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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%"
)
```
# miRminer
<!-- badges: start -->
[![R build status](https://github.com/jvfe/miRminer/workflows/R-CMD-check/badge.svg)](https://github.com/jvfe/miRminer/actions)
[![license](https://img.shields.io/badge/license-MIT-lightgrey)](https://github.com/jvfe/miRminer/blob/master/LICENSE.md)
<!-- badges: end -->
Scrapes disease-associated miRNA data.
Databases of miRNA-disease association, like [HMDD](http://www.cuilab.cn/hmdd) or [miRTarBase](http://mirtarbase.cuhk.edu.cn/php/), provide
easily downloadable data dumps, but no easy way to query it programmatically, such
as an API, this package exists to alleviate some of those issues.
## Installation
You can install the latest version of miRminer from Github with:
```{r install_github, eval=FALSE}
install.packages("remotes")
remotes::install_github("jvfe/miRminer")
```
## Example usage
If you want to get causality information from HMDD3:
```{r hmdd-causal, eval=FALSE}
library(miRminer)
sepsis_causal <- get_hmdd_causality("sepsis")
hm101_causal <- get_hmdd_causality("hsa-mir-101")
```
Or miRNA-target interaction networks:
```{r hmdd-net, eval=FALSE}
silicosis_net <- get_hmdd_net("silicosis")
hm101_net <- get_hmdd_net("hsa-mir-101")
```
Or maybe miRNA-disease association from mirTarBase:
```{r mirtar-examp, eval=FALSE}
carcinoma_mirnas <- get_mirtar_disease("carcinoma")
```