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The Top 23 Python Microbiome Open Source Projects

Open source projects categorized as Python Microbiome
Categories > Microbiome
Metagem ⭐ 155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
most recent commit 4 months ago
Qiita ⭐ 118
Qiita - A multi-omics databasing effort
total releases 3most recent commit 4 months ago
Micom ⭐ 73
Python package to study microbial communities using metabolic modeling.
dependent packages 1total releases 101most recent commit 4 months agopypi micom} Downloads
Ganon ⭐ 73
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
most recent commit 3 months ago
Deepmicrobes ⭐ 61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
most recent commit 2 years ago
Gemelli ⭐ 60
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
most recent commit 3 months ago
Woltka ⭐ 58
Woltka: a versatile meta'omic data classifier
total releases 4most recent commit 4 months ago
Emperor ⭐ 52
Emperor a tool for the analysis and visualization of large microbial ecology datasets
total releases 34most recent commit 10 months ago
Redbiom ⭐ 42
Sample search by metadata and features
dependent packages 1total releases 10most recent commit 8 months agopypi redbiom} Downloads
Microbiomehd ⭐ 40
Cross-disease comparison of case-control gut microbiome studies
most recent commit 5 years ago
Mmlong2 ⭐ 26
An all-in-one genome-centric metagenomics workflow using long reads
most recent commit 7 months ago
Q2 Qemistree ⭐ 24
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
most recent commit a year ago
Stag Mwc ⭐ 24
StaG Metagenomic Workflow Collaboration
most recent commit 3 months ago
Ghost Tree ⭐ 23
creating hybrid-gene phylogenetic trees for diversity analyses
most recent commit 2 years ago
Nmdc Schema ⭐ 23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
dependent packages 1total releases 70most recent commit 3 months agopypi nmdc-schema} Downloads
Calour ⭐ 23
exploratory and interactive microbiome analyses based on heatmaps
most recent commit a year ago
Mitre ⭐ 22
The Microbiome Interpretable Temporal Rule Engine
most recent commit 4 years ago
Birdman ⭐ 21
Bayesian Inferential Regression for Differential Microbiome Analysis
most recent commit 4 months ago
Super Focus ⭐ 19
A tool for agile functional analysis of shotgun metagenomic data
total releases 10most recent commit 3 months ago
Amon ⭐ 17
Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data
total releases 3most recent commit 3 months ago
Microbiome Mvib ⭐ 16
Microbiome-based disease prediction with multimodal variational information bottlenecks, Grazioli et al., PLOS Computational Biology 2022
most recent commit 2 years ago
Metasub_cap ⭐ 16
A comprehensive pipeline for short read metagenomic data
most recent commit 4 years ago
Micone ⭐ 15
The Microbial Co-occurrence Network Explorer
total releases 20most recent commit 7 months ago
The 3 Most Depended On Python Microbiome Open Source Projects
Nmdc Schema ⭐ 23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
dependent packages 1total releases 70latest release June 16, 2022most recent commit 3 months agopypi nmdc-schema} Downloads
Micom ⭐ 73
Python package to study microbial communities using metabolic modeling.
dependent packages 1total releases 101latest release October 29, 2023most recent commit 4 months agopypi micom} Downloads
Redbiom ⭐ 42
Sample search by metadata and features
dependent packages 1total releases 10latest release December 20, 2022most recent commit 8 months agopypi redbiom} Downloads
The 10 Latest Releases In Python Microbiome Open Source Projects
Micom ⭐ 73
Python package to study microbial communities using metabolic modeling.
dependent packages 1total releases 101latest release October 29, 2023most recent commit 4 months agopypi micom} Downloads
Woltka ⭐ 58
Woltka: a versatile meta'omic data classifier
total releases 4latest release December 26, 2022most recent commit 4 months ago
Redbiom ⭐ 42
Sample search by metadata and features
dependent packages 1total releases 10latest release December 20, 2022most recent commit 8 months agopypi redbiom} Downloads
Qupid ⭐ 7
Case-control matching for microbiome data
total releases 3latest release June 23, 2022most recent commit 2 years ago
Nmdc Schema ⭐ 23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
dependent packages 1total releases 70latest release June 16, 2022most recent commit 3 months agopypi nmdc-schema} Downloads
Xebec ⭐ 5
Snakemake pipeline for microbiome diversity effect size benchmarking
total releases 2latest release June 08, 2022most recent commit a year ago
Super Focus ⭐ 19
A tool for agile functional analysis of shotgun metagenomic data
total releases 10latest release April 11, 2022most recent commit 3 months ago
Micone ⭐ 15
The Microbial Co-occurrence Network Explorer
total releases 20latest release April 05, 2022most recent commit 7 months ago
Microbiome Toolbox ⭐ 8
Early Life Microbiome Toolbox
total releases 12latest release February 24, 2022most recent commit 4 months ago
Focus ⭐ 5
FOCUS: An Agile Profiler for Metagenomic Data
total releases 5latest release December 28, 2021most recent commit 2 years ago
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