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Open Source Science

https://github.com/biojulia/singlecellprojections.jl

Analysis of Single Cell Expression data in Julia

https://github.com/biojulia/singlecellprojections.jl

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    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
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary

Keywords from Contributors

biology bioinformatics julialang numerical programming-language biojulia fastq fastq-files fastq-format
Last synced: 11 months ago · JSON representation

Repository

Analysis of Single Cell Expression data in Julia

Basic Info
  • Host: GitHub
  • Owner: BioJulia
  • License: other
  • Language: Julia
  • Default Branch: main
  • Size: 1.41 MB
Statistics
  • Stars: 21
  • Watchers: 3
  • Forks: 3
  • Open Issues: 4
  • Releases: 21
Created over 3 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.md

SingleCellProjections.jl

Stable Dev Build Status Coverage

SingleCellProjections.jl is an easy to use and powerful package for analysis of Single Cell Expression data in Julia. It is faster and uses less memory than existing solutions since the data is internally represented as expressions of sparse and low rank matrices, instead of storing huge dense matrices. In particular, it efficiently performs PCA (Principal Component Analysis), a natural starting point for downstream analysis, and supports both standard workflows and projections onto a base data set.

Installation

Install SingleCellProjections.jl by running the following commands in Julia:

julia using Pkg Pkg.add("SingleCellProjections")

Threading

SingleCellProjections.jl relies heavily on threading. Please make sure to enable threading in Julia to dramatically improve computation speed.

Tutorial

Here is a tutorial, showcasing SingleCellProjections.jl functionality using a PBMC (Peripheral Blood Mononuclear Cell) data set.

force_layout

Force layout plot of the PBMC data.

Documentation

For more information, please refer to the documentation.

Owner

  • Name: BioJulia
  • Login: BioJulia
  • Kind: organization

Bioinformatics and Computational Biology in Julia

GitHub Events

Total
  • Create event: 4
  • Commit comment event: 3
  • Release event: 2
  • Watch event: 5
  • Issue comment event: 10
  • Push event: 40
  • Pull request event: 2
Last Year
  • Create event: 4
  • Commit comment event: 3
  • Release event: 2
  • Watch event: 5
  • Issue comment event: 10
  • Push event: 40
  • Pull request event: 2

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 192
  • Total Committers: 4
  • Avg Commits per committer: 48.0
  • Development Distribution Score (DDS): 0.016
Past Year
  • Commits: 19
  • Committers: 1
  • Avg Commits per committer: 19.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Rasmus Henningsson r****n@g****m 189
Tim Holy t****y@g****m 1
Kevin Bonham k****m@g****m 1
Michael Persico m****o@g****m 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 7
  • Total pull requests: 14
  • Average time to close issues: 2 days
  • Average time to close pull requests: 7 days
  • Total issue authors: 6
  • Total pull request authors: 4
  • Average comments per issue: 3.29
  • Average comments per pull request: 0.43
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 3
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 10 days
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 5.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kescobo (2)
  • pmodv (1)
  • pywugate (1)
  • aadimator (1)
  • rasmushenningsson (1)
  • akhst7 (1)
Pull Request Authors
  • github-actions[bot] (8)
  • rasmushenningsson (6)
  • M-PERSIC (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • julia 3 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 21
juliahub.com: SingleCellProjections

Analysis of Single Cell Expression data in Julia

  • Versions: 21
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 3 Total
Rankings
Dependent repos count: 9.9%
Average: 24.4%
Dependent packages count: 38.9%
Last synced: 11 months ago

Dependencies

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.github/workflows/TagBot.yml actions
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.github/workflows/CompatHelper.yml actions