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SimBu

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data

https://github.com/omnideconv/simbu

Science Score: 49.0%

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
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 10 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.8%) to scientific vocabulary

Keywords from Contributors

transcriptomics single-cell microscopy particles bioconductor-package bioconductor anndata bioinformatics genomics tracking
Last synced: 7 months ago · JSON representation

Repository

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data

Basic Info
Statistics
  • Stars: 17
  • Watchers: 5
  • Forks: 1
  • Open Issues: 7
  • Releases: 0
Created almost 5 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



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

# SimBu


[![tests](https://github.com/omnideconv/SimBu/actions/workflows/test.yml/badge.svg)](https://github.com/omnideconv/SimBu/actions/workflows/test.yml)
[![license](https://img.shields.io/badge/license-LGPLv3-blue.svg)](https://github.com/omnideconv/SimBu/blob/master/LICENSE.md)
[![docs](https://img.shields.io/badge/docs-pkgdown-blue.svg)](https://omnideconv.github.io/SimBu)
[![Codecov test coverage](https://codecov.io/gh/omnideconv/SimBu/branch/master/graph/badge.svg)](https://app.codecov.io/gh/omnideconv/SimBu?branch=master)


The goal of SimBu is to simulate pseudo-bulk RNAseq datasets with variable cell-type fractions baed on public or private single-cell RNAseq datasets.

## Installation

To install the developmental version of the package, run:

```{r, eval=FALSE}
install.packages("devtools")
devtools::install_github("omnideconv/SimBu")
```

To install from Bioconductor:

```{r, eval=FALSE}
if (!require("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install("SimBu")
```

## Usage

Create a dataset-object with local data and simulate a pseudo-bulk dataset

```{r example, eval=FALSE}
library(SimBu)
# use local data to build dataset
dataset <- dataset(annotation = annotation_dataframe, count_matrix = expression_matrix, name = "test_dataset")
simulation <- simulate_bulk(data = dataset, scenario = "random", scaling_factor = "NONE")
```


For more detailed usage instructions, check out [Getting started](http://omnideconv.org/SimBu/articles/simulator_documentation.html). 

You can find more information on the simulation setup and mRNA bias in our [SimBu publication](https://doi.org/10.1093/bioinformatics/btac499).

Owner

  • Name: omnideconv
  • Login: omnideconv
  • Kind: organization

GitHub Events

Total
  • Watch event: 5
  • Push event: 13
  • Create event: 1
Last Year
  • Watch event: 5
  • Push event: 13
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 222
  • Total Committers: 10
  • Avg Commits per committer: 22.2
  • Development Distribution Score (DDS): 0.315
Past Year
  • Commits: 15
  • Committers: 2
  • Avg Commits per committer: 7.5
  • Development Distribution Score (DDS): 0.133
Top Committers
Name Email Commits
Alexander Dietrich a****h@n****e 152
alex-d13 d****0@g****m 23
Alexander Dietrich 4****3 19
Gregor Sturm m****l@g****e 10
Alexander Dietrich a****h@a****e 7
Federico Marini m****f@u****e 4
J Wokaty j****y@s****u 2
pre-commit-ci[bot] 6****] 2
omnideconv-bot o****t 2
grst g****t 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 uni-mainz.de: 1 alfred.exbio.wzw.tum.de: 1 gregor-sturm.de: 1 norm.exbio.wzw.tum.de: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 37
  • Total pull requests: 16
  • Average time to close issues: 4 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 12
  • Total pull request authors: 4
  • Average comments per issue: 7.43
  • Average comments per pull request: 0.88
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 1
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
  • alex-d13 (13)
  • grst (8)
  • FFinotello (5)
  • ZheFrench (2)
  • mea2712 (1)
  • MengjurJ (1)
  • orange-whale (1)
  • arielah (1)
  • slieped (1)
  • AlmogAngel (1)
  • mlist (1)
  • saketkc (1)
Pull Request Authors
  • alex-d13 (11)
  • federicomarini (4)
  • pre-commit-ci[bot] (1)
  • grst (1)
Top Labels
Issue Labels
bug (3) enhancement (2) question (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 6,884 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: SimBu

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 6,884 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 9.8%
Forks count: 18.4%
Average: 24.6%
Downloads: 94.6%
Maintainers (1)
alex.dietrich@tum.de
Last synced: 8 months ago

Dependencies

DESCRIPTION cran
  • BiocParallel * imports
  • Matrix >= 1.3.3 imports
  • RColorBrewer * imports
  • RCurl * imports
  • SummarizedExperiment * imports
  • basilisk * imports
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  • dplyr * imports
  • ggplot2 * imports
  • methods * imports
  • phyloseq * imports
  • proxyC * imports
  • reticulate * imports
  • sparseMatrixStats * imports
  • tidyr * imports
  • tools * imports
  • Seurat * suggests
  • curl * suggests
  • knitr * suggests
  • matrixStats * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
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  • actions/checkout v2 composite
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.github/workflows/pkgdown.yml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
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.github/workflows/test-coverage.yml actions
  • actions/checkout v2 composite
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.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite