Package: girafe 1.59.1

J. Toedling

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.

Authors:Joern Toedling, with contributions from Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang Huber

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girafe.pdf |girafe.html✨
girafe/json (API)
NEWS

# Install 'girafe' in R:
install.packages('girafe', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:girafe-1.59.0(bioc 3.21)girafe-1.58.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing

3.60 score 1 scripts 296 downloads 1 mentions 48 exports 57 dependencies

Last updated 26 days agofrom:8e022377c1. Checks:OK: 1 NOTE: 5 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 26 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTENov 26 2024
R-4.4-mac-x86_64NOTENov 26 2024
R-4.4-mac-aarch64NOTENov 26 2024
R-4.3-win-x86_64WARNINGNov 26 2024
R-4.3-mac-x86_64WARNINGNov 26 2024
R-4.3-mac-aarch64WARNINGNov 26 2024

Exports:addNBSignificanceagiFromBamAlignedGenomeIntervalschrlengthschrlengths<-chromosomeclusterscoercecountReadsAnnotatedcoveragecoverageOneStranddetailexportextendfracOverlapgetFeatureCountshistidid<-interval_includedinterval_overlapintPhredmatchesmatches<-medianByPositionncharorganismorganism<-perWindowplotplotAlignedplotNegBinomFitreadsreads<-reducesamplescorescore<-seqnamesshowsortstrandstrand<-subsetsummarytrimAdapterwhich_nearestwidth

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArraydeldirformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDatagenomeIntervalsGenomicAlignmentsGenomicRangeshttrhwriterinterpintervalsIRangesjpegjsonlitelambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatsmimeopensslpngpwalignR6RColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

Genome intervals and read alignments for functional exploration

Rendered fromgirafe.Rnwusingutils::Sweaveon Nov 26 2024.

Last update: 2024-04-24
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
assess significance of sliding-window read countsaddNBSignificance estimateNBParams
Create AlignedGenomeIntervals objects from BAM files.agiFromBam
Class 'AlignedGenomeIntervals'AlignedGenomeIntervals AlignedGenomeIntervals-class c,AlignedGenomeIntervals-method c.AlignedGenomeIntervals chrlengths chrlengths,AlignedGenomeIntervals-method chrlengths<- chrlengths<-,AlignedGenomeIntervals,numeric-method chromosome,AlignedGenomeIntervals-method chromosome,Genome_intervals-method clusters,AlignedGenomeIntervals-method clusters,Genome_intervals-method coerce,AlignedRead,AlignedGenomeIntervals-method coverage,AlignedGenomeIntervals-method detail,AlignedGenomeIntervals-method export export,AlignedGenomeIntervals,character,character-method export,Genome_intervals,character,ANY-method extend extend,AlignedGenomeIntervals-method extend,Genome_intervals-method extend,Genome_intervals_stranded-method hist,AlignedGenomeIntervals-method id,AlignedGenomeIntervals-method id<- id<-,AlignedGenomeIntervals,character-method interval_included,AlignedGenomeIntervals,AlignedGenomeIntervals-method interval_included,AlignedGenomeIntervals,Genome_intervals_stranded-method interval_included,Genome_intervals_stranded,AlignedGenomeIntervals-method interval_overlap,AlignedGenomeIntervals,AlignedGenomeIntervals-method interval_overlap,AlignedGenomeIntervals,Genome_intervals-method interval_overlap,AlignedGenomeIntervals,Genome_intervals_stranded-method interval_overlap,Genome_intervals,AlignedGenomeIntervals-method interval_overlap,Genome_intervals_stranded,AlignedGenomeIntervals-method matches matches,AlignedGenomeIntervals-method matches<- matches<-,AlignedGenomeIntervals,integer-method nchar,AlignedGenomeIntervals-method organism organism,AlignedGenomeIntervals-method organism<- organism<-,AlignedGenomeIntervals,character-method organism<-,AlignedGenomeIntervals-method plot,AlignedGenomeIntervals,ANY-method plot,AlignedGenomeIntervals,Genome_intervals_stranded-method plot,AlignedGenomeIntervals,missing-method plot,AlignedGenomeIntervals-method reads reads,AlignedGenomeIntervals-method reads<- reads<-,AlignedGenomeIntervals,character-method reduce,AlignedGenomeIntervals-method reduce,Genome_intervals-method sample,AlignedGenomeIntervals-method score,AlignedGenomeIntervals-method score<- score<-,AlignedGenomeIntervals,numeric-method score<-,AlignedGenomeIntervals-method seqnames seqnames,AlignedGenomeIntervals-method show,AlignedGenomeIntervals-method sort,AlignedGenomeIntervals-method strand,AlignedGenomeIntervals-method strand<-,AlignedGenomeIntervals,factor-method strand<-,AlignedGenomeIntervals,vector-method subset subset,AlignedGenomeIntervals-method summary summary,AlignedGenomeIntervals-method width,AlignedGenomeIntervals-method [,AlignedGenomeIntervals,ANY,ANY,ANY-method [,AlignedGenomeIntervals,ANY,ANY-method
Sum up aligned reads per category of genome featurecountReadsAnnotated
Retrieve intervals overlapping by fraction of widthfracOverlap
Extract integer Phred score values from FastQ dataintPhred
Compute median quality for each nucleotide positionmedianByPosition
Investigate aligned reads in genome intervals with sliding windowsperWindow
Remove 3' adapter contaminationtrimAdapter
Methods for function 'which_nearest' and genome intervalswhich_nearest which_nearest,AlignedGenomeIntervals,Genome_intervals_stranded-method which_nearest,Genome_intervals,Genome_intervals-method which_nearest,Genome_intervals_stranded,Genome_intervals_stranded-method