seqbias

DOI: 10.18129/B9.bioc.seqbias    

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

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

Bioconductor version: Development (3.10)

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>

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

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.33.0
In Bioconductor since BioC 2.8 (R-2.13) (8.5 years)
License LGPL-3
Depends R (>= 3.0.2), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0), methods
Imports
LinkingTo Rhtslib(>= 1.15.3)
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_1.33.0.tar.gz
Windows Binary seqbias_1.33.0.zip
Mac OS X 10.11 (El Capitan) seqbias_1.33.0.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

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