girafe: Genome Intervals and Read Alignments for Functional Exploration

The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.

AuthorJoern Toedling, with contributions from Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang Huber
Date of publicationNone
MaintainerJ. Toedling <jtoedling@yahoo.de>
LicenseArtistic-2.0
Version1.26.0

View on Bioconductor

Files in this package

girafe/DESCRIPTION
girafe/NAMESPACE
girafe/NEWS
girafe/R
girafe/R/AllGenerics.R girafe/R/alignedGenomeIntervals.R girafe/R/countReadsAnnotated.R girafe/R/coverageFun.R girafe/R/export.R girafe/R/fracOverlap.R girafe/R/genome_intervals_extensions.R girafe/R/includedMethod.R girafe/R/input.R girafe/R/intPhred.R girafe/R/negbinom.R girafe/R/overlap.R girafe/R/perWindow.R girafe/R/plotAligned.R girafe/R/plotAllChrom.R girafe/R/reduceMethod.R girafe/R/trimAdapter.R girafe/R/util.R girafe/R/whichNearestMethods.R girafe/R/zzz.R
girafe/build
girafe/build/vignette.rds
girafe/inst
girafe/inst/CITATION
girafe/inst/doc
girafe/inst/doc/girafe.R
girafe/inst/doc/girafe.Rnw
girafe/inst/doc/girafe.pdf
girafe/inst/extdata
girafe/inst/extdata/aravinSRNA_23_no_adapter_excerpt_mm9_unmasked.bwtmap
girafe/inst/extdata/aravinSRNA_23_plus_adapter_excerpt.fastq
girafe/inst/extdata/mgi_gi.RData
girafe/inst/scripts
girafe/inst/scripts/colourspace.R
girafe/inst/scripts/prepareAnnotation.R
girafe/inst/scripts/readAlignedExtras.R
girafe/man
girafe/man/AlignedGenomeIntervals-class.Rd girafe/man/agiFromBam.Rd girafe/man/countReadsAnnotated.Rd girafe/man/fracOverlap.Rd girafe/man/getFeatureCounts.Rd girafe/man/girafe-internal.Rd girafe/man/intPhred.Rd girafe/man/medianByPosition.Rd girafe/man/negbinomsig.Rd girafe/man/perWindow.Rd girafe/man/plotAligned.Rd girafe/man/plotReads.Rd girafe/man/plotnegbinomfit.Rd girafe/man/reduce-extras.Rd girafe/man/trimAdapter.Rd girafe/man/weightedConsensusMatrix.Rd girafe/man/whichNearestMethods.Rd
girafe/src
girafe/src/coverage.cpp
girafe/src/girafe.h
girafe/src/girafe_init.c
girafe/vignettes
girafe/vignettes/Makefile
girafe/vignettes/girafe.Rnw
girafe/vignettes/girafe.tex
girafe/vignettes/ngs.bib

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

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