Package: girafe 1.59.0
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:
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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')) |
On BioConductor:girafe-1.57.0(bioc 3.20)girafe-1.56.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 23 days agofrom:595754b718. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 31 2024 |
Exports:addNBSignificanceagiFromBamAlignedGenomeIntervalschrlengthschrlengths<-chromosomeclusterscoercecountReadsAnnotatedcoveragecoverageOneStranddetailexportextendfracOverlapgetFeatureCountshistidid<-interval_includedinterval_overlapintPhredmatchesmatches<-medianByPositionncharorganismorganism<-perWindowplotplotAlignedplotNegBinomFitreadsreads<-reducesamplescorescore<-seqnamesshowsortstrandstrand<-subsetsummarytrimAdapterwhich_nearestwidth
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArraydeldirformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDatagenomeIntervalsGenomicAlignmentsGenomicRangeshttrhwriterinterpintervalsIRangesjpegjsonlitelambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatsmimeopensslpngpwalignR6RColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| assess significance of sliding-window read counts | addNBSignificance 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 feature | countReadsAnnotated |
| Retrieve intervals overlapping by fraction of width | fracOverlap |
| Extract integer Phred score values from FastQ data | intPhred |
| Compute median quality for each nucleotide position | medianByPosition |
| Investigate aligned reads in genome intervals with sliding windows | perWindow |
| Remove 3' adapter contamination | trimAdapter |
| Methods for function 'which_nearest' and genome intervals | which_nearest which_nearest,AlignedGenomeIntervals,Genome_intervals_stranded-method which_nearest,Genome_intervals,Genome_intervals-method which_nearest,Genome_intervals_stranded,Genome_intervals_stranded-method |
