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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( # nolint: extraction_operator_linter.
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# drugfindR
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml)
[](https://github.com/CogDisResLab/drugfindR/releases/latest)
[](https://github.com/CogDisResLab/drugfindR/blob/main/LICENSE)
[](https://zenodo.org/badge/latestdoi/338354715)
[](https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel)
<!-- badges: end -->
drugfindR allows convenient access to the iLINCS Gene Knockdown, Gene Overexpression and Chemical Perturbagen databases and allows you to generate and investigate signatures to identify relevant genes and drugs.
## Installation
You can install the released version of drugfindR from [r-universe](https://cogdisreslab.r-universe.dev/drugfindR) with:
```{r, eval = FALSE}
install.packages("drugfindR",
repos = c(
"https://cogdisreslab.r-universe.dev",
"https://cran.r-project.org"
)
)
```
And the development version from [GitHub](https://github.com/) with:
```{r, eval = FALSE}
if (!requireNamespace("devtools", quietly = TRUE)) {
install.packages("devtools")
}
devtools::install_github("CogDisResLab/drugfindR")
```
## Usage
This package has two different interfaces that can be used to generate the results:
1. The first way is to use the individual building block functions to generate results.
This is useful if you want to use the results in your own analysis pipeline or want more
control over the results.
2. The second way is to use one of the convenience functions (`investigateSignatures` or `investigateTarget`)
to generate results.
This approach uses the building block functions under the hood with sensible defaults and
returns a final result that can be used for further analysis.