bamsignals: Extract read count signals from bam files

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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.

Author
Alessandro Mammana [aut, cre], Johannes Helmuth [aut]
Date of publication
None
Maintainer
Alessandro Mammana <mammana@molgen.mpg.de>
License
GPL-2
Version
1.6.0

View on Bioconductor

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

Files in this package

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