BioCor

Package to calculate functional similarity between genes https://biocor.llrs.dev

Science Score: 54.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
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1 of 14 committers (7.1%) from academic institutions
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Low similarity (17.9%) to scientific vocabulary

Keywords

bioconductor-packages bioinformatics functional-similarity gene gene-sets pathway-analysis pathways similarity similarity-measurement

Keywords from Contributors

bioconductor bioconductor-package biomarker-discovery biostatistics causal-inference computational-biology targeted-learning cheminformatics chromatography gc-fid

Last synced: 6 months ago · JSON representation ·

Repository

Package to calculate functional similarity between genes https://biocor.llrs.dev

Basic Info

Host: GitHub
Owner: llrs
License: other
Language: R
Default Branch: devel
Homepage: https://www.bioconductor.org/packages/BioCor/
Size: 9.97 MB

Statistics

Stars: 14
Watchers: 3
Forks: 1
Open Issues: 4
Releases: 3

Topics

bioconductor-packages bioinformatics functional-similarity gene gene-sets pathway-analysis pathways similarity similarity-measurement

Created about 9 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog Contributing License Citation Codemeta

README.Rmd

---
output: github_document
---



```{r echo=FALSE, message=FALSE, warning=FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "README-"
)
library("BioCor")
```

# BioCor 


[![R-CMD-check](https://github.com/llrs/BioCor/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/llrs/BioCor/actions/workflows/R-CMD-check.yaml)
[![codecov](https://codecov.io/gh/llrs/BioCor/branch/master/graph/badge.svg)](https://codecov.io/gh/llrs/BioCor/)
[![Build Status](https://www.bioconductor.org/shields/build/devel/bioc/BioCor.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/BioCor/)
[![Bioc](https://www.bioconductor.org/shields/years-in-bioc/BioCor.svg)](https://www.bioconductor.org/packages/devel/bioc/html/BioCor.html#since)
[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/1913/badge)](https://bestpractices.coreinfrastructure.org/projects/1913)



This project wants to allow the user to calculate functional similarities (or biological correlation as it was named originally hence the name) and 
use them for network building or other purposes.

# Installation

It is an R package you can install it from the Bioconductor project with:

```{r eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")
  }
BiocManager::install("BioCor")
```
You can install this version of *BioCor* with:
```{r eval=FALSE}
if (!requireNamespace("devtools", quietly = TRUE)) {
      install.packages("devtools")
  }
devtools::install_github("llrs/BioCor")
```

# How to use BioCor?

See the [vignette](https://bioconductor.org/packages/release/bioc/vignettes/BioCor/inst/doc/BioCor_1_basics.html) in Bioconductor site and the [advanced vignette](https://bioconductor.org/packages/release/bioc/vignettes/BioCor/inst/doc/BioCor_2_advanced.html).  
Here is a minimum example:
```{r message=FALSE, warning=FALSE, include=FALSE}
library("reactome.db")
genesReact <- as.list(reactomeEXTID2PATHID)
# Remove genes and pathways which are not from human pathways
genesReact <- sapply(genesReact, function(x) {
    unique(grep("R-HSA-", x, value = TRUE))
})
genesReact <- genesReact[lengths(genesReact) >= 1]
```

```{r}
# The data must be provided, see the vignette for more details.
# Get some pathways from the pathway data
(pathways <- sample(unlist(genesReact, use.names = FALSE), 5))
# Calculate the pathway similarity of them
mpathSim(pathways, genesReact, NULL)
```

# Who might use this package?

It is intended for bioinformaticians, both people interested in *knowing* the functionally *similarity of some genes* or clusters and people *developing* some other analysis at the top of it.


# What is the goal of this project?

The goal of this project is to provide methods to calculate functional similarities based on pathways. 

# What can be BioCor used for?

Here is a non-comprehensive list:

 - Diseases or drug:  
  By observing which genes with the same pathways are more affected
 - Gene/protein functional analysis:  
  By testing how new pathways are similar to existing pathways
 - Protein-protein interaction:   
  By testing if they are involved in the same pathways
 - miRNA-mRNA interaction:   
  By comparing clusters they affect
 - sRNA regulation:  
  By observing the relationship between sRNA and genes
 - Evolution:  
  By comparing similarities of genes between species
 - Networks improvement:  
  By adding information about the known relationship between genes
 - Evaluate pathways databases:  
  By comparing scores of the same entities

See the [advanced vignette](https://bioconductor.org/packages/release/bioc/vignettes/BioCor/inst/doc/BioCor_2_advanced.html)

# Contributing

Please read [how to contribute](.github/CONTRIBUTING.md) for details on the code of conduct, and the process for submitting pull requests.

# Acknowledgments

Anyone that has contributed to make this package be as is, specially my advisor.

Owner

Name: Lluís Revilla
Login: llrs
Kind: user
Location: Spain
Company: @irsi-tiv

Website: https://llrs.dev
Twitter: Lluis_Revilla
Repositories: 140
Profile: https://github.com/llrs

Bioinformatician, data scientist/engineer making data accessible & useful, be it in pharma, research, open source or government data.

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "BioCor" in publications use:'
type: software
license: MIT
title: 'BioCor: Functional similarities'
version: 1.27.1
abstract: Calculates functional similarities based on the pathways described on KEGG
  and REACTOME or in gene sets. These similarities can be calculated for pathways
  or gene sets, genes, or clusters and combined with other similarities. They can
  be used to improve networks, gene selection, testing relationships...
authors:
- family-names: Revilla Sancho
  given-names: Lluís
  email: lluis.revilla@gmail.com
  orcid: https://orcid.org/0000-0001-9747-2570
repository: https://bioconductor.org/
repository-code: https://github.com/llrs/BioCor
url: https://bioconductor.org/packages/BioCor
contact:
- family-names: Revilla Sancho
  given-names: Lluís
  email: lluis.revilla@gmail.com
  orcid: https://orcid.org/0000-0001-9747-2570
keywords:
- bioconductor-packages
- bioinformatics
- functional-similarity
- gene
- gene-sets
- pathway-analysis
- pathways
- similarity
- similarity-measurement
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
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    name: Vienna, Austria
  year: '2024'
  institution:
    name: R Foundation for Statistical Computing
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    given-names: Valerie
  - family-names: Lang
    given-names: Michel
    email: michellang@gmail.com
  - family-names: Thompson
    given-names: Ryan
    email: rct@thompsonclan.org
  - family-names: Turaga
    given-names: Nitesh
  year: '2024'
  doi: 10.18129/B9.bioc.BiocParallel
- type: software
  title: GSEABase
  abstract: 'GSEABase: Gene set enrichment data structures and methods'
  notes: Imports
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Falcon
    given-names: Seth
  - family-names: Gentleman
    given-names: Robert
  year: '2024'
  doi: 10.18129/B9.bioc.GSEABase
- type: software
  title: Matrix
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  notes: Imports
  url: https://R-forge.R-project.org/tracker/?atid=294&group_id=61
  repository: https://CRAN.R-project.org/package=Matrix
  authors:
  - family-names: Bates
    given-names: Douglas
    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Maechler
    given-names: Martin
    email: mmaechler+Matrix@gmail.com
    orcid: https://orcid.org/0000-0002-8685-9910
  - family-names: Jagan
    given-names: Mikael
    orcid: https://orcid.org/0000-0002-3542-2938
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  year: '2024'
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: airway
  abstract: 'airway: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle
    cells, by Himes et al PLoS One 2014'
  notes: Suggests
  repository: https://bioconductor.org/
  authors:
  - family-names: Love
    given-names: Michael
  year: '2024'
  doi: 10.18129/B9.bioc.airway
- type: software
  title: BiocStyle
  abstract: 'BiocStyle: Standard styles for vignettes and other Bioconductor documents'
  notes: Suggests
  url: https://github.com/Bioconductor/BiocStyle
  repository: https://bioconductor.org/
  authors:
  - family-names: Oleś
    given-names: Andrzej
    orcid: https://orcid.org/0000-0003-0285-2787
  year: '2024'
  doi: 10.18129/B9.bioc.BiocStyle
- type: software
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  abstract: 'boot: Bootstrap Functions (Originally by Angelo Canty for S)'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=boot
  authors:
  - family-names: Canty
    given-names: Angelo
    email: cantya@mcmaster.ca
  - family-names: Ripley
    given-names: Brian
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  year: '2024'
- type: software
  title: DESeq2
  abstract: 'DESeq2: Differential gene expression analysis based on the negative binomial
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  notes: Suggests
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  repository: https://bioconductor.org/
  authors:
  - family-names: Love
    given-names: Michael
    email: michaelisaiahlove@gmail.com
  - family-names: Anders
    given-names: Simon
  - family-names: Huber
    given-names: Wolfgang
  year: '2024'
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  repository: https://CRAN.R-project.org/package=ggplot2
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  - family-names: Wickham
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  - family-names: Dunnington
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  - family-names: van den Brand
    given-names: Teun
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  version: '>= 3.4.1'
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  year: '2024'
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  abstract: 'spelling: Tools for Spell Checking in R'
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  url: https://docs.ropensci.org/spelling/
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  year: '2024'
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- type: software
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  url: https://testthat.r-lib.org
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identifiers:
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      "identifier": "Hmisc",
      "name": "Hmisc",
      "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=Hmisc"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "spelling",
      "name": "spelling",
      "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=spelling"
    }
  ],
  "softwareRequirements": [
    {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 3.4.0"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "BiocParallel",
      "name": "BiocParallel",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "BioConductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/BiocParallel.html"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "Matrix",
      "name": "Matrix",
      "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=Matrix"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "methods",
      "name": "methods"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "GSEABase",
      "name": "GSEABase",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "BioConductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/GSEABase.html"
    }
  ],
  "relatedLink": [
    "https://llrs.github.io/BioCor/",
    "https://bioconductor.org/packages/release/bioc/html/BioCor.html"
  ],
  "releaseNotes": "https://github.com/llrs/BioCor/blob/master/NEWS.md",
  "readme": "https://github.com/llrs/BioCor/blob/master/README.md",
  "fileSize": "0KB",
  "contIntegration": [
    "https://travis-ci.org/llrs/BioCor",
    "https://ci.appveyor.com/projects/llrs/BioCor",
    "https://codecov.io/gh/llrs/BioCor/"
  ],
  "developmentStatus": [
    "https://www.repostatus.org/#active",
    "https://www.tidyverse.org/lifecycle/#stable"
  ],
  "keywords": [
    "similarity-measurement",
    "similarity",
    "functional-similarity",
    "bioinformatics",
    "pathway-analysis",
    "gene-sets",
    "bioconductor-packages",
    "gene",
    "pathways"
  ]
}

GitHub Events

Total

Push event: 4

Last Year

Push event: 4

Committers

Last synced: over 2 years ago

All Time

Total Commits: 506
Total Committers: 14
Avg Commits per committer: 36.143
Development Distribution Score (DDS): 0.121

Past Year

Commits: 25
Committers: 5
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.48

Top Committers

Name	Email	Commits
Lluís Revilla	l**a@g**m	445
Lluís	l****s	17
Nitesh Turaga	n**a@g**m	14
Lluís Revilla	l**a@i**s	13
david mas	d**p@g**m	2
Herve Pages	h**s@f**g	2
J Wokaty	j**y@s**u	2
vobencha	v**n@r**g	2
vobencha	v**a@g**m	2
Hervé Pagès	h**s@f**g	2
J Wokaty	j****y	2
Martin Morgan	m**n@f**g	1
LiNk-NY	m**9@g**m	1
Lori Shepherd	l**d@r**g	1

Committer Domains (Top 20 + Academic)

roswellpark.org: 2 fhcrc.org: 2 fredhutch.org: 1 sph.cuny.edu: 1 irsicaixa.es: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 29
Total pull requests: 2
Average time to close issues: 6 months
Average time to close pull requests: about 1 hour
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 1.52
Average comments per pull request: 1.5
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

llrs (28)

Pull Request Authors

llrs (1)
davidmasp (1)

Top Labels

Issue Labels

enhancement (18) bug (5) question (2) Bioconductor (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- bioconductor 18,922 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 5
Total maintainers: 1

bioconductor.org: BioCor

Functional similarities

Homepage: https://bioconductor.org/packages/BioCor https://llrs.github.io/BioCor/
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/BioCor/inst/doc/BioCor.pdf
License: MIT + file LICENSE
Latest release: 1.32.0
published 9 months ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 18,922 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 0.0%

Stargazers count: 7.3%

Average: 16.5%

Forks count: 18.4%

Downloads: 56.9%

Maintainers (1)

lluis.revilla@gmail.com

Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/update-citation-cff.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

DESCRIPTION cran

R >= 3.4.0 depends
BiocParallel * imports
GSEABase * imports
Matrix * imports
methods * imports
BiocStyle * suggests
DESeq2 * suggests
GOSemSim * suggests
Hmisc * suggests
WGCNA * suggests
airway * suggests
boot * suggests
knitr >= 1.35 suggests
org.Hs.eg.db * suggests
reactome.db * suggests
rmarkdown * suggests
spelling * suggests
targetscan.Hs.eg.db * suggests
testthat * suggests