bcSeq

DOI: 10.18129/B9.bioc.bcSeq    

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

PDF	R Script	bcSeq
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, Alignment, CRISPR, ImmunoOncology, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software
Version	1.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (4 years)
License	GPL (>= 2)
Depends	R (>= 3.4.0)
Imports	Rcpp (>= 0.12.12), Matrix, Biostrings
LinkingTo	Rcpp, Matrix
Suggests	knitr
SystemRequirements
Enhances
URL	https://github.com/jl354/bcSeq
BugReports	https://support.bioconductor.org
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	bcSeq_1.16.0.tar.gz
Windows Binary	bcSeq_1.16.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	bcSeq_1.16.0.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	https://bioconductor.org/packages/bcSeq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive