micutio/innit

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

Language: Rust - Size: 3.35 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 46 - Forks: 3

YuLab-SMU/MMINP

Microbe-Metabolite INteractions-based metabolic profiles Predictor

Language: R - Size: 11.8 MB - Last synced at: 26 days ago - Pushed at: about 2 years ago - Stars: 13 - Forks: 4

amarinderthind/decontaminer

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: 1.45 MB - Last synced at: 23 days ago - Pushed at: 24 days ago - Stars: 9 - Forks: 0

email-clm/CLM-Microbe

This is the code repository for CLM-Microbe model.

Language: Fortran - Size: 64.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 13

SysBioChalmers/ecFactory

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

Language: MATLAB - Size: 524 KB - Last synced at: 16 days ago - Pushed at: 2 months ago - Stars: 8 - Forks: 4

BCCDC-PHL/fluflo

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

Language: Nextflow - Size: 1.59 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - 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 at: 10 months ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 1

BCCDC-PHL/WasteFlow

Nextflow pipeline for pathogen surveillance in wastewater

Language: Nextflow - Size: 956 KB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 5 - Forks: 1

hip-satomi/ObiWan-Microbi

Omero based integrated Workflow for annotating Microbes in the Cloud

Language: Dockerfile - Size: 12.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

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 at: over 1 year ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 7

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 at: about 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

cguccione/NeutralEvolutionModeling

Neutral evolution modeling of microbes.

Language: Jupyter Notebook - Size: 2.55 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

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 at: about 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

RoshniRanaDS27/Belly_Button_Biodiversity_INTERACTIVE_DASHBOARD

INTERACTIVE DASHBOARD to explore the Belly Button Biodiversity datasetLinks to an external site., which catalogs the microbes that colonize human navels.

Language: JavaScript - Size: 77.1 KB - Last synced at: 9 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

JoshuaIszatt/bakorder

Python script to reorder bacterial genomes from bakta output

Language: Python - Size: 15.6 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

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 at: about 1 month ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 2

pbradleylab/phylogenize

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

Language: HTML - Size: 23.3 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

bioatmosphere/NM-GHGs

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

Size: 2.93 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

kenan-erol/MicrobeClassification

Classification model predicting the type of microbe from provided features

Language: Jupyter Notebook - Size: 1.18 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ArjunChakrawal/Stoichiometry-and-Thermodynamics

This repository contains python code used to create figures in the accompanying manuscript.

Language: Python - Size: 16.5 MB - Last synced at: about 1 year ago - Pushed at: almost 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 at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - 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 at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 2

CALeDNA/POUR

Size: 40.6 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

kk-deng/Biodiversity-Dashboard-Plotly

Build an interactive dashboard to explore the Belly Button Biodiversity dataset, which catalogues the microbes that colonize human navels by using Plotly and D3.js libraries.

Language: JavaScript - Size: 326 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - 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 at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

knowledgebaum/periodictable_node

Trying out Node with Express using the periodic table of microbes. See notes in HTML for more details.

Last synced at: 9 months ago - Stars: 0 - Forks: 0