Package: wiggleplotr 1.37.0

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:Kaur Alasoo [aut, cre]

wiggleplotr_1.37.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
wiggleplotr/json (API)

# Install 'wiggleplotr' in R:

install.packages('wiggleplotr', repos = c('https://bioc.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.

immunooncology coverage rnaseq chipseq sequencing visualization geneexpression transcription alternativesplicing

6.49 score 3 packages 34 scripts 4 mentions 10 exports 76 dependencies

Last updated from:fc07c2398b. Checks:6 WARNING, 2 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	261
linux-devel-x86_64	ERROR	351
source / vignettes	OK	339
linux-release-x86_64	WARNING	361
macos-release-arm64	WARNING	203
macos-oldrel-arm64	WARNING	178
windows-devel	ERROR	207
windows-release	WARNING	187
windows-oldrel	WARNING	208
wasm-release	OK	216

Exports:extractCoverageData getGenotypePalette makeManhattanPlot plotCoverage plotCoverageData plotCoverageFromEnsembldb plotCoverageFromUCSC plotTranscripts plotTranscriptsFromEnsembldb plotTranscriptsFromUCSC

Dependencies:abind askpass assertthat BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo cli codetools cowplot cpp11 crayon curl DelayedArray dplyr farver formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig purrr R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml

Introduction to wiggleplotr

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

Rendered fromwiggleplotr.Rmdusingknitr::rmarkdown

Last update: 2026-03-18
Started: 2017-01-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract read coverage data from the bigWig files	extractCoverageData
Returns a three-colour palette suitable for visualising read coverage stratified by genotype	getGenotypePalette
Make a Manahattan plot of p-values	makeManhattanPlot
Coding sequences from 9 protein coding transcripts of NCOA7	ncoa7_cdss
Exons from 9 protein coding transcripts of NCOA7	ncoa7_exons
Gene metadata for NCOA7	ncoa7_metadata
Paste two factors together and preserved their joint order.	pasteFactors
Plot read coverage across a genomic region	plotCoverage
Plot read coverage across a genomic region	plotCoverageData
Plot read coverage directly from ensembldb object.	plotCoverageFromEnsembldb
Plot read coverage directly from UCSC OrgDb and TxDb objects.	plotCoverageFromUCSC
Quickly plot transcript structure without read coverage tracks	plotTranscripts
Plot transcripts directly from ensembldb object.	plotTranscriptsFromEnsembldb
Plot transcripts directly from UCSC OrgDb and TxDb objects.	plotTranscriptsFromUCSC
wiggleplotr	wiggleplotr