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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# MOSuite <a href="https://ccbr.github.io/MOSuite/"><img src="inst/extdata/logo/mosuite_logo_with_text.png" align="right" height="160" alt="MOSuite website" /></a>
R package for differential multi-omics analysis
<!-- badges: start -->
[](https://github.com/CCBR/MOSuite/actions/workflows/R-CMD-check.yaml)
[](https://codecov.io/gh/CCBR/MOSuite)
[](https://github.com/CCBR/MOSuite/actions/workflows/github-code-scanning/codeql)
[](https://github.com/CCBR/MOSuite/releases/latest)
[](https://hub.docker.com/r/nciccbr/mosuite)
[](https://doi.org/10.5281/zenodo.16371580)
<!-- badges: end -->
Multi-Omics Suite provides a suite of functions to clean, filter, batch-correct,
normalize, visualize, and perform differential expression analysis. While the
package is designed for differential [RNA-seq](https://github.com/CCBR/RENEE)
analysis and multi-omics datasets, it can be used for any data represented in a
counts table. See the website for more information, documentation, and examples:
<https://ccbr.github.io/MOSuite/>
## Installation
You can install the development version of MOSuite from [GitHub](https://github.com/CCBR/MOSuite) with:
```r
# install.packages("remotes")
remotes::install_github("CCBR/MOSuite", dependencies = TRUE)
```
Or install a specific version:
```r
remotes::install_github("CCBR/MOSuite", dependencies = TRUE, ref = "v0.3.0")
```
There is also a Docker container available at <https://hub.docker.com/r/nciccbr/mosuite>
```sh
singularity exec docker://nciccbr/mosuite:v0.3.0 R -s -e \
'cat("MOSuite version:", installed.packages()["MOSuite",][["Version"]])'
```
## Usage
Please see the [introductory vignette](https://ccbr.github.io/MOSuite/articles/intro.html)
for a quick start tutorial.
Take a look at the [reference documentation](https://ccbr.github.io/MOSuite/reference/index.html)
for detailed information on each function in the package.
## Help & Contributing
Come across a **bug**? Open an [issue](https://github.com/CCBR/MOSuite/issues) and include a minimal reproducible example.
Have a **question**? Ask it in [discussions](https://github.com/CCBR/MOSuite/discussions).
Want to **contribute** to this project? Check out the [contributing guidelines](.github/CONTRIBUTING.md).
## Development Roadmap
- [dev spreadsheet](https://nih-my.sharepoint.com/:x:/g/personal/homanpj_nih_gov/ETvHXgnwxExEpcP57Jj9_EwBHBvZBqNuZ_c3eu51w-SlnA?e=PcXKU8)
- [project board](https://github.com/orgs/CCBR/projects/32)