bamsignals: Extract read count signals from bam files
Version 1.8.0

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

AuthorAlessandro Mammana [aut, cre], Johannes Helmuth [aut]
Bioconductor views Alignment Coverage DataImport Sequencing
Date of publicationNone
MaintainerAlessandro Mammana <mammana@molgen.mpg.de>
LicenseGPL-2
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bamsignals")

Getting started

README.md
Introduction to the bamsignals package

Popular man pages

as.list.CountSignals: Converts the container to a list 'l' such that 'l[[i]]' is...
bamsignals: Efficient counting of reads in a bam file
bamsignals-methods: Functions for extracting count signals from a bam file.
CountSignals-class: Container for count signals
See all...

All man pages Function index File listing

Man pages

as.list.CountSignals: Converts the container to a list 'l' such that 'l[[i]]' is...
bamsignals: Efficient counting of reads in a bam file
bamsignals-methods: Functions for extracting count signals from a bam file.
CountSignals-class: Container for count signals

Functions

CountSignals Man page
CountSignals-class Man page
[,CountSignals,ANY-method Man page
alignSignals Man page
alignSignals,CountSignals-method Man page
as.list Man page
as.list,CountSignals-method Man page
as.list.CountSignals Man page Source code
bamCount Man page
bamCount,character,GenomicRanges-method Man page
bamCoverage Man page
bamCoverage,character,GenomicRanges-method Man page
bamProfile Man page
bamProfile,character,GenomicRanges-method Man page
bamsignals Man page
bamsignals-methods Man page
bamsignals-package Man page
checkList Source code
coverage_core Source code
fastWidth Source code
flagMask Source code
length Man page
length,CountSignals-method Man page
pileup_core Source code
printStupidSentence Source code
showCountSignals Source code
showCounts Source code
tlenFilter Source code
width Man page
width,CountSignals-method Man page
writeSamAsBamAndIndex Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/wrappers.R
R/zzzCountSignals.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/bamsignals.R
inst/doc/bamsignals.Rmd
inst/doc/bamsignals.html
inst/examples
inst/examples/class_example.R
inst/examples/methods_example.R
inst/extdata
inst/extdata/randomAnnot.Rdata
inst/extdata/randomBam.bam
inst/extdata/randomBam.bam.bai
man
man/CountSignals-class.Rd
man/as.list.CountSignals.Rd
man/bamsignals-methods.Rd
man/bamsignals.Rd
scripts
scripts/generateCode.R
src
src/CountSignals.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/bamsignals.cpp
src/bamsignals_init.c
tests
tests/testthat
tests/testthat.R
tests/testthat/randomReads.RData
tests/testthat/test_CountSignals.R
tests/testthat/test_methods.R
tests/testthat/utils.R
vignettes
vignettes/bamsignals.Rmd
bamsignals documentation built on May 20, 2017, 9:30 p.m.

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