seqbias

DOI: 10.18129/B9.bioc.seqbias    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see seqbias.

Estimation of per-position bias in high-throughput sequencing data

Bioconductor version: 3.8

This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

Author: Daniel Jones <dcjones at cs.washington.edu>

Maintainer: Daniel Jones <dcjones at cs.washington.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("seqbias")

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("seqbias")

 

PDF	R Script	Assessing and Adjusting for Technical Bias in High Throughput Sequencing Data
PDF		Reference Manual

Details

biocViews	Sequencing, Software
Version	1.30.0
In Bioconductor since	BioC 2.8 (R-2.13) (8 years)
License	LGPL-3
Depends	R (>= 2.13.0), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0), methods
Imports	zlibbioc
LinkingTo	Rsamtools(>= 1.19.38)
Suggests	Rsamtools, ggplot2
SystemRequirements
Enhances
URL
Depends On Me	ReQON
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	seqbias_1.30.0.tar.gz
Windows Binary	seqbias_1.30.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	seqbias_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seqbias
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqbias
Package Short Url	http://bioconductor.org/packages/seqbias/
Package Downloads Report	Download Stats