To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("bcSeq")

In most cases, you don't need to download the package archive at all.

bcSeq

DOI: 10.18129/B9.bioc.bcSeq    

This is the development version of bcSeq; to use it, please install the devel version of Bioconductor.

Fast Sequence Alignment for High-Throughput shRNA and CRISPR Screens

Bioconductor version: Development (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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("bcSeq")

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 Alignment, CRISPR, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software
Version 1.0.0
License GPL (>= 2)
Depends R (>= 3.4)
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
Build Report  

Package Archives

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

Source Package bcSeq_1.0.0.tar.gz
Windows Binary bcSeq_0.99.7.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) bcSeq_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bcSeq
Package Short Url http://bioconductor.org/packages/bcSeq/
Package Downloads Report Download Stats

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