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scDiffCom

Difference in Intercellular Communication from scRNA-seq data

https://github.com/cyrillagger/scdiffcom

Science Score: 20.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: nature.com
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Difference in Intercellular Communication from scRNA-seq data

Basic Info
Statistics
  • Stars: 22
  • Watchers: 4
  • Forks: 1
  • Open Issues: 3
  • Releases: 0
Created over 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



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

# scDiffCom


[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![CRAN status](https://www.r-pkg.org/badges/version/scDiffCom)](https://CRAN.R-project.org/package=scDiffCom)
[![Codecov test coverage](https://codecov.io/gh/CyrilLagger/scDiffCom/branch/master/graph/badge.svg)](https://app.codecov.io/gh/CyrilLagger/scDiffCom?branch=master)
[![R-CMD-check](https://github.com/CyrilLagger/scDiffCom/workflows/R-CMD-check/badge.svg)](https://github.com/CyrilLagger/scDiffCom/actions)


scDiffCom stands for "single-cell Differential Communication" and infers 
changes in intercellular communication between two biological 
conditions from scRNA-seq data (as [Seurat](https://satijalab.org/seurat/)
objects). The package relies on an internal collection of ligand-receptor 
interactions (available for human, mouse and rat) retrieved from seven 
curated databases.



Display LRI databases
* [CellChat](http://www.cellchat.org/)
* [CellPhoneDB](https://www.cellphonedb.org/)
* [CellTalkDB](http://tcm.zju.edu.cn/celltalkdb/)
* [connectomeDB2020](https://github.com/forrest-lab/NATMI)
* [ICELLNET](https://github.com/soumelis-lab/ICELLNET)
* [NicheNet](https://github.com/saeyslab/nichenetr)
* [SingleCellSignalR](https://www.bioconductor.org/packages/release/bioc/html/SingleCellSignalR.html)

 

## Installation

``` r
# Install the development version from GitHub
devtools::install_github("CyrilLagger/scDiffCom")

# Install release version from CRAN
install.packages("scDiffCom")
```

## Usage

As an introduction, please look at the
[documentation](https://cyrillagger.github.io/scDiffCom/) and this [vignette](https://cyrillagger.github.io/scDiffCom/articles/scDiffCom-vignette.html).

For a concrete and large-scale project that used scDiffCom, please look at
[scagecom.org](https://scagecom.org/), our murine atlas of
age-related changes in intercellular communication.


## Citation

Please consider reading and citing our Nature Aging paper:
[here](https://www.nature.com/articles/s43587-023-00514-x).

Owner

  • Name: Cyril Lagger
  • Login: CyrilLagger
  • Kind: user

Computational Scientist at Altos Labs

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 402
  • Total Committers: 3
  • Avg Commits per committer: 134.0
  • Development Distribution Score (DDS): 0.06
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Cyril Lagger l****l@g****m 378
ursueugen u****n@h****m 22
Cyril Lagger c****r@l****k 2
Committer Domains (Top 20 + Academic)
liverpool.ac.uk: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 13
  • Total pull requests: 9
  • Average time to close issues: 9 days
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 10
  • Total pull request authors: 2
  • Average comments per issue: 1.38
  • Average comments per pull request: 0.0
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: about 19 hours
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • CyrilLagger (4)
  • aosakwe (1)
  • alvarezprado (1)
  • trusha0911 (1)
  • lef2158 (1)
  • majeex233 (1)
  • Gesmira (1)
  • Brawni (1)
  • suanzaoren (1)
Pull Request Authors
  • CyrilLagger (8)
  • ursueugen (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 297 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: scDiffCom

Differential Analysis of Intercellular Communication from scRNA-Seq Data

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 297 Last month
Rankings
Stargazers count: 19.8%
Forks count: 28.8%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 36.1%
Downloads: 66.6%
Maintainers (1)
lagger.cyril@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • DelayedArray * imports
  • Seurat >= 4.0.0 imports
  • data.table * imports
  • future * imports
  • future.apply * imports
  • magrittr * imports
  • methods * imports
  • stats * imports
  • utils * imports
  • DT * suggests
  • GOSemSim * suggests
  • KEGGREST * suggests
  • RColorBrewer * suggests
  • SingleCellSignalR * suggests
  • biomaRt * suggests
  • covr * suggests
  • ggplot2 * suggests
  • igraph * suggests
  • kableExtra * suggests
  • knitr * suggests
  • ontoProc * suggests
  • ontologyIndex * suggests
  • pkgdown * suggests
  • plotly * suggests
  • rmarkdown * suggests
  • rrvgo * suggests
  • shiny * suggests
  • shinyWidgets * suggests
  • shinythemes * suggests
  • spelling * suggests
  • testthat >= 3.0.0 suggests
  • visNetwork * suggests