Science Score: 77.0%
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 1 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary
Repository
Metagenomic Binning Algorithm
Basic Info
- Host: GitHub
- Owner: rhysnewell
- License: bsd-3-clause
- Language: Rust
- Default Branch: main
- Size: 4.75 MB
Statistics
- Stars: 47
- Watchers: 5
- Forks: 3
- Open Issues: 11
- Releases: 22
Metadata Files
README.md
Rosella
Rosella is a metagenomic binning algorithm using UMAP and HDBSCAN. It is written in Rust with a python component that handles calls to UMAP and HDBSCAN. Rosella aims to be as user friendly as possible with multiple usage modes and installation methods.
Please note that Rosella is under active development with new commits often providing much improved results. If you would like
the most up to date version of Rosella please pull the code from dev branch. Hopefully releases will stabilise very soon.
Quick Install
Option 1: Conda
It's recommended that you create a new environment to ensure conda can correctly handle of the rosella's dependencies:
bash
conda create -n rosella -c bioconda rosella
conda activate rosella
rosella --version
Option 2: Install manually
After cloning the repo with rust and cargo installed on your system
bash
cd rosella
cargo install --path .
Create the conda environment
bash
mamba env create -f rosella.yml -n rosella
mamba activate rosella
rosella --help
Documentation
Please refer to documentation for installation and usage instructions.
Owner
- Name: Rhys Newell
- Login: rhysnewell
- Kind: user
- Location: Sydney, Australia
- Company: Microba LifeSciences
- Website: rhysnewell.github.io
- Twitter: rhysnewell
- Repositories: 11
- Profile: https://github.com/rhysnewell
Bioinformatics Software Engineer @ Microba. Awaiting for my PhD to be examined. Specialises in software development and analysis of big genomic data
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Newell
given-names: Rhys J. P.
orcid: https://orcid.org/0000-0002-1300-6116
- family-names: Tyson
given-names: Gene W.
orcid: https://orcid.org/0000-0001-8559-9427
- family-names: Woodcroft
given-names: Ben J.
orcid: https://orcid.org/0000-0003-0670-7480
title: "Rosella: Metagenomic binning using UMAP and HDBSCAN"
version: 0.5.3
doi: 10.5281/zenodo.10460259
date-released: 2023-11-05
GitHub Events
Total
- Issues event: 4
- Watch event: 8
- Delete event: 1
- Issue comment event: 4
- Push event: 4
- Pull request event: 4
- Create event: 2
Last Year
- Issues event: 4
- Watch event: 8
- Delete event: 1
- Issue comment event: 4
- Push event: 4
- Pull request event: 4
- Create event: 2
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Rhys Newell | r****l@h****u | 195 |
| Rhys Newell | r****l@m****m | 5 |
| Ben Woodcroft | b****t@g****m | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 36
- Total pull requests: 25
- Average time to close issues: 5 months
- Average time to close pull requests: about 22 hours
- Total issue authors: 25
- Total pull request authors: 2
- Average comments per issue: 4.81
- Average comments per pull request: 0.04
- Merged pull requests: 25
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 3
- Average time to close issues: 6 days
- Average time to close pull requests: less than a minute
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 1.25
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jvollme (3)
- michoug (3)
- jianshu93 (3)
- Rridley7 (2)
- wwood (2)
- aljazdzy (2)
- Valentin-Bio (2)
- Valentin-Bio-zz (1)
- gabrieleghiotto (1)
- schmigle (1)
- dpryan79 (1)
- alienzj (1)
- greenmna (1)
- StevenJRobbins (1)
- mmac0026 (1)
Pull Request Authors
- rhysnewell (26)
- wwood (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cargo 6,140 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
crates.io: rosella
Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN
- Homepage: https://rhysnewell.github.io/rosella/
- Documentation: https://docs.rs/rosella/
- License: GPL-3.0
-
Latest release: 0.5.4
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- assert_cli 0.6.* development
- ansi_term 0.12.1
- bio 0.35.0
- bio-types 0.12.0
- bird_tool_utils 0.3.0
- clap 2
- csv 1
- derive-new 0.5
- derive_builder 0.9
- env_logger 0.6
- galah 0.3.0
- glob 0.3.*
- indicatif *
- itertools 0.8
- lazy_static 1.3.0
- log 0.4
- ndarray 0.15.3
- ndarray-npy 0.8.0
- needletail 0.4.1
- nix 0.24
- openssl 0.10
- openssl-sys 0.9
- ordered-float 1
- pest 2
- pest_derive 2
- rand 0.6
- rayon 1.5.1
- rust-htslib 0.38.2
- scoped_threadpool *
- seq_io 0.3.*
- serde 1
- serde_derive 1
- serde_json 1
- serde_yaml 0.8
- statrs 0.13
- strum 0.17.1
- strum_macros 0.17.1
- tempdir 0.3
- tempfile 3.0
- actions/checkout master composite
- crazy-max/ghaction-github-pages v3.0.0 composite
- actions/checkout main composite
- actions/upload-artifact v2 composite
- marvinpinto/action-automatic-releases latest composite
- master-atul/tar-action v1.0.2 composite
- rhysnewell/rust-cargo-musl-action v0.1.20 composite