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GeDi

Geneset distances project

https://github.com/annekathrinsilvia/gedi

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    26 of 32 committers (81.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (20.6%) to scientific vocabulary

Keywords from Contributors

bioconductor-package
Last synced: 10 months ago · JSON representation

Repository

Geneset distances project

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created over 4 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog License Code of conduct

README.Rmd 

---
output: github_document
---





```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# GeDi


[![R build status](https://github.com/AnnekathrinSilvia/GeDi/workflows/R-CMD-check/badge.svg)](https://github.com/AnnekathrinSilvia/GeDi/actions)

[![](https://img.shields.io/github/last-commit/AnnekathrinSilvia/GeDi.svg)](https://github.com/AnnekathrinSilvia/GeDi/commits/devel)
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
[![CodeCov.io codecov status](https://codecov.io/github/AnnekathrinSilvia/GeDi/coverage.svg?branch=master)](https://codecov.io/github/AnnekathrinSilvia/GeDi)


The goal of GeDi is to provide a user-friendly platform for exploring and analyzing the results of functional annotation and enrichment analyses. By integrating various enrichment methods and offering interactive visualizations, GeDi aims to streamline the process of interpreting biological data and identifying meaningful patterns within it. Through features like distance score calculation, clustering, and bookmarking, GeDi empowers users to gain deeper insights into their data and make informed decisions in their research endeavors.

## Installation

You can install the development version of GeDi from [GitHub](https://github.com/AnnekathrinSilvia/GeDi) with:

```{r, eval = FALSE}
install.packages("devtools")
devtools::install_github("AnnekathrinSilvia/GeDi")
```

## Example

If you want to give GeDi a testrun on a demo dataset, you can simply launch the Shiny application and load the demo data in the **Data input** panel. To start the Shiny Application, you can use the following code:

```{r, eval = FALSE}
library("GeDi")
GeDi()
```

## Usage Overview

You can find the rendered version of the documentation of `GeDi` at the project website https://AnnekathrinSilvia.github.io/GeDi, created with `pkgdown`.                            


## Development

If you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an [issue](https://github.com/AnnekathrinSilvia/GeDi/issues).

## Code of Conduct
  
Please note that the GeDi project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

## License

MIT © Annekathrin Silvia Nedwed

Owner

  • Login: AnnekathrinSilvia
  • Kind: user

GitHub Events

Total
  • Delete event: 5
  • Push event: 9
  • Create event: 3
Last Year
  • Delete event: 5
  • Push event: 9
  • Create event: 3

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 276
  • Total Committers: 32
  • Avg Commits per committer: 8.625
  • Development Distribution Score (DDS): 0.576
Past Year
  • Commits: 159
  • Committers: 8
  • Avg Commits per committer: 19.875
  • Development Distribution Score (DDS): 0.579
Top Committers
Name Email Commits
Annekathrin Silvia Ludt a****n@a****p 117
Federico Marini m****f@u****e 63
AnnekathrinSilvia 3****a 24
Annekathrin Silvia Ludt a****n@A****l 16
Annekathrin Silvia Ludt a****n@e****E 7
J Wokaty j****y@s****u 4
Annekathrin Silvia Ludt a****n@z****E 4
Annekathrin Silvia Ludt a****n@A****x 3
Annekathrin Silvia Ludt a****n@z****E 3
Annekathrin Silvia Ludt a****n@z****E 3
Annekathrin Silvia Ludt a****n@z****E 3
Leon Dammer l****r@g****e 3
Annekathrin Silvia Ludt a****n@z****E 2
Annekathrin Silvia Ludt a****n@z****E 2
Annekathrin Silvia Ludt a****n@z****E 2
Annekathrin Silvia Ludt a****n@z****E 2
Annekathrin Silvia Ludt a****n@z****E 2
Annekathrin Silvia Ludt a****n@z****E 2
Annekathrin Silvia Ludt a****n@A****x 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
Annekathrin Silvia Ludt a****n@z****E 1
and 2 more...
Committer Domains (Top 20 + Academic)
zdv-vpn01-36-221.zdv.uni-mainz.de: 1 zdv-vpn01-38-95.zdv.uni-mainz.de: 1 zdv-vpn01-38-70.zdv.uni-mainz.de: 1 zdv-vpn01-38-27.zdv.uni-mainz.de: 1 zdv-vpn01-38-150.zdv.uni-mainz.de: 1 zdv-vpn01-38-149.zdv.uni-mainz.de: 1 zdv-vpn01-37-3.zdv.uni-mainz.de: 1 zdv-vpn01-36-27.zdv.uni-mainz.de: 1 zdv-vpn01-36-182.zdv.uni-mainz.de: 1 zdv-vpn01-36-161.zdv.uni-mainz.de: 1 zdv-vpn01-36-151.zdv.uni-mainz.de: 1 zdv-vpn01-36-104.zdv.uni-mainz.de: 1 zdv-vpn01-36-100.zdv.uni-mainz.de: 1 annekathrinsmbp.fritz.box: 1 zdv-vpn01-39-162.zdv.uni-mainz.de: 1 zdv-vpn01-38-29.zdv.uni-mainz.de: 1 zdv-vpn01-38-210.zdv.uni-mainz.de: 1 zdv-vpn01-38-182.zdv.uni-mainz.de: 1 zdv-vpn01-36-96.zdv.uni-mainz.de: 1 zdv-vpn01-36-201.zdv.uni-mainz.de: 1 zdv-vpn01-39-40.zdv.uni-mainz.de: 1 zdv-vpn01-38-177.zdv.uni-mainz.de: 1 zdv-vpn01-36-108.zdv.uni-mainz.de: 1 zdv-vpn01-36-204.zdv.uni-mainz.de: 1 sph.cuny.edu: 1 eduroam-119-237.zdv.uni-mainz.de: 1 uni-mainz.de: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 18
  • Total pull requests: 9
  • Average time to close issues: 6 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 4
  • Total pull request authors: 3
  • Average comments per issue: 0.94
  • Average comments per pull request: 0.56
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 1
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 10 days
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • AnnekathrinSilvia (15)
  • NajlaAbassi (2)
  • LTLA (1)
  • federicomarini (1)
Pull Request Authors
  • AnnekathrinSilvia (7)
  • federicomarini (7)
  • ldammer (2)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 3,541 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
bioconductor.org: GeDi

Defining and visualizing the distances between different genesets

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 3,541 Total
Rankings
Dependent repos count: 0.0%
Average: 15.6%
Dependent packages count: 31.3%
Maintainers (1)
anneludt@uni-mainz.de
Last synced: 11 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • grimbough/bioc-actions/build-install-check v1 composite
  • grimbough/bioc-actions/run-BiocCheck v1 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/setup-pandoc v2 composite
.github/workflows/r.yml actions
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  • r-lib/actions/setup-r f57f1301a053485946083d7a45022b278929a78a composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 3.5.0 depends
  • BiocNeighbors * imports
  • ComplexHeatmap * imports
  • DT * imports
  • GOSemSim * imports
  • GeneTonic * imports
  • InteractiveComplexHeatmap * imports
  • Matrix * imports
  • RColorBrewer * imports
  • STRINGdb * imports
  • bs4Dash * imports
  • dplyr * imports
  • fontawesome * imports
  • ggdendro * imports
  • ggplot2 * imports
  • grDevices * imports
  • igraph * imports
  • org.Hs.eg.db * imports
  • parallel * imports
  • plotly * imports
  • readxl * imports
  • rintrojs * imports
  • scales * imports
  • shiny * imports
  • shinyAce * imports
  • shinyBS * imports
  • shinyWidgets * imports
  • shinycssloaders * imports
  • stats * imports
  • stringr * imports
  • tm * imports
  • utils * imports
  • visNetwork * imports
  • wordcloud2 * imports
  • AnnotationDbi * suggests
  • DESeq2 * suggests
  • ReactomePA * suggests
  • biomaRt * suggests
  • clusterProfiler * suggests
  • htmltools * suggests
  • ideal * suggests
  • knitr * suggests
  • macrophage * suggests
  • pcaExplorer * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
  • topGO * suggests