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bcSeq

This is the development version of bcSeq; for the stable release version, see bcSeq.

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens


Bioconductor version: Development (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 duke.edu>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("bcSeq")

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

Documentation

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

browseVignettes("bcSeq")
bcSeq PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, Alignment, CRISPR, ImmunoOncology, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software
Version 1.25.0
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
System Requirements
URL https://github.com/jl354/bcSeq
Bug Reports https://support.bioconductor.org
See More
Suggests knitr
Linking To Rcpp, Matrix
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package bcSeq_1.25.0.tar.gz
Windows Binary bcSeq_1.25.0.zip (64-bit only)
macOS Binary (x86_64) bcSeq_1.25.0.tgz
macOS Binary (arm64) bcSeq_1.25.0.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/
Package Downloads Report Download Stats