Extract read coverage from parquet files instead of bigWig files | Overlaying multiple conditions | Plotting other types of data | Extract transcript annotations automatically from Ensembl and UCSC annotations objects
Package: wiggleplotr 1.36.0
Kaur Alasoo
wiggleplotr: Make read coverage plots from BigWig files
Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.
Authors:
wiggleplotr_1.36.0.tar.gz
wiggleplotr_1.36.0.zip(r-4.7-any)wiggleplotr_1.36.0.zip(r-4.6-any)wiggleplotr_1.36.0.zip(r-4.5-any)
wiggleplotr_1.36.0.tgz(r-4.6-any)wiggleplotr_1.36.0.tgz(r-4.5-any)
wiggleplotr_1.36.0.tar.gz(r-4.7-any)wiggleplotr_1.36.0.tar.gz(r-4.6-any)
wiggleplotr_1.36.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
wiggleplotr/json (API)
| # Install 'wiggleplotr' in R: |
| install.packages('wiggleplotr', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- ncoa7_cdss - Coding sequences from 9 protein coding transcripts of NCOA7
- ncoa7_exons - Exons from 9 protein coding transcripts of NCOA7
- ncoa7_metadata - Gene metadata for NCOA7
On BioConductor:wiggleplotr-1.37.0(bioc 3.24)wiggleplotr-1.36.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologycoveragernaseqchipseqsequencingvisualizationgeneexpressiontranscriptionalternativesplicing
Last updated from:17d23cc5e7 (on RELEASE_3_23). Checks:6 WARNING, 2 ERROR, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 275 | ||
| linux-devel | ERROR | 333 | ||
| source / vignettes | OK | 340 | ||
| linux-release | WARNING | 362 | ||
| macos-release | WARNING | 230 | ||
| macos-oldrel | WARNING | 207 | ||
| windows-devel | ERROR | 195 | ||
| windows-release | WARNING | 207 | ||
| windows-oldrel | WARNING | 196 | ||
| wasm-release | OK | 199 |
Exports:extractCoverageDatagetGenotypePalettemakeManhattanPlotplotCoverageplotCoverageDataplotCoverageFromEnsembldbplotCoverageFromUCSCplotTranscriptsplotTranscriptsFromEnsembldbplotTranscriptsFromUCSC
Dependencies:abindaskpassassertthatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscowplotcpp11crayoncurlDelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpurrrR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml
