dyngen

Simulating single-cell data using gene regulatory networks 📠

https://github.com/dynverse/dyngen

Science Score: 23.0%

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
Found 5 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
1 of 8 committers (12.5%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (19.2%) to scientific vocabulary

Keywords

benchmarking single-cell single-cell-analysis single-cell-omics

Keywords from Contributors

bioinformatics scrna-seq bioconductor

Last synced: 6 months ago · JSON representation

Repository

Simulating single-cell data using gene regulatory networks 📠

Basic Info

Host: GitHub
Owner: dynverse
License: other
Language: HTML
Default Branch: master
Homepage: https://dyngen.dynverse.org
Size: 607 MB

Statistics

Stars: 75
Watchers: 2
Forks: 6
Open Issues: 20
Releases: 0

Topics

benchmarking single-cell single-cell-analysis single-cell-omics

Created almost 9 years ago · Last pushed almost 2 years ago

Metadata Files

Readme License

README.Rmd

---
output:
  github_document:
    html_preview: false
editor_options: 
  chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(fig.path = "man/figures/README_", warning=FALSE, message=FALSE, error=FALSE, echo = TRUE)

library(tidyverse)
submission_to_cran <- FALSE
```

# dyngen 



[![CRAN Status](https://www.r-pkg.org/badges/version/dyngen)](https://cran.r-project.org/package=dyngen)
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/dyngen)](https://cran.r-project.org/package=dyngen)
[![DOI](https://img.shields.io/badge/doi-10.1038%2Fs41467--021--24152--2-green)](https://doi.org/10.1038/s41467-021-24152-2)
[![R-CMD-check](https://github.com/dynverse/dyngen/workflows/R-CMD-check/badge.svg)](https://github.com/dynverse/dyngen/actions?query=workflow%3AR-CMD-check)
[![Coverage Status](https://app.codecov.io/gh/dynverse/dyngen/branch/master/graph/badge.svg)](https://app.codecov.io/gh/dynverse/dyngen?branch=master)


dyngen is a novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods.

dyngen is now published (CC-BY, [doi:10.1038/s41467-021-24152-2](https://doi.org/10.1038/s41467-021-24152-2)). Run `citation("dyngen")` to obtain the corresponding citation information. All source code for reproducing the results in this manuscript are available on [GitHub](https://github.com/dynverse/dyngen_manuscript).

```{r out.width = '60%', echo = FALSE}
knitr::include_graphics("man/figures/overview.png")
```

## Installation
dyngen should work straight out of the CRAN box by running `install.packages("dyngen")`. Having said that, you should definitely configure a few system variables for optimal speed. Check the [installation guide](https://dyngen.dynverse.org/articles/installation.html) for more information!

## Getting started

Check out [this guide](https://dyngen.dynverse.org/articles/getting_started.html) on how to get started with dyngen. You can find more guides by clicking any of the links below:

```{r vignettes, results='asis', echo=FALSE}
vign <- list.files("vignettes", pattern = "*.Rmd", recursive = TRUE)
walk(
  c(vign[!grepl("^advan", vign)], vign[grepl("^advan", vign)]),
  function(file) {
    title <- 
      read_lines(paste0("vignettes/", file)) %>% 
      keep(~grepl("^title: ", .)) %>% 
      gsub("title: \"(.*)\"", "\\1", .)
    vignette_name <- gsub("\\.Rmd", "", file)
    html_name <- gsub("\\.Rmd", ".html", file)
    
    cat("* [", title, "](https://dyngen.dynverse.org/articles/", html_name, ")\n", sep = "")
  }
)
```

## Latest changes

A full list of changes is available on our [changelog](https://dyngen.dynverse.org/news/index.html).

Owner

Name: dynverse: benchmarking, constructing and interpreting single-cell trajectories
Login: dynverse
Kind: organization
Location: The dynverse

Website: https://dynverse.org
Repositories: 15
Profile: https://github.com/dynverse

The dynverse is an open set of packages to benchmark, construct and interpret single-cell trajectories. See https://dynverse.org for an overview

GitHub Events

Total

Issues event: 1
Watch event: 4

Last Year

Issues event: 1
Watch event: 4

Committers

Last synced: over 2 years ago

All Time

Total Commits: 1,098
Total Committers: 8
Avg Commits per committer: 137.25
Development Distribution Score (DDS): 0.382

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Robrecht Cannoodt	r**d@g**m	679
Wouter Saelens	w**s@g**m	316
Robrecht Cannoodt	b**s@g**m	68
Robrecht Cannoodt	r**t@u**e	28
Louise Deconinck	l**k@g**m	4
Helena Todorov	h**t@h**r	1
Wouter Saelens	W**s@U**e	1
george-hall-ucl	g**l@u**k	1

Committer Domains (Top 20 + Academic)

ugent.be: 2 ucl.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 40
Total pull requests: 20
Average time to close issues: 4 months
Average time to close pull requests: 7 days
Total issue authors: 31
Total pull request authors: 4
Average comments per issue: 2.28
Average comments per pull request: 1.0
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

rcannood (3)
Pinolinoo (3)
koenvandenberge (2)
XiaPoppy (2)
spriyansh (2)
lila167 (2)
HectorRDB (2)
cameronraysmith (1)
No2Ross (1)
YinoZ (1)
cakeinspace (1)
masastat (1)
christinedien (1)
zouter (1)
mvinyard (1)

Pull Request Authors

rcannood (13)
zouter (4)
LouiseDck (2)
george-hall-ucl (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 329 last-month
Total docker downloads: 61

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 7
Total maintainers: 1

cran.r-project.org: dyngen

A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses

Homepage: https://dyngen.dynverse.org
Documentation: http://cran.r-project.org/web/packages/dyngen/dyngen.pdf
License: MIT + file LICENSE
Latest release: 1.0.5
published over 3 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 329 Last month
Docker Downloads: 61

Rankings

Stargazers count: 5.6%

Forks count: 9.7%

Dependent repos count: 24.2%

Average: 24.5%

Dependent packages count: 29.0%

Downloads: 53.9%

Maintainers (1)

rcannood@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
GillespieSSA2 >= 0.2.6 imports
Matrix * imports
assertthat * imports
dplyr * imports
dynutils >= 1.0.4 imports
ggplot2 * imports
ggraph >= 2.0 imports
ggrepel * imports
grDevices * imports
grid * imports
igraph * imports
lmds * imports
methods * imports
patchwork * imports
pbapply * imports
purrr * imports
rlang >= 0.4.1 imports
stats * imports
tibble * imports
tidygraph * imports
tidyr * imports
utils * imports
viridis * imports
R.rsp * suggests
Seurat * suggests
SingleCellExperiment >= 1.5.3 suggests
SummarizedExperiment * suggests
anndata * suggests
covr * suggests
dynwrap >= 1.2.0 suggests
rmarkdown * suggests
testthat * suggests

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

actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/check-r-package v1 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

.github/workflows/docker_build.yml actions

actions/checkout v2 composite

.github/workflows/pkgdown.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

.github/workflows/test_coverage.yml actions

actions/checkout v2 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

docker/Dockerfile docker

rocker/tidyverse 4.0.3 build

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

dyngen

Science Score: 23.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: dyngen

Rankings

Maintainers (1)

Dependencies