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Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("bcSeq")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

bcSeq PDF R Script
Reference Manual PDF


biocViews ATACSeq, Alignment, CRISPR, ImmunoOncology, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software
Version 1.26.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL (>= 2)
Depends R (>= 3.4.0)
Imports Rcpp (>= 0.12.12), Matrix, Biostrings
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Follow Installation instructions to use this package in your R session.

Source Package bcSeq_1.26.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) bcSeq_1.26.0.tgz
macOS Binary (arm64) bcSeq_1.26.0.tgz
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Source Repository (Developer Access) git clone
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