Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
2 of 12 committers (16.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Multiview Intercellular SpaTial modeling framework
Basic Info
- Host: GitHub
- Owner: saezlab
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://saezlab.github.io/mistyR/
- Size: 126 MB
Statistics
- Stars: 64
- Watchers: 2
- Forks: 12
- Open Issues: 3
- Releases: 12
Topics
Metadata Files
README.md
MISTy - Multiview Intercellular SpaTial modeling framework 
Overview
The advancement of technologies for measurement of highly multiplexed spatial data require the development of scalable methods that can leverage the availability of the spatial context. Multiview Intercellular SpaTial modeling framework (MISTy) is an explainable machine learning framework for knowledge extraction and analysis of single-cell, highly multiplexed, spatially resolved data.
MISTy facilitates an in-depth understanding of marker interactions by profiling the intra- and intercellular relationships. MISTy is a flexible framework able to process a custom number of views. Each of these views can describe a different spatial context, i.e., define a relationship among the observed expressions of the markers, such as intracellular regulation or paracrine regulation. However, the views can also capture cell-type specific relationships, capture relations between functional footprints or focus on relations between different anatomical regions. Each MISTy view is considered as a potential source of variability in the measured marker expressions. Each MISTy view is then analyzed for its contribution to the total expression of each marker and is explained in terms of the interactions with other measurements that led to the observed contribution. Our approach is modular, easily parallelizable and thus scalable to samples with millions of cells and thousands of measured markers.
mistyR is a R package implementing MISTy.
System Requirements
mistyR requires a standard configuration and enough RAM to store the analyzed dataset and to support in-memory operations.
The package requires R version 4.0 or higher. This package is developed on macOS Big Sur. The package should be compatible with Windows, Linux and maxOS operating systems.
Installation
Install from Bioconductor:
```r
install.packages("BiocManager")
BiocManager::install("mistyR") ```
You can install the latest stable and development versions from GitHub with remotes:
- stable
```r
install.packages("remotes")
remotes::install_github("saezlab/mistyR") ```
- development
R
remotes::install_github("saezlab/mistyR@devel")
Docker
For the released and the latest stable and development versions we also provide Docker images based on the Rocker project - rocker/r-base image.
To create and start a container from the latest docker image and run R in interactive mode:
bash
docker run -it tanevski/mistyr:latest
Usage
Start by reading vignette("mistyR") to learn how to run mistyR. To learn how to use the package with commonly used objects for spatial omics data see the articles.
Example pipelines and synthetic data for mistyR are also available from this repository. To run mistyR on the provided synthetic data run the script synthetic_pipeline.R.
Citation
If you use mistyR for your research please cite the following publication:
Jovan Tanevski, Ricardo Omar Ramirez Flores, Attila Gabor, Denis Schapiro, Julio Saez-Rodriguez. Explainable multiview framework for dissecting spatial relationships from highly multiplexed data. Genome Biology 23, 97 (2022). https://doi.org/10.1186/s13059-022-02663-5
Owner
- Name: Saez Lab
- Login: saezlab
- Kind: organization
- Email: pub.saez@uni-heidelberg.de
- Location: Germany
- Website: saezlab.org
- Repositories: 241
- Profile: https://github.com/saezlab
Institute for Computational Biomedicine - Julio Saez-Rodriguez's group
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 13
- Watch event: 14
- Issue comment event: 6
- Fork event: 1
Last Year
- Create event: 1
- Release event: 1
- Issues event: 13
- Watch event: 14
- Issue comment event: 6
- Fork event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jovan Tanevski | t****i@g****m | 308 |
| schae211 | s****1@m****u | 54 |
| Nitesh Turaga | n****a@g****m | 6 |
| J Wokaty | j****y@s****u | 4 |
| Christian | c****8@g****m | 3 |
| deeenes | t****s@g****m | 3 |
| Olga Ivanova | i****9@g****m | 2 |
| J Wokaty | j****y | 2 |
| Jovan Tanevski | 4****i | 2 |
| Philipp SL Schäfer | 6****1 | 1 |
| Nathan Steenbuck | 7****k | 1 |
| NP | N****c | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 21
- Total pull requests: 26
- Average time to close issues: about 2 months
- Average time to close pull requests: 28 days
- Total issue authors: 18
- Total pull request authors: 10
- Average comments per issue: 1.9
- Average comments per pull request: 0.69
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 5
- Average time to close issues: about 2 months
- Average time to close pull requests: about 6 hours
- Issue authors: 6
- Pull request authors: 1
- Average comments per issue: 1.83
- Average comments per pull request: 0.8
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Jwong684 (2)
- HenrikBengtsson (2)
- LynnChan99 (2)
- deconvolute (2)
- Li-ZhiD (1)
- YaobangWang (1)
- lengfei5 (1)
- archanabhardwaj (1)
- wangyiqing50 (1)
- CAUiKUN (1)
- whitneyt1 (1)
- spatts14 (1)
- Pentayouth (1)
- zhumengyan (1)
- Peasent007 (1)
Pull Request Authors
- leotenshii (8)
- schae211 (5)
- ivanovaos (5)
- christianholland (3)
- jtanevski (3)
- gabora (1)
- nathansteenbuck (1)
- Nic-Nic (1)
- deeenes (1)
- roramirezf (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 9,285 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: mistyR
Multiview Intercellular SpaTial modeling framework
- Homepage: https://saezlab.github.io/mistyR/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/mistyR/inst/doc/mistyR.pdf
- License: GPL-3
-
Latest release: 1.16.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
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