locuszoomr: Gene Locus Plot with Gene Annotations
Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
| Version: | 0.3.8 |
| Depends: | R (≥ 3.5) |
| Imports: | AnnotationFilter, BiocGenerics, cowplot, dplyr, ensembldb, GenomeInfoDb, GenomicRanges, gggrid, ggplot2, ggrepel, graphics, grDevices, grid, IRanges, LDlinkR, memoise, plotly, rlang, rtracklayer, zoo |
| Suggests: | AnnotationHub, EnsDb.Hsapiens.v75, knitr, rmarkdown |
| Published: | 2025-03-03 |
| DOI: | 10.32614/CRAN.package.locuszoomr |
| Author: | Myles Lewis  [aut,
cre] |
| Maintainer: | Myles Lewis <myles.lewis at qmul.ac.uk> |
| BugReports: | https://github.com/myles-lewis/locuszoomr/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/myles-lewis/locuszoomr |
| NeedsCompilation: | no |
| Language: | en-gb |
| Citation: | locuszoomr citation info |
| Materials: | README, NEWS |
| CRAN checks: | locuszoomr results |
Documentation:
| Reference manual: | locuszoomr.html , locuszoomr.pdf |
| Vignettes: |
locuszoomr (source, R code) |
Downloads:
| Package source: | locuszoomr_0.3.8.tar.gz |
| Windows binaries: | r-devel: locuszoomr_0.3.8.zip, r-release: locuszoomr_0.3.8.zip, r-oldrel: locuszoomr_0.3.8.zip |
| macOS binaries: | r-release (arm64): locuszoomr_0.3.8.tgz, r-oldrel (arm64): locuszoomr_0.3.8.tgz, r-release (x86_64): locuszoomr_0.3.8.tgz, r-oldrel (x86_64): locuszoomr_0.3.8.tgz |
| Old sources: | locuszoomr archive |
Linking:
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