seqbias

DOI: 10.18129/B9.bioc.seqbias  

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

Bioconductor version: Release (3.16)

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 <djones3 at fredhutch.org>

Maintainer: Daniel Jones <djones3 at fredhutch.org>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	1.46.0
In Bioconductor since	BioC 2.8 (R-2.13) (12 years)
License	LGPL-3
Depends	R (>= 3.0.2), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0), methods
Imports
LinkingTo	Rhtslib(>= 1.99.1), zlibbioc
Suggests	Rsamtools, ggplot2
SystemRequirements	GNU make
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_1.46.0.tar.gz
Windows Binary	seqbias_1.46.0.zip (64-bit only)
macOS Binary (x86_64)	seqbias_1.46.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/seqbias
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqbias
Bioc Package Browser	https://code.bioconductor.org/browse/seqbias/
Package Short Url	https://bioconductor.org/packages/seqbias/
Package Downloads Report	Download Stats