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.

AuthorAlessandro Mammana [aut, cre], Johannes Helmuth [aut]
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

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

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

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

All documentation is copyright its authors; we didn't write any of that.