Data

Tools

Indexes

Applications

Experiments

Open Source Science

tmod

tmod – Gene set enrichments

https://github.com/january3/tmod

Science Score: 13.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.8%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

tmod – Gene set enrichments

Basic Info
Statistics
  • Stars: 3
  • Watchers: 0
  • Forks: 1
  • Open Issues: 1
  • Releases: 1
Created about 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



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


# tmod 



[![R-CMD-check](https://github.com/january3/tmod/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/january3/tmod/actions/workflows/R-CMD-check.yaml)
[![test-coverage](https://github.com/january3/tmod/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/january3/tmod/actions/workflows/test-coverage.yaml)
[![CRAN status](https://www.r-pkg.org/badges/version/tmod)](https://CRAN.R-project.org/package=tmod)


Tmod is a suite of gene set enrichment algorithms, visualizations and
utilities which comes bundled with a few libraries of gene sets
("modules"). Following features distinguish tmod from other packages:

 * "panel plot" visualizations which allow to compare results of gene set
   enrichments;
 * several enrichment algorithms are implemented in tmod, in particular the
   very efficient, versatile and
   [reproducible](https://academic.oup.com/bioinformatics/article/35/24/5146/5511403)
   algorithm called "CERNO";
 * it includes a library of gene sets derived from clustering of gene
   expression data from human blood, which is especially useful in
   functional analysis in infection and immune responses.

## Installation

You can install the released version of tmod from [CRAN](https://CRAN.R-project.org/) with:

``` r
install.packages("tmod")
```

And the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("january3/tmod")
```
## Tmod manual

 * Access the documentation using `vignette("tmod")`
 * Full user manual is found [here](https://tmod.online/articles/user_manual/tmod_user_manual.html)

## Example usage


```{r include=FALSE}
library(ggplot2)
library(cowplot)
theme_set(theme_minimal())
```





```{r}
library(tmod)
data(EgambiaResults)
tt <- EgambiaResults

## gene set enrichment analysis
res <- tmodCERNOtest(tt$GENE_SYMBOL)
head(res)
```

Owner

  • Name: January Weiner
  • Login: january3
  • Kind: user
  • Company: CUBI / BIH @bihealth

GitHub Events

Total
  • Push event: 1
Last Year
  • Push event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 120
  • Total Committers: 1
  • Avg Commits per committer: 120.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
January Weiner j****r@g****m 120

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: 4 days
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 1.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • Dereth-Pirout (1)
  • TzuTingWei (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 257 last-month
  • Total docker downloads: 21,661
  • Total dependent packages: 3
  • Total dependent repositories: 1
  • Total versions: 12
  • Total maintainers: 1
cran.r-project.org: tmod

Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

  • Versions: 12
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Downloads: 257 Last month
  • Docker Downloads: 21,661
Rankings
Docker downloads count: 0.6%
Dependent packages count: 18.3%
Average: 20.1%
Forks count: 21.2%
Dependent repos count: 24.2%
Stargazers count: 27.9%
Downloads: 28.5%
Maintainers (1)
january.weiner@gmail.com
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • RColorBrewer * imports
  • XML * imports
  • beeswarm * imports
  • colorDF * imports
  • ggplot2 * imports
  • ggrepel * imports
  • gplots * imports
  • methods * imports
  • pheatmap * imports
  • plotwidgets * imports
  • purrr * imports
  • rlang * imports
  • tagcloud * imports
  • tibble * imports
  • tidyr * imports
  • tidyselect * imports
  • dplyr * suggests
  • knitr * suggests
  • limma * suggests
  • pca3d * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 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
.github/workflows/pr-commands.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/pr-fetch v2 composite
  • r-lib/actions/pr-push v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite