seqbias: Estimation of per-position bias in high-throughput sequencing data
Version 1.24.0

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.

AuthorDaniel Jones <dcjones@cs.washington.edu>
Bioconductor views Sequencing
Date of publicationNone
MaintainerDaniel Jones <dcjones@cs.washington.edu>
LicenseLGPL-3
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("seqbias")

Getting started

Package overview

Popular man pages

count_reads: Counting reads across intervals
kmer_freq: Measuring positional kmer frequencies
random_intervals: Generating random genomic intervals
seqbias-class: The seqbias model
seqbias_fit: Fitting seqbias models
seqbias-package: 'seqbias' modeling bias in high-throughput sequencing data
seqbias_predict: Predicting sequencing bias
See all...

All man pages Function index File listing

Man pages

count_reads: Counting reads across intervals
kmer_freq: Measuring positional kmer frequencies
random_intervals: Generating random genomic intervals
seqbias-class: The seqbias model
seqbias_fit: Fitting seqbias models
seqbias_load: Loading seqbias models
seqbias-package: 'seqbias' modeling bias in high-throughput sequencing data
seqbias_predict: Predicting sequencing bias
seqbias_save: Saving seqbias models

Functions

count.reads Man page
kmer.freq Man page
random.intervals Man page
seqbias Man page
seqbias-class Man page
seqbias-package Man page
seqbias.fit Man page
seqbias.load Man page
seqbias.predict Man page
seqbias.save Man page

Files

DESCRIPTION
NAMESPACE
R
R/seqbias.R
build
build/vignette.rds
configure
inst
inst/CITATION
inst/doc
inst/doc/overview.R
inst/doc/overview.Rnw
inst/doc/overview.pdf
inst/extra
inst/extra/example.bam
inst/extra/example.bam.bai
inst/extra/example.fa
inst/extra/example.fa.fai
man
man/count_reads.Rd
man/kmer_freq.Rd
man/random_intervals.Rd
man/seqbias-class.Rd
man/seqbias-package.Rd
man/seqbias_fit.Rd
man/seqbias_load.Rd
man/seqbias_predict.Rd
man/seqbias_save.Rd
src
src/Makevars
src/Makevars.common
src/Makevars.win
src/common.c
src/common.h
src/config.h
src/kmer_matrix.cpp
src/kmer_matrix.hpp
src/logger.cpp
src/logger.h
src/logger.hpp
src/miscmath.c
src/miscmath.h
src/motif.cpp
src/motif.hpp
src/pos_table.c
src/pos_table.h
src/samtools_extra.c
src/samtools_extra.h
src/seqbias.cpp
src/sequencing_bias.cpp
src/sequencing_bias.hpp
src/twobitseq.cpp
src/twobitseq.hpp
src/yaml-cpp
src/yaml-cpp/COPYING
src/yaml-cpp/aliasmanager.cpp
src/yaml-cpp/aliasmanager.h
src/yaml-cpp/anchor.h
src/yaml-cpp/collectionstack.h
src/yaml-cpp/conversion.cpp
src/yaml-cpp/conversion.h
src/yaml-cpp/directives.cpp
src/yaml-cpp/directives.h
src/yaml-cpp/dll.h
src/yaml-cpp/emitfromevents.cpp
src/yaml-cpp/emitfromevents.h
src/yaml-cpp/emitter.cpp
src/yaml-cpp/emitter.h
src/yaml-cpp/emittermanip.h
src/yaml-cpp/emitterstate.cpp
src/yaml-cpp/emitterstate.h
src/yaml-cpp/emitterutils.cpp
src/yaml-cpp/emitterutils.h
src/yaml-cpp/eventhandler.h
src/yaml-cpp/exceptions.h
src/yaml-cpp/exp.cpp
src/yaml-cpp/exp.h
src/yaml-cpp/indentation.h
src/yaml-cpp/iterator.cpp
src/yaml-cpp/iterator.h
src/yaml-cpp/iterpriv.h
src/yaml-cpp/license.txt
src/yaml-cpp/ltnode.h
src/yaml-cpp/mark.h
src/yaml-cpp/node.cpp
src/yaml-cpp/node.h
src/yaml-cpp/nodebuilder.cpp
src/yaml-cpp/nodebuilder.h
src/yaml-cpp/nodeimpl.h
src/yaml-cpp/nodeownership.cpp
src/yaml-cpp/nodeownership.h
src/yaml-cpp/nodereadimpl.h
src/yaml-cpp/nodeutil.h
src/yaml-cpp/noncopyable.h
src/yaml-cpp/null.cpp
src/yaml-cpp/null.h
src/yaml-cpp/ostream.cpp
src/yaml-cpp/ostream.h
src/yaml-cpp/parser.cpp
src/yaml-cpp/parser.h
src/yaml-cpp/ptr_stack.h
src/yaml-cpp/ptr_vector.h
src/yaml-cpp/regex.cpp
src/yaml-cpp/regex.h
src/yaml-cpp/regeximpl.h
src/yaml-cpp/scanner.cpp
src/yaml-cpp/scanner.h
src/yaml-cpp/scanscalar.cpp
src/yaml-cpp/scanscalar.h
src/yaml-cpp/scantag.cpp
src/yaml-cpp/scantag.h
src/yaml-cpp/scantoken.cpp
src/yaml-cpp/setting.h
src/yaml-cpp/simplekey.cpp
src/yaml-cpp/singledocparser.cpp
src/yaml-cpp/singledocparser.h
src/yaml-cpp/stlemitter.h
src/yaml-cpp/stlnode.h
src/yaml-cpp/stream.cpp
src/yaml-cpp/stream.h
src/yaml-cpp/streamcharsource.h
src/yaml-cpp/stringsource.h
src/yaml-cpp/tag.cpp
src/yaml-cpp/tag.h
src/yaml-cpp/token.h
src/yaml-cpp/traits.h
src/yaml-cpp/yaml.h
vignettes
vignettes/overview.Rnw
vignettes/overview.bib
seqbias documentation built on May 20, 2017, 10:51 p.m.

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