README.Rmd

---
output: github_document
---

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knitr::opts_chunk$set(
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# tmod <a href='https://january3.github.com/tmod/'><img src='man/figures/logo.png' align="right" height="138.5" /></a>


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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://january3.github.io/tmod/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)
```