bcSeq: Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

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.

Package details

AuthorJiaxing 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]
Bioconductor views ATACSeq Alignment CRISPR ImmunoOncology MultipleSequenceAlignment SequenceMatching Sequencing Software
MaintainerJiaxing Lin <jiaxing.lin@duke.edu>
LicenseGPL (>= 2)
URL https://github.com/jl354/bcSeq
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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bcSeq documentation built on Nov. 8, 2020, 8:03 p.m.