Package: wiggleplotr 1.31.0

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]

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NEWS

# 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-1.31.0(bioc 3.21)wiggleplotr-1.30.0(bioc 3.20)

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

5.49 score 1 packages 26 scripts 398 downloads 4 mentions 8 exports 80 dependencies

Last updated 2 months agofrom:aad27cceaa. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 17 2024
R-4.5-win	NOTE	Dec 17 2024
R-4.5-linux	NOTE	Dec 17 2024
R-4.4-win	NOTE	Dec 17 2024
R-4.4-mac	NOTE	Dec 17 2024
R-4.3-win	NOTE	Dec 17 2024
R-4.3-mac	NOTE	Dec 17 2024

Exports:getGenotypePalette makeManhattanPlot plotCoverage plotCoverageFromEnsembldb plotCoverageFromUCSC plotTranscripts plotTranscriptsFromEnsembldb plotTranscriptsFromUCSC

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

Introduction to wiggleplotr

Kaur Alasoo

Rendered fromwiggleplotr.Rmdusingknitr::rmarkdownon Dec 17 2024.

Last update: 2020-06-08
Started: 2017-01-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 genomic regions	plotCoverage
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-package wiggleplotr