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

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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@cs.washington.edu>
Date of publication
None
Maintainer
Daniel Jones <dcjones@cs.washington.edu>
License
LGPL-3
Version
1.22.0

View on Bioconductor

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

Files in this package

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