bamsignals: Extract read count signals from bam files

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bamsignals")
AuthorAlessandro Mammana [aut, cre], Johannes Helmuth [aut]
Bioconductor views Alignment Coverage DataImport Sequencing
Date of publicationNone
MaintainerAlessandro Mammana <mammana@molgen.mpg.de>
LicenseGPL-2
Version1.6.0

View on Bioconductor

Functions

alignSignals Man page
alignSignals,CountSignals-method Man page
as.list Man page
as.list.CountSignals Man page
as.list,CountSignals-method Man page
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
CountSignals Man page
[,CountSignals,ANY-method Man page
CountSignals-class Man page
length Man page
length,CountSignals-method Man page
width Man page
width,CountSignals-method Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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