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g3viz

Lollipop-diagram to interactively visualize genetic mutations

https://github.com/g3viz/g3viz

Science Score: 13.0%

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    CITATION.cff file
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    .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary

Keywords

bioinformatics genomics-visualization lollipop-plot variants visualize-mutation-data
Last synced: 6 months ago · JSON representation

Repository

Lollipop-diagram to interactively visualize genetic mutations

Basic Info
Statistics
  • Stars: 31
  • Watchers: 1
  • Forks: 19
  • Open Issues: 19
  • Releases: 0
Topics
bioinformatics genomics-visualization lollipop-plot variants visualize-mutation-data
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram

Date: 2024-09-04

Build Status CRAN status CRAN_monthly_download

Live demo

Introduction

Intuitively and effectively visualizing genetic mutation data can help researchers to better understand genomic data and validate findings. G3viz is an R package which provides an easy-to-use lollipop-diagram tool. It enables users to interactively visualize detailed translational effect of genetic mutations in RStudio or a web browser, without having to know any HTML5/JavaScript technologies.

The features of g3viz include

  • Interactive (zoom & pan, tooltip, brush selection tool, and interactive legend)
  • Highlight and label positional mutations
  • 8 ready-to-use chart themes
  • Highly customizable with over 50 chart options and over 35 color schemes
  • Save charts in PNG or high-quality SVG format
  • Built-in function to retrieve protein domain information and resolve gene isoforms
  • Built-in function to map genetic mutation type (a.k.a, variant classification) to mutation class

Install g3viz

Install from R repository ```r

install package

install.packages("g3viz", repos = "http://cran.us.r-project.org") or install development version from github r

Check if "devtools" installed

if("devtools" %in% rownames(installed.packages()) == FALSE){ install.packages("devtools") }

install from github

devtools::install_github("g3viz/g3viz") ```

Reference

Guo, X., et al. (2020). G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram. Bioinformatics, 36(3), 928-929.

What's new

1.2.0 - [x] Updated Pfam (v37.0) (date: 2024-07-29) - [x] Updated UniProtKB (date: 2024-07-29) - [x] Updated hgnc2pfam.df.rda (date: 2024-07-29)

1.1.5 - [x] Updated getMutationsFromCbioportal (date: 2022-06-23) - [x] Remove Dependency cgdsr; Add Dependency cBioPortalData (date: 2022-06-23) - [x] Updated hgnc2pfam.df.rda (date: 2022-06-24)

Owner

  • Name: g3viz
  • Login: G3viz
  • Kind: organization

Visualize G3 (gene/genome/genetics) for fun

GitHub Events

Total
  • Issues event: 1
  • Watch event: 4
Last Year
  • Issues event: 1
  • Watch event: 4

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 113
  • Total Committers: 3
  • Avg Commits per committer: 37.667
  • Development Distribution Score (DDS): 0.018
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
phoeguo p****o@g****m 111
zhangrener z****r@g****m 1
Rener Zhang 8****r 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 22
  • Total pull requests: 0
  • Average time to close issues: 14 days
  • Average time to close pull requests: N/A
  • Total issue authors: 20
  • Total pull request authors: 0
  • Average comments per issue: 0.82
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • diegollarrull (2)
  • ytakemon (2)
  • azizhamid (1)
  • Nitin123-4 (1)
  • dgautheret (1)
  • inodb (1)
  • fsnibs10 (1)
  • Eugene79 (1)
  • jxchong (1)
  • jpinero (1)
  • Ben-JWL (1)
  • AHTARazzak (1)
  • rdmorin (1)
  • nicolehl (1)
  • Jidgdoi (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 350 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 11
  • Total maintainers: 1
cran.r-project.org: g3viz

Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 350 Last month
Rankings
Forks count: 4.8%
Stargazers count: 10.7%
Average: 21.0%
Dependent repos count: 24.2%
Dependent packages count: 29.0%
Downloads: 36.5%
Maintainers (1)
g3viz.group@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.0 depends
  • cgdsr * imports
  • htmlwidgets * imports
  • jsonlite * imports
  • stringr * imports
  • kableExtra * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • shiny >= 1.0.0 suggests