rira
The Rhesus Immune Reference Atlas: multi-tissue scRNA-seq atlas and code for cell type/state classification
Science Score: 67.0%
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 -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov, zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary
Repository
The Rhesus Immune Reference Atlas: multi-tissue scRNA-seq atlas and code for cell type/state classification
Statistics
- Stars: 8
- Watchers: 1
- Forks: 3
- Open Issues: 1
- Releases: 1
Metadata Files
README.md
Rhesus Immune Reference Atlas (RIRA): A multi-tissue single-cell landscape of immune cells
Table of Contents
Overview
RIRA is a multi-tissue single-cell RNA-seq atlas from Rhesus macaque cells, including data from 7 tissues and 47 animals. It provides highly annotated reference data, and a number of pipelines to assign cell type to your data using RIRA's built-in models. Finally, it includes pipelines to replicate the process used to generate RIRA's reference labels, which might be useful for generating a similar reference for another species.
The raw expression data are available, including a seurat object, through the NIH GEO database under accession GSE277821.
Please see our documentation for more detail and usage examples
Installation
```
Make sure to update your Rprofile to include Bioconductor repos, such as adding this line to ~/.Rprofile:
local({options(repos = BiocManager::repositories())})
Latest version:
devtools::install_github(repo = 'bimberlab/RIRA', ref = 'master', dependencies = TRUE, upgrade = 'always') ```
Pre-packaged Docker images with all needed dependencies installed can be found on our GitHub Packages page:
docker pull ghcr.io/bimberlab/rira:latest
Owner
- Name: Bimber Lab
- Login: BimberLab
- Kind: organization
- Repositories: 11
- Profile: https://github.com/BimberLab
Software created by the Bimber Lab of OHSU
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as follows."
title: "RIRA: Rhesus Immunome Reference Atlas"
authors:
- name: "Bimber Lab"
email: "bimber@ohsu.edu"
affiliation: "Oregon Health & Science University"
date-released: "2025-03-05"
version: "1.0.0"
repository-code: "https://github.com/BimberLab/RIRA"
license: "GPL-3"
url: "https://bimberlab.github.io/RIRA/"
GitHub Events
Total
- Create event: 17
- Issues event: 1
- Release event: 1
- Watch event: 4
- Delete event: 13
- Issue comment event: 5
- Push event: 101
- Pull request review event: 2
- Pull request review comment event: 2
- Pull request event: 25
- Fork event: 1
Last Year
- Create event: 17
- Issues event: 1
- Release event: 1
- Watch event: 4
- Delete event: 13
- Issue comment event: 5
- Push event: 101
- Pull request review event: 2
- Pull request review comment event: 2
- Pull request event: 25
- Fork event: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 11
- Average time to close issues: N/A
- Average time to close pull requests: about 11 hours
- Total issue authors: 1
- Total pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.18
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 11
- Average time to close issues: N/A
- Average time to close pull requests: about 11 hours
- Issue authors: 1
- Pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.18
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- bbimber (1)
- jccarado (1)
Pull Request Authors
- bbimber (11)
- eisascience (1)
- Chaunzwa-maker (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 4.1.0 depends
- UCell * depends
- scGate * depends
- DALEX * imports
- DALEXtra * imports
- DropletUtils * imports
- ExperimentHub * imports
- Matrix * imports
- Seurat * imports
- SeuratDisk * imports
- SingleCellExperiment * imports
- cFIT * imports
- caret * imports
- dplyr * imports
- egg * imports
- future * imports
- ggplot2 * imports
- knitr * imports
- methods * imports
- mlr3 * imports
- mlr3learners * imports
- naturalsort * imports
- patchwork * imports
- ranger * imports
- reticulate * imports
- stats * imports
- utils * imports
- SeuratData * suggests
- devtools * suggests
- testthat >= 2.1.0 suggests