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seqbias

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see seqbias.

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
Assessing and Adjusting for Technical Bias in High Throughput Sequencing Data PDF R Script
Reference Manual PDF

Details

biocViews Sequencing, Software
Version 1.50.0
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License LGPL-3
Depends R (>= 3.0.2), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0), methods
Imports
System Requirements GNU make
URL
See More
Suggests Rsamtools, ggplot2
Linking To Rhtslib(>= 1.99.1), zlibbioc
Enhances
Depends On Me ReQON
Imports Me
Suggests Me
Links To Me
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Package Archives

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

Source Package seqbias_1.50.0.tar.gz
Windows Binary seqbias_1.50.0.zip (64-bit only)
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/seqbias/
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