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

Functions

addNBSignificance Man page
agiFromBam Man page
AlignedGenomeIntervals Man page
[,AlignedGenomeIntervals,ANY,ANY-method Man page
AlignedGenomeIntervals-class Man page
alongChromTicks Man page
c.AlignedGenomeIntervals Man page
c,AlignedGenomeIntervals-method Man page
chrlengths Man page
chrlengths<- Man page
chrlengths,AlignedGenomeIntervals-method Man page
chrlengths<-,AlignedGenomeIntervals,numeric-method Man page
chromosome,AlignedGenomeIntervals-method Man page
chromosome,Genome_intervals-method Man page
clusters,AlignedGenomeIntervals-method Man page
clusters,Genome_intervals-method Man page
coerce,AlignedGenomeIntervals,RangedData-method Man page
coerce,AlignedRead,AlignedGenomeIntervals-method Man page
countReadsAnnotated Man page
coverage,AlignedGenomeIntervals-method Man page
coverageOneStrand Man page
detail,AlignedGenomeIntervals-method Man page
estimateNBParams Man page
export Man page
export,AlignedGenomeIntervals,character,character-method Man page
export,Genome_intervals,character,ANY-method Man page
extend Man page
extend,AlignedGenomeIntervals-method Man page
extend,Genome_intervals-method Man page
extend,Genome_intervals_stranded-method Man page
featureColors Man page
fracOverlap Man page
getChromLengths Man page
getFeatureCounts Man page
getReadPosDf Man page
hist,AlignedGenomeIntervals-method Man page
id<- Man page
id<-,AlignedGenomeIntervals,character-method Man page
id,AlignedGenomeIntervals-method Man page
interval_included,AlignedGenomeIntervals,AlignedGenomeIntervals- Man page
interval_included,AlignedGenomeIntervals,Genome_intervals_strand Man page
interval_included,Genome_intervals_stranded,AlignedGenomeInterva Man page
interval_overlap,AlignedGenomeIntervals,AlignedGenomeIntervals-m Man page
interval_overlap,AlignedGenomeIntervals,Genome_intervals-method Man page
interval_overlap,AlignedGenomeIntervals,Genome_intervals_strande Man page
interval_overlap,Genome_intervals,AlignedGenomeIntervals-method Man page
interval_overlap,Genome_intervals_stranded,AlignedGenomeInterval Man page
intPhred Man page
matches Man page
matches<- Man page
matches<-,AlignedGenomeIntervals,integer-method Man page
matches,AlignedGenomeIntervals-method Man page
medianByPosition Man page
nchar,AlignedGenomeIntervals-method Man page
newVP Man page
organism Man page
organism<- Man page
organism<-,AlignedGenomeIntervals,character-method Man page
organism<-,AlignedGenomeIntervals-method Man page
organism,AlignedGenomeIntervals-method Man page
perWindow Man page
plotAligned Man page
plot,AlignedGenomeIntervals,ANY-method Man page
plot,AlignedGenomeIntervals,Genome_intervals_stranded-method Man page
plot,AlignedGenomeIntervals-method Man page
plot,AlignedGenomeIntervals,missing-method Man page
plotAllChrom Man page
plotAlongChromLegend Man page
plotNegBinomFit Man page
plotReads Man page
reads Man page
reads<- Man page
reads<-,AlignedGenomeIntervals,character-method Man page
reads,AlignedGenomeIntervals-method Man page
reduce,AlignedGenomeIntervals-method Man page
reduce,CompressedIRangesList-method Man page
reduce,Genome_intervals-method Man page
reduce,IRanges-method Man page
reduce-methods Man page
reduceOneEnd Man page
reduceOneExact Man page
reduce,RangedData-method Man page
reduce,RangesList-method Man page
reduce,Ranges-method Man page
sample,AlignedGenomeIntervals-method Man page
score<- Man page
score<-,AlignedGenomeIntervals-method Man page
score,AlignedGenomeIntervals-method Man page
score<-,AlignedGenomeIntervals,numeric-method Man page
seqnames Man page
seqnames,AlignedGenomeIntervals-method Man page
show,AlignedGenomeIntervals-method Man page
sort,AlignedGenomeIntervals-method Man page
strand<-,AlignedGenomeIntervals,factor-method Man page
strand,AlignedGenomeIntervals-method Man page
strand<-,AlignedGenomeIntervals,vector-method Man page
subset Man page
subset,AlignedGenomeIntervals-method Man page
summary Man page
summary,AlignedGenomeIntervals-method Man page
trimAdapter Man page
weightedConsensusMatrix Man page
which_nearest Man page
which_nearest,AlignedGenomeIntervals,Genome_intervals_stranded-m Man page
which_nearest,Genome_intervals,Genome_intervals-method Man page
which_nearest,Genome_intervals_stranded,Genome_intervals_strande Man page
width,AlignedGenomeIntervals-method Man page
windowCountAndGC Man page
writeExportData Man page

Files

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

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