DOI: 10.18129/B9.bioc.bcSeq  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see bcSeq.

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

Bioconductor version: 3.17

This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes' classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading.

Author: Jiaxing Lin [aut, cre], Jeremy Gresham [aut], Jichun Xie [aut], Kouros Owzar [aut], Tongrong Wang [ctb], So Young Kim [ctb], James Alvarez [ctb], Jeffrey S. Damrauer [ctb], Scott Floyd [ctb], Joshua Granek [ctb], Andrew Allen [ctb], Cliburn Chan [ctb]

Maintainer: Jiaxing Lin <jiaxing.lin at duke.edu>

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PDF R Script bcSeq
PDF   Reference Manual
Text   NEWS


biocViews ATACSeq, Alignment, CRISPR, ImmunoOncology, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software
Version 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 years)
License GPL (>= 2)
Depends R (>= 3.4.0)
Imports Rcpp (>= 0.12.12), Matrix, Biostrings
LinkingTo Rcpp, Matrix
Suggests knitr
URL https://github.com/jl354/bcSeq
BugReports https://support.bioconductor.org
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package bcSeq_1.22.0.tar.gz
Windows Binary bcSeq_1.22.0.zip (64-bit only)
macOS Binary (x86_64) bcSeq_1.22.0.tgz
macOS Binary (arm64) bcSeq_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bcSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bcSeq
Bioc Package Browser https://code.bioconductor.org/browse/bcSeq/
Package Short Url https://bioconductor.org/packages/bcSeq/
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