girafe: Genome Intervals and Read Alignments for Functional Exploration

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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.

Author
Joern Toedling, with contributions from Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang Huber
Date of publication
None
Maintainer
J. Toedling <jtoedling@yahoo.de>
License
Artistic-2.0
Version
1.26.0

View on Bioconductor

Man pages

agiFromBam
Create AlignedGenomeIntervals objects from BAM files.
AlignedGenomeIntervals-class
Class 'AlignedGenomeIntervals'
countReadsAnnotated
Sum up aligned reads per category of genome feature
fracOverlap
Retrieve intervals overlapping by fraction of width
getFeatureCounts
get the read counts for a supplied set of genomic features
girafe-internal
Internal girafe functions
intPhred
Extract integer Phred score values from FastQ data
medianByPosition
Compute median quality for each nucleotide position
negbinomsig
assess significance of sliding-window read counts
perWindow
Investigate aligned reads in genome intervals with sliding...
plotAligned
Visualise reads aligned to genome intervals
plotnegbinomfit
Plot Negative Binomial Fit
plotReads
Function to plot aligned reads along the chromosome
reduce-extras
Auxiliary methods for Function reduce in Package 'girafe'
trimAdapter
Remove 3' adapter contamination
weightedConsensusMatrix
compute weighted consensus matrix
whichNearestMethods
Methods for function 'which_nearest' and genome intervals

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