drugfindr

Repository holding the code for the drugfindR R package

https://github.com/cogdisreslab/drugfindr

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (18.2%) to scientific vocabulary

Keywords

bioinformatics bioinformatics-pipeline ilincs r transcriptomics

Last synced: 6 months ago · JSON representation

Repository

Repository holding the code for the drugfindR R package

Basic Info

Host: GitHub
Owner: CogDisResLab
License: gpl-3.0
Language: R
Default Branch: devel
Size: 7.38 MB

Statistics

Stars: 8
Watchers: 1
Forks: 3
Open Issues: 19
Releases: 41

Topics

bioinformatics bioinformatics-pipeline ilincs r transcriptomics

Created about 5 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Codemeta Zenodo

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set( # nolint: extraction_operator_linter.
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# drugfindR


[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

[![Continuous Integration / R Workflows](https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml/badge.svg)](https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml)
[![latest-version](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fcogdisreslab.r-universe.dev%2Fapi%2Fpackages%2FdrugfindR&query=%24.Version&style=flat&label=latest-release&color=orange)](https://github.com/CogDisResLab/drugfindR/releases/latest)
[![license](https://img.shields.io/github/license/CogDisResLab/drugfindR)](https://github.com/CogDisResLab/drugfindR/blob/main/LICENSE)
[![DOI](https://zenodo.org/badge/338354715.svg)](https://zenodo.org/badge/latestdoi/338354715)
[![Codecov test coverage](https://codecov.io/gh/CogDisResLab/drugfindR/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel)


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.

Owner

Name: Cognitive Disorders Research Lab
Login: CogDisResLab
Kind: organization
Email: contact@cdrl-ut.org
Location: United States of America

Website: www.cdrl-ut.org
Repositories: 52
Profile: https://github.com/CogDisResLab

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GitHub Events

Total

Create event: 51
Issues event: 1
Release event: 12
Watch event: 1
Delete event: 25
Issue comment event: 94
Push event: 57
Pull request review event: 2
Pull request event: 73

Last Year

Create event: 51
Issues event: 1
Release event: 12
Watch event: 1
Delete event: 25
Issue comment event: 94
Push event: 57
Pull request review event: 2
Pull request event: 73

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 23
Total pull requests: 51
Average time to close issues: 9 months
Average time to close pull requests: 2 days
Total issue authors: 4
Total pull request authors: 3
Average comments per issue: 0.22
Average comments per pull request: 1.24
Merged pull requests: 35
Bot issues: 0
Bot pull requests: 14

Past Year

Issues: 1
Pull requests: 34
Average time to close issues: N/A
Average time to close pull requests: about 1 hour
Issue authors: 1
Pull request authors: 2
Average comments per issue: 0.0
Average comments per pull request: 1.68
Merged pull requests: 23
Bot issues: 0
Bot pull requests: 11

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Top Authors

Issue Authors

AliSajid (25)
willgryan (2)
cventophd (1)
evelynb4565 (1)
renovate[bot] (1)

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AliSajid (66)
renovate[bot] (46)
pre-commit-ci[bot] (2)

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Issue Labels

bioconductor (12) documentation (7) enhancement (6) good first issue (5) help wanted (4) dependencies (1) renovate (1)

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Dependencies

DESCRIPTION cran

R >= 2.10 depends
dplyr * imports
httr * imports
magrittr * imports
purrr * imports
readr * imports
rlang * imports
stringr * imports
tibble * imports
tidyr * imports
testthat >= 3.0.0 suggests

.github/workflows/rworkflows.yml actions

neurogenomics/rworkflows master composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

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