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README.Rmd
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README.Rmd
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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%"
)
```
# MolEvolvR 📦
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
<!-- badges: end -->
The _MolEvolvR_ R-package provides a framework for characterizing proteins using molecular evolution and phylogeny. Check out our pkgdown page here: [jravilab.github.io/MolEvolvR](https://jravilab.github.io/MolEvolvR)
## Installation
You can install the development version of MolEvolvR from [GitHub](https://github.com/) with:
```{r, eval=FALSE}
# Install Bioconductor
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.19")
# Install Development Version of MolEvolvR
BiocManager::install("JRaviLab/MolEvolvR")
```
### Loading the package
```{r eval=FALSE}
library(MolEvolvR)
```
## Example
This is a basic example which shows you how to analyze your favorite protein:
```{r example, eval=FALSE}
library(MolEvolvR)
## basic example code
## ⏳ Stay tuned!
```
## Companion repos & projects
### Related MolEvolvR codebases
- MolEvolvR web-app 1.0 | 🔒[Repo](https://github.com/jravilab/molevol1.0/) | [Live web-app](//jravilab.org/molevolvr) | [Preprint](https://doi.org/10.1101/2022.02.18.461833) | [Case studies](https://jravilab.cuanschutz.edu/molevolvr/?r=&p=help)
- MolEvolvR web-app 2.0 | 🔒[Repo](https://github.com/jravilab/molevolvr2.0/)
### Specific use cases
- PSP evolution across the tree of life | 🔒[Repo](https://github.com/jravilab/psp_app/) | [Live web-app](//jravilab.org/psp) | [PubMed](https://pubmed.ncbi.nlm.nih.gov/38809013)
- Bacterial phage defense system, avcDI | [Repo](https://github.com/JRaviLab/phage_defense_avcd) | [PubMed](https://pubmed.ncbi.nlm.nih.gov/35817890/)
- DciA evolution across bacteria | [Repo](https://github.com/JRaviLab/dcia_evolution) | [PubMed](https://pubmed.ncbi.nlm.nih.gov/35880876/)
- Internalins in Listeria | [Repo](https://github.com/JRaviLab/inlp_listeria) | [PubMed](https://pubmed.ncbi.nlm.nih.gov/35904424/)
## Current contributors
- [David Mayer](//github.com/the-mayer) | R-package, back-end
- [Faisal Alquaddoomi](//github.com/falquaddoomi) | Front-end 1.0, back-end
- [Evan Brenner](//github.com/epbrenner) | MolEvolvR functionality
- [Vince Rubinetti](//github.com/vincerubinetti) | Front-end 2.0
- [Dave Bunten](//github.com/d33bs) | Data management, engineering
- [Janani Ravi](//github.com/jananiravi) | PI
### Contribution guidelines
We welcome contributions from the community! To ensure a smooth and collaborative process, please follow these [guidelines](https://github.com/JRaviLab/MolEvolvR/blob/main/.github/CONTRIBUTING.md). Outreachy interns, please check out these [pointers](https://github.com/JRaviLab/MolEvolvR/blob/main/.github/outreachy_guidelines.md) to get started.
📜 [License](https://github.com/JRaviLab/MolEvolvR/blob/main/LICENSE.md)
### Code of Conduct
Please note that the MolEvolvR project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.