Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: microbes

Repositories

pbradleylab/phylogenize

A tool for phylogenetic comparison and analysis of microbe including gene's environmental association

Language: HTML - Size: 23 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

BCCDC-PHL/WasteFlow

Nextflow pipeline for pathogen surveillance in wastewater

Language: Nextflow - Size: 837 KB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 4 - Forks: 0

ruthhinkle/belly-button-biodiversity

Interactive dashboard to explore the Belly Button Biodiversity dataset using Plotly for Javascript.

Language: JavaScript - Size: 341 KB - Last synced: 3 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 2

SysBioChalmers/ecFactory

A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism

Language: MATLAB - Size: 359 KB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 6 - Forks: 2

joshualiuxu/qcmi

To explore biotic associations of microbes at the community level. See the detailed package tutorial (https://joshualiuxu.github.io/).

Language: HTML - Size: 13.1 MB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 4 - Forks: 7

micutio/innit

A roguelike game where you play a micro organism inside a larger organism!

Language: Rust - Size: 3.35 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 46 - Forks: 3

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x

Language: Perl - Size: 1.44 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 6 - Forks: 0

YuLab-SMU/MMINP

Microbe-Metabolite INteractions-based metabolic profiles Predictor

Language: R - Size: 11.8 MB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 8 - Forks: 1

bioatmosphere/microbiome-drought-legacy

A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.

Language: Jupyter Notebook - Size: 329 MB - Last synced: 4 months ago - Pushed: about 1 year ago - Stars: 3 - Forks: 0

mocchicone/Plotly-Interactive-Dashboard

Using Plotly, JavaScript, d3, and Bootstrap, created an interactive dashboard to explore the Belly Button Biodiversity dataset, which catalogs the microbes that colonize human navels. The dataset reveals that a small handful of microbial species (also called operational taxonomic units, or OTUs, in the study) were present in more than 70% of people, while the rest were relatively rare.

Language: JavaScript - Size: 1.76 MB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

Asplund-Samuelsson/fitml

Classification of stressful microbial growth conditions using gene fitness data and support vector machines

Language: R - Size: 5.86 KB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

JoshuaIszatt/bakorder

Python script to reorder bacterial genomes from bakta output

Language: Python - Size: 15.6 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

hip-satomi/ObiWan-Microbi

Omero based integrated Workflow for annotating Microbes in the Cloud

Language: Dockerfile - Size: 12.4 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 4 - Forks: 1

BCCDC-PHL/fluflo

Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

Language: Nextflow - Size: 1.57 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 3 - Forks: 4

hip-satomi/microbeSEG

Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data

Language: Python - Size: 8.44 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1

bioatmosphere/NM-GHGs

Significance of non-microbial processes in organic matter decompositon in ecosystems across scales

Size: 2.93 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

TheJacksonLaboratory/MA-GenTA Fork of cometsong/MA-GenTA

Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.

Language: Python - Size: 18.5 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0