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GeneTonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

https://github.com/federicomarini/genetonic

Science Score: 59.0%

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

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    CITATION.cff file
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    Found codemeta.json file
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    Found .zenodo.json file
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    Found 9 DOI reference(s) in README
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    Academic publication links
    Links to: biorxiv.org
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    6 of 9 committers (66.7%) from academic institutions
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    Low similarity (19.5%) to scientific vocabulary

Keywords

bioconductor bioconductor-package data-exploration data-visualization functional-enrichment-analysis gene-expression gui pathway-analysis r reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome transcriptomics user-friendly

Keywords from Contributors

genomics gene proteomics single-cell immune-repertoire sequencing grna-sequence core-package u24ca289073 core-services
Last synced: 6 months ago · JSON representation

Repository

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Basic Info
Statistics
  • Stars: 78
  • Watchers: 4
  • Forks: 11
  • Open Issues: 19
  • Releases: 1
Topics
bioconductor bioconductor-package data-exploration data-visualization functional-enrichment-analysis gene-expression gui pathway-analysis r reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome transcriptomics user-friendly
Created over 6 years ago · Last pushed 10 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%"
)
```

# GeneTonic






[![R build status](https://github.com/federicomarini/GeneTonic/workflows/R-CMD-check/badge.svg)](https://github.com/federicomarini/GeneTonic/actions)
[![](https://bioconductor.org/shields/build/devel/bioc/GeneTonic.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/GeneTonic/)
[![](https://img.shields.io/github/last-commit/federicomarini/GeneTonic.svg)](https://github.com/federicomarini/GeneTonic/commits/master)
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[![Codecov.io coverage status](https://codecov.io/github/federicomarini/GeneTonic/coverage.svg?branch=master)](https://codecov.io/github/federicomarini/GeneTonic)


The goal of GeneTonic is to analyze and integrate the results from Differential Expression analysis and functional enrichment analysis.

This package provides a Shiny application that aims to combine at different levels the existing pieces of the transcriptome data and results, in a way that makes it easier to generate insightful observations and hypothesis - combining the benefits of interactivity and reproducibility, e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist.

GeneTonic can be found on Bioconductor (https://www.bioconductor.org/packages/GeneTonic).

If you use GeneTonic in your work, please refer to the original publication :page_facing_up: on BMC Bioinformatics (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04461-5, doi: [10.1186/s12859-021-04461-5](https://doi.org/10.1186/s12859-021-04461-5)).

A preprint :page_facing_up: on GeneTonic is available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1.

## Installation

You can install the development version of GeneTonic from GitHub with:

```{r eval=FALSE}
library("remotes")
remotes::install_github("federicomarini/GeneTonic", 
                        dependencies = TRUE, build_vignettes = TRUE)
```

## Example

This is a basic example which shows you how to use `GeneTonic` on a demo dataset (the one included in the `macrophage` package).

```{r eval=FALSE}
library("GeneTonic")
example("GeneTonic")

# which will in the end run
library("macrophage")
library("DESeq2")
library("org.Hs.eg.db")
library("AnnotationDbi")

# dds object
data("gse", package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~line + condition)
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)

# annotation object
anno_df <- data.frame(
  gene_id = rownames(dds_macrophage),
  gene_name = mapIds(org.Hs.eg.db,
                     keys = rownames(dds_macrophage),
                     column = "SYMBOL",
                     keytype = "ENSEMBL"),
  stringsAsFactors = FALSE,
  row.names = rownames(dds_macrophage)
)

# res object
data(res_de_macrophage, package = "GeneTonic")
res_de <- res_macrophage_IFNg_vs_naive

# res_enrich object
data(res_enrich_macrophage, package = "GeneTonic")
res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)

GeneTonic(dds = dds_macrophage,
          res_de = res_de,
          res_enrich = res_enrich,
          annotation_obj = anno_df,
          project_id = "my_first_genetonic")
```

## Usage overview

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

## Sneak peek?

Please visit http://shiny.imbei.uni-mainz.de:3838/GeneTonic/ to see a small demo instance running, on the `macrophage` dataset.

## 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/federicomarini/GeneTonic/issues).

## Code of Conduct

Please note that the GeneTonic project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

## License

MIT © Federico Marini

Owner

  • Name: Federico Marini
  • Login: federicomarini
  • Kind: user
  • Location: Mainz
  • Company: University Medical Center, Mainz

Virchow Fellow, Bioinformatician @ Institute of Medical Biostatistics, Epidemiology and Informatics, Mainz (@imbeimainz)

GitHub Events

Total
  • Issues event: 1
  • Watch event: 2
  • Member event: 1
  • Issue comment event: 10
  • Push event: 31
  • Pull request event: 6
  • Fork event: 2
  • Create event: 3
Last Year
  • Issues event: 1
  • Watch event: 2
  • Member event: 1
  • Issue comment event: 10
  • Push event: 31
  • Pull request event: 6
  • Fork event: 2
  • Create event: 3

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 1,077
  • Total Committers: 9
  • Avg Commits per committer: 119.667
  • Development Distribution Score (DDS): 0.032
Past Year
  • Commits: 58
  • Committers: 5
  • Avg Commits per committer: 11.6
  • Development Distribution Score (DDS): 0.138
Top Committers
Name Email Commits
Federico Marini m****f@u****e 1,042
Nitesh Turaga n****a@g****m 10
J Wokaty j****y@s****u 10
Ludt a****t@U****e 7
“edo98811” “****e@u****” 3
A Wokaty a****y@s****u 2
SimonTStahl S****l@g****m 1
Najla Abassi a****6@g****m 1
Annekathrin Silvia Ludt a****n@z****E 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2 uni-mainz.de: 2 zdv-vpn01-38-62.zdv.uni-mainz.de: 1 uni-mainz.de”: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 27
  • Total pull requests: 42
  • Average time to close issues: 3 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 21
  • Total pull request authors: 6
  • Average comments per issue: 3.63
  • Average comments per pull request: 0.88
  • Merged pull requests: 38
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 8
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 days
  • Issue authors: 2
  • Pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.63
  • Merged pull requests: 7
  • Bot issues: 0
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View more stats
Top Authors
Issue Authors
  • AnnekathrinSilvia (3)
  • lucolotto (2)
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Pull Request Authors
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Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 17,541 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: GeneTonic

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 17,541 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 21.8%
Downloads: 65.4%
Maintainers (1)
marinif@uni-mainz.de
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • AnnotationDbi * imports
  • ComplexHeatmap * imports
  • ComplexUpset * imports
  • DESeq2 * imports
  • DT * imports
  • GO.db * imports
  • RColorBrewer * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • backbone * imports
  • bs4Dash >= 2.0.0 imports
  • circlize * imports
  • colorspace * imports
  • colourpicker * imports
  • dendextend * imports
  • dplyr * imports
  • dynamicTreeCut * imports
  • expm * imports
  • ggforce * imports
  • ggplot2 * imports
  • ggrepel * imports
  • grDevices * imports
  • graphics * imports
  • grid * imports
  • igraph * imports
  • matrixStats * imports
  • methods * imports
  • plotly * imports
  • rintrojs * imports
  • rlang * imports
  • rmarkdown * imports
  • scales * imports
  • shiny * imports
  • shinyAce * imports
  • shinyWidgets * imports
  • shinycssloaders * imports
  • stats * imports
  • tidyr * imports
  • tippy * imports
  • tools * imports
  • utils * imports
  • viridis * imports
  • visNetwork * imports
  • BiocStyle * suggests
  • clusterProfiler * suggests
  • htmltools * suggests
  • knitr * suggests
  • macrophage * suggests
  • magrittr * suggests
  • org.Hs.eg.db * suggests
  • testthat >= 2.1.0 suggests
.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