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geneviewer

An R package designed for drawing gene arrow maps

https://github.com/nvelden/geneviewer

Science Score: 26.0%

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary

Keywords

genetics r
Last synced: 6 months ago · JSON representation

Repository

An R package designed for drawing gene arrow maps

Basic Info
Statistics
  • Stars: 85
  • Watchers: 1
  • Forks: 4
  • Open Issues: 3
  • Releases: 0
Topics
genetics r
Created over 2 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

geneviewer - Gene Cluster Visualizations in R

R-CMD-check CRAN status Metacran downloads License: MIT

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:

r install.packages("geneviewer")

And the development version from GitHub with:

``` r

install.packages("devtools")

devtools::install_github("nvelden/geneviewer") ```

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.

``` r 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

GCchart(genecluster, 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.

Owner

  • Login: nvelden
  • Kind: user

GitHub Events

Total
  • Release event: 1
  • Issues event: 6
  • Watch event: 50
  • Issue comment event: 7
  • Push event: 41
  • Pull request event: 1
  • Fork event: 1
Last Year
  • Release event: 1
  • Issues event: 6
  • Watch event: 50
  • Issue comment event: 7
  • Push event: 41
  • Pull request event: 1
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 14
  • Total pull requests: 2
  • Average time to close issues: 25 days
  • Average time to close pull requests: 4 months
  • Total issue authors: 13
  • Total pull request authors: 1
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 2
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 4 months
  • Issue authors: 5
  • Pull request authors: 1
  • Average comments per issue: 1.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • shengqiangJ (1)
  • yamn29302 (1)
  • jonng2024 (1)
  • ETaSky (1)
  • FroJaTy (1)
  • Jessica1080 (1)
  • cbendett (1)
  • rayab1993 (1)
  • jhastie (1)
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  • RohanNathHERE (1)
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  • Johnny254 (1)
Pull Request Authors
  • RohanNathHERE (2)
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 226 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: geneviewer

Gene Cluster Visualizations

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 226 Last month
Rankings
Dependent packages count: 27.4%
Dependent repos count: 33.8%
Average: 49.4%
Downloads: 86.9%
Maintainers (1)
n.s.j.vandervelden@gmail.com
Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • htmlwidgets * imports
  • magrittr * imports
  • biomaRt * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • shiny * suggests