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Experiments

Open Sustainable Technology

https://github.com/BigDataBiology/SemiBin

SemiBin: metagenomics binning with self-supervised deep learning
assembly-binning bioinformatics deep-learning metagenomics self-supervised-learning
Added: about 1 year ago - Last Synced: 11 months ago - Created: November 18, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 478
  • Committers: 6
  • Issues: 94
  • Pull Requests: 37
  • Owner: BigDataBiology
  • Stars: 101
  • Forks: 11
  • Packages: 1
  • Downloads: 107
https://github.com/vini2/phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
assembly-graphs bacteriophages bioinformatics genomics metagenomics
Added: over 1 year ago - Last Synced: 11 months ago - Created: July 21, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 545
  • Committers: 2
  • Issues: 37
  • Pull Requests: 15
  • Owner: Vini2
  • Stars: 64
  • Forks: 6
  • Packages: 1
  • Downloads: 57
https://github.com/gibsramen/qadabra

Snakemake workflow for comparison of differential abundance ranks
bioinformatics differential-abundance machine-learning metagenomics microbiome pipeline snakemake workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: May 04, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 60
  • Committers: 3
  • Issues: 16
  • Pull Requests: 23
  • Owner: biocore
  • Stars: 13
  • Forks: 4
  • Packages: 1
  • Downloads: 8
https://github.com/biocore/qadabra

Snakemake workflow for comparison of differential abundance ranks
bioinformatics differential-abundance machine-learning metagenomics microbiome pipeline snakemake workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: May 04, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 96
  • Committers: 4
  • Issues: 41
  • Pull Requests: 51
  • Owner: biocore
  • Stars: 13
  • Forks: 4
  • Packages: 0
https://github.com/fpusan/superpang

Non-redundant pangenome assemblies from multiple genomes or bins
bioinformatics genomics metagenomics pangenome
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 14, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 89
  • Committers: 1
  • Issues: 11
  • Pull Requests: 1
  • Owner: fpusan
  • Stars: 13
  • Forks: 2
  • Packages: 1
  • Downloads: 25
https://github.com/WrightonLabCSU/DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
annotation bioinformatics genomics metagenome-assembled-genomes metagenomics microbiome viral-genomics viral-metagenomics
Added: over 1 year ago - Last Synced: 11 months ago - Created: February 11, 2019

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 765
  • Committers: 18
  • Issues: 165
  • Pull Requests: 12
https://github.com/unipept/umgap

A taxonomic classifier for shotgun metagenomics reads
metagenomics taxonomy
Added: over 1 year ago - Last Synced: 11 months ago - Created: January 01, 2017

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Rust
  • Commits: 592
  • Committers: 15
  • Issues: 5
  • Pull Requests: 2
  • Owner: unipept
  • Stars: 10
  • Forks: 6
  • Packages: 1
  • Downloads: 1,876