DOI: 10.18129/B9.bioc.bcSeq    

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

Bioconductor version: Release (3.7)

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 Alignment, CRISPR, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software
Version 1.2.0
License GPL (>= 2)
Depends R (>= 3.4)
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
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Source Package bcSeq_1.2.0.tar.gz
Windows Binary bcSeq_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) bcSeq_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bcSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bcSeq
Package Short Url http://bioconductor.org/packages/bcSeq/
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