Package: geneviewer 0.1.10
geneviewer: Gene Cluster Visualizations
Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>; Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.
Authors:
geneviewer_0.1.10.tar.gz
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geneviewer_0.1.10.tgz(r-4.4-any)geneviewer_0.1.10.tgz(r-4.3-any)
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geneviewer_0.1.10.tgz(r-4.4-emscripten)geneviewer_0.1.10.tgz(r-4.3-emscripten)
geneviewer.pdf |geneviewer.html✨
geneviewer/json (API)
NEWS
# Install 'geneviewer' in R: |
install.packages('geneviewer', repos = c('https://nvelden.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nvelden/geneviewer/issues4 issues
- BRCA1_splice_variants - BRCA1 Splice Variants
- erythromycin_BlastP - Erythromycin BlastP results
- erythromycin_cluster - Erythromycin Gene Cluster Data
- hs_dystrophin_transcripts - Human Dystrophin Transcripts Data
- human_hox_genes - Human HOX Gene Cluster Data
- ophA_clusters - OphA Gene Cluster from Omphalotus olearius
On CRAN:geneviewer-0.1.10(2025-01-10)
Last updated 5 hours agofrom:9d2273ec8e. Checks:5 OK, 2 ERROR. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Jan 20 2025 |
R-4.5-win | OK | Jan 20 2025 |
R-4.5-linux | OK | Jan 20 2025 |
R-4.4-win | OK | Jan 20 2025 |
R-4.4-mac | OK | Jan 20 2025 |
R-4.3-win | ERROR | Jan 20 2025 |
R-4.3-mac | ERROR | Jan 20 2025 |
Exports:%>%gbk_features_to_dfGC_alignGC_annotationGC_chartGC_chartOutputGC_clusterGC_clusterFooterGC_clusterLabelGC_clusterTitleGC_colorGC_coordinatesGC_genesGC_gridGC_labelsGC_legendGC_linksGC_normalizeGC_scaleGC_scaleBarGC_sequenceGC_titleGC_tooltipGC_trackMouseGC_transcriptgenbank_to_fastaget_intronsmummer_alignmentprotein_blastread_bedread_fastaread_gbkread_gffrenderGC_chart
Dependencies:base64encbslibcachemclicpp11digestdplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimepillarpkgconfigpurrrR6rappdirsrlangrmarkdownsassstringistringrtibbletidyrtidyselecttinytexutf8vctrswithrxfunyaml
Citation
To cite package ‘geneviewer’ in publications use:
van der Velden N (2025). geneviewer: Gene Cluster Visualizations. R package version 0.1.10, https://github.com/nvelden/geneviewer.
Corresponding BibTeX entry:
@Manual{, title = {geneviewer: Gene Cluster Visualizations}, author = {Niels {van der Velden}}, year = {2025}, note = {R package version 0.1.10}, url = {https://github.com/nvelden/geneviewer}, }
Readme and manuals
geneviewer - Gene Cluster Visualizations in Rgeneviewer
geneviewer
geneviewer is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. To explore all features visit the package website.
Installation
You can install the released version of geneviewer from CRAN with:
install.packages("geneviewer")
And the development version from GitHub with:
# install.packages("devtools")
# devtools::install_github("nvelden/geneviewer")
install.packages("geneviewer", repos = c('https://nvelden.r-universe.dev', 'https://cloud.r-project.org'))
Usage
The below example demonstrates using geneviewer to plot a gene cluster on a genomic sequence, using the start and end positions of each gene. The genes are grouped by class and labels are added using the GC_labels
function.
library(geneviewer)
# Data
gene_cluster <- data.frame(
name = c("ophB1", "ophC", "ophA", "ophD", "ophB2", "ophP", "ophE"),
start = c(2522, 5286, 9536, 12616, 13183, 19346, 20170),
end = c(4276, 4718, 10904, 11859, 15046, 16016, 21484),
class = c("Monooxygenase", "NTF2-like", "Methyltransferase",
"O-acyltransferase", "Monooxygenase", "Prolyloligopeptidase",
"F-box/RNHI-like")
)
# Chart
GC_chart(gene_cluster, group = "class", height = "100px") %>%
GC_labels("name")
Examples
For additional examples and the corresponding code to create the plots, please visit the Examples section.
Issues
If you encounter any issues or have feature requests, please open an Issue.