

Details

  • Operation: Mapping
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v>=2
  • Cost: Free
  • Version name: 1.8.0
  • Maturity: Stable
  • Credit: National Cancer Institute.
  • Contact: Jiaxing Lin jiaxing.lin _at_ duke.edu
  • Collection: BioConductor

Publications

Lin J, Gresham J, Wang T, Kim SY, Alvarez J, Damrauer JS, Floyd S, Granek J, Allen A, Chan C, Xie J, Owzar K "bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens." Bioinformatics. 2018 Oct 15;34(20):3581-3583. https://doi.org/10.1093/bioinformatics/bty402
PMID: 29790906
PMCID: PMC6184561


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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