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 <email@example.com>|
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