Science Score: 54.0%
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
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○Academic publication links
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✓Committers with academic emails
2 of 8 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary
Keywords
Repository
Muon for Julia
Basic Info
- Host: GitHub
- Owner: scverse
- License: bsd-3-clause
- Language: Julia
- Default Branch: main
- Homepage: https://scverse.github.io/Muon.jl/dev
- Size: 1.11 MB
Statistics
- Stars: 27
- Watchers: 3
- Forks: 6
- Open Issues: 1
- Releases: 4
Topics
Metadata Files
README.md
Muon for Julia
Muon is originally a Python library to work with multimodal data. Muon.jl brings the ability to work with the same data structures to Julia.
Muon.jl implements I/O for .h5mu and .h5ad files as well as basic operations on the multimodal objects.
Introduction
Datasets can usually be represented as matrices with values for the variables measured in different samples, or observations. Variables and observations tend to have annotations attached to them, a typical example would be metadata annotating samples. Such a dataset with the matrix in its centre and different kinds of annotations associated with it can be stored conveniently in an annotated data object, AnnData for short.
Multimodal datasets are characterised by the variables coming from different generative processes. Each of these modalities is an annotated dataset by itself, but they can be managed and analyzed together within a MuData object.
Examples
MuData objects can be created from .h5mu files:
```julia using Muon
mdata = readh5mu("pbmc10k.h5mu"); ```
Individual modalities can be accessed directly by their name:
```julia mdata["rna"]
=> AnnData object 10110 ✕ 101001
```
Low-dimensional representations of the data can be plotted with the plotting library of choice:
```julia using DataFrames using GLMakie using AlgebraOfGraphics
df = DataFrame(LF1 = mdata.obsm["X_umap"][1,:], LF2 = mdata.obsm["X_umap"][2,:]);
data(df) * mapping(:LF1, :LF2) * visual(Scatter) |> draw ```
Muon.jl is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
Owner
- Name: scverse
- Login: scverse
- Kind: organization
- Website: https://scverse.org
- Twitter: scverse_team
- Repositories: 28
- Profile: https://github.com/scverse
Foundational tools for omics data in the life sciences
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Bredikhin"
given-names: "Danila"
orcid: "https://orcid.org/0000-0001-8089-6983"
- family-names: "Kats"
given-names: "Ilia"
orcid: "https://orcid.org/0000-0001-5220-5671"
title: "muon"
version: 1.0.0
date-released: 2021-06-01
url: "https://github.com/scverse/muon"
preferred-citation:
type: article
authors:
- family-names: "Bredikhin"
given-names: "Danila"
orcid: "https://orcid.org/0000-0001-8089-6983"
- family-names: "Kats"
given-names: "Ilia"
orcid: "https://orcid.org/0000-0001-5220-5671"
- family-names: "Stegle"
given-names: "Oliver"
orcid: "https://orcid.org/0000-0002-8818-7193"
doi: "10.1186/s13059-021-02577-8"
journal: "Genome Biology"
month: 2
title: "MUON: multimodal omics analysis framework"
year: 2022
GitHub Events
Total
- Watch event: 2
- Delete event: 2
- Issue comment event: 2
- Push event: 27
- Pull request review comment event: 2
- Pull request review event: 4
- Pull request event: 5
- Fork event: 1
- Create event: 3
Last Year
- Watch event: 2
- Delete event: 2
- Issue comment event: 2
- Push event: 27
- Pull request review comment event: 2
- Pull request review event: 4
- Pull request event: 5
- Fork event: 1
- Create event: 3
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ilia Kats | i****s@g****t | 119 |
| Danila Bredikhin | d****n@e****e | 48 |
| Daniel C. Jones | d****3@f****g | 8 |
| Wouter-Michiel Vierdag | w****v@h****m | 3 |
| Douglas Bates | d****s@g****m | 2 |
| jdm204 | j****4@c****k | 1 |
| Simon Bil | S****l@u****e | 1 |
| jdm204 | j****4@m****m | 1 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 17
- Total pull requests: 15
- Average time to close issues: about 2 months
- Average time to close pull requests: about 1 month
- Total issue authors: 9
- Total pull request authors: 7
- Average comments per issue: 2.0
- Average comments per pull request: 1.0
- Merged pull requests: 12
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 5
- Average time to close issues: 14 days
- Average time to close pull requests: 4 days
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 0.4
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- gtca (4)
- ilia-kats (3)
- orenbenkiki (3)
- zhanglab2008 (2)
- dmbates (1)
- lbotecur (1)
- ivirshup (1)
- JuliaTagBot (1)
- timholy (1)
Pull Request Authors
- dcjones (5)
- jdm204 (4)
- dmbates (4)
- ilia-kats (1)
- gtca (1)
- smnbl (1)
- jberkh (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- julia 15 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 4
juliahub.com: Muon
Muon for Julia
- Homepage: https://scverse.github.io/Muon.jl/dev
- Documentation: https://docs.juliahub.com/General/Muon/stable/
- License: BSD-3-Clause
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Latest release: 0.2.1
published over 1 year ago
Rankings
Dependencies
- JuliaRegistries/TagBot v1 composite
- actions/checkout v2 composite
- julia-actions/setup-julia latest composite
- actions/cache v2 composite
- actions/checkout v2 composite
- julia-actions/julia-runtest v1 composite
- julia-actions/setup-julia v1 composite