drugfindr

This is a read-only mirror of the git repos at https://bioconductor.org

https://github.com/bioc/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
○
Scientific vocabulary similarity
Low similarity (18.2%) to scientific vocabulary

Last synced: 9 months ago · JSON representation

Repository

This is a read-only mirror of the git repos at https://bioconductor.org

Basic Info

Host: GitHub
Owner: bioc
License: gpl-3.0
Language: R
Default Branch: devel
Size: 6.81 MB

Statistics

Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Created about 2 years ago · Last pushed over 1 year 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: bioc
Login: bioc
Kind: organization

Repositories: 1
Profile: https://github.com/bioc

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "drugfindR",
  "description": "This package provides a convenient way to access the LINCS Signatures available in the iLINCS database. These signatures include Consensus Gene Knockdown Signatures, Gene Overexpression signatures and Chemical Perturbagen Signatures. It also provides a way to enter your own transcriptomic signatures and identify concordant and discordant signatures in the LINCS database.",
  "name": "drugfindR: Investigate iLINCS for candidate repurposable drugs",
  "codeRepository": "https://github.com/CogDisResLab/drugfindR",
  "issueTracker": "https://github.com/CogDisResLab/drugfindR/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "0.99.1017",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.4.2 (2024-10-31)",
  "author": [
    {
      "@type": "Person",
      "givenName": [
        "Ali",
        "Sajid"
      ],
      "familyName": "Imami",
      "email": "Ali.Sajid.Imami@gmail.com",
      "@id": "https://orcid.org/0000-0003-3684-3539"
    },
    {
      "@type": "Person",
      "givenName": "Smita",
      "familyName": "Sahay",
      "email": "Smita.Sahay@rockets.utoledo.edu",
      "@id": "https://orcid.org/0009-0003-4377-8963"
    },
    {
      "@type": "Person",
      "givenName": [
        "Justin",
        "Fortune"
      ],
      "familyName": "Creeden",
      "email": "Justin.Creeden@rockets.utoledo.edu",
      "@id": "https://orcid.org/0000-0003-3123-8401"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": [
        "Ali",
        "Sajid"
      ],
      "familyName": "Imami",
      "email": "Ali.Sajid.Imami@gmail.com",
      "@id": "https://orcid.org/0000-0003-3684-3539"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "AnnotationDbi",
      "name": "AnnotationDbi",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "Bioconductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "BiocStyle",
      "name": "BiocStyle",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "Bioconductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/BiocStyle.html"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "biocthis",
      "name": "biocthis",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "Bioconductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/biocthis.html"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "codemetar",
      "name": "codemetar",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=codemetar"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "devtools",
      "name": "devtools",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=devtools"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "version": ">= 3.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "tidyverse",
      "name": "tidyverse",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tidyverse"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "usethis",
      "name": "usethis",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=usethis"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "vcr",
      "name": "vcr",
      "version": ">= 0.6.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=vcr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "webmockr",
      "name": "webmockr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=webmockr"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "magrittr",
      "name": "magrittr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=magrittr"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "tibble",
      "name": "tibble",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tibble"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "rlang",
      "name": "rlang",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rlang"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "dplyr",
      "name": "dplyr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=dplyr"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "purrr",
      "name": "purrr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=purrr"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "readr",
      "name": "readr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=readr"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "stringr",
      "name": "stringr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=stringr"
    },
    "8": {
      "@type": "SoftwareApplication",
      "identifier": "stats",
      "name": "stats"
    },
    "9": {
      "@type": "SoftwareApplication",
      "identifier": "lifecycle",
      "name": "lifecycle",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=lifecycle"
    },
    "10": {
      "@type": "SoftwareApplication",
      "identifier": "S4Vectors",
      "name": "S4Vectors",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "Bioconductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/S4Vectors.html"
    },
    "11": {
      "@type": "SoftwareApplication",
      "identifier": "httr2",
      "name": "httr2",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=httr2"
    },
    "12": {
      "@type": "SoftwareApplication",
      "identifier": "curl",
      "name": "curl",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=curl"
    },
    "13": {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 4.4.0"
    },
    "SystemRequirements": null
  },
  "applicationCategory": "Genomics",
  "isPartOf": "https://bioconductor.org",
  "keywords": [
    "LINCS",
    "iLINCS",
    "drugrepurposing",
    "drugdiscovery",
    "transcriptomics",
    "geneexpression",
    "geneknockdown",
    "geneoverexpression",
    "chemicalperturbagen",
    "drugfindR",
    "r",
    "ilincs",
    "bioinformatics",
    "bioinformatics-pipeline"
  ],
  "fileSize": "2087.859KB",
  "readme": "https://github.com/CogDisResLab/drugfindR/blob/devel/README.md",
  "contIntegration": [
    "https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml",
    "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"
  ],
  "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental"
}

GitHub Events

Total

Push event: 2

Last Year

Push event: 2

Dependencies

.github/workflows/create_github_release.yaml actions

actions/checkout 692973e3d937129bcbf40652eb9f2f61becf3332 composite
r-lib/actions/setup-r 929c772977a3a13c8733b363bf5a2f685c25dd91 composite
r-lib/actions/setup-renv 929c772977a3a13c8733b363bf5a2f685c25dd91 composite

.github/workflows/rworkflows.yml actions

neurogenomics/rworkflows master composite

.github/workflows/test-coverage.yaml actions

actions/checkout 692973e3d937129bcbf40652eb9f2f61becf3332 composite
actions/upload-artifact 65462800fd760344b1a7b4382951275a0abb4808 composite
r-lib/actions/setup-r 929c772977a3a13c8733b363bf5a2f685c25dd91 composite
r-lib/actions/setup-r-dependencies 929c772977a3a13c8733b363bf5a2f685c25dd91 composite

DESCRIPTION cran

R >= 4.4.0 depends
S4Vectors * imports
dplyr * imports
httr * imports
lifecycle * imports
magrittr * imports
purrr * imports
readr * imports
rlang * imports
stats * imports
stringr * imports
tibble * imports
AnnotationDbi * suggests
BiocStyle * suggests
biocthis * suggests
codemetar * suggests
devtools * suggests
knitr * suggests
rmarkdown * suggests
testthat >= 3.0.0 suggests
tidyverse * suggests
usethis * suggests
vcr >= 0.6.0 suggests
webmockr * suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science