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https://github.com/mschubert/ebits
R bioinformatics toolkit incubator
https://github.com/mschubert/ebits
Last synced: about 12 hours ago
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R bioinformatics toolkit incubator
- Host: GitHub
- URL: https://github.com/mschubert/ebits
- Owner: mschubert
- License: apache-2.0
- Created: 2014-04-11T15:03:11.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2025-01-20T12:26:22.000Z (2 days ago)
- Last Synced: 2025-01-20T13:35:10.011Z (2 days ago)
- Language: R
- Homepage:
- Size: 726 KB
- Stars: 6
- Watchers: 41
- Forks: 3
- Open Issues: 18
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
ebits: bioinformatics-related R modules
=======================================
[](https://github.com/mschubert/ebits/actions)
This repository is meant as a collection of bioinformatics-related R
code that simplify workflows and can be shared with other people.
For details, see the `README.md` files and API documentation in the respective
directories.
Requirements
------------
This collection of tools requires `modules`, install using using `devtools`:
```r
# install.packages('devtools')
devtools::install_github('klmr/modules')
```
The scripts also depend on a range of R packages. If using only a few modules,
you may want to install only the packages you need. Otherwise you can
list/install all of them by typing:
```sh
./dependencies.sh # list all packages
make install-deps # install all packages (warning: there's a lot)
```
Setup
-----
```bash
cd your_local_directory
git clone https://github.com/EBI-predocs/ebits.git
cd ebits && git submodule --init --recursive
```
Additionally, you need load the `modules` package and tell R where to find the
`ebits` module. In order to do this, set your `import.path` in your
*~/.Rprofile*:
```r
library(modules) # can also load manually
options(import.path=c("/path/to/ebits",
"/path/to/other/module")
```
Usage
-----
Modules can be imported and used as described in the
[`modules` documentation](https://github.com/klmr/modules)
```r
mod = import('module') # imports the module
mod$func(x=5) # calls the module function
```