microbes

There are 26 repositories under microbes topic.

  • innit

    micutio/innit

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

    Language:Rust46533

  • YuLab-SMU/MMINP

    Microbe-Metabolite INteractions-based metabolic profiles Predictor

    Language:R13404
  • decontaminer

    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:Perl9270

  • email-clm/CLM-Microbe

    This is the code repository for CLM-Microbe model.

    Language:Fortran99113

  • BCCDC-PHL/fluflo

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

    Language:Nextflow8164

  • joshualiuxu/qcmi

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

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  • SysBioChalmers/ecFactory

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

    Language:MATLAB8114

  • hip-satomi/microbeSEG

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

    Language:Python75151

  • BCCDC-PHL/WasteFlow

    Nextflow pipeline for pathogen surveillance in wastewater

    Language:Nextflow5221

  • hip-satomi/ObiWan-Microbi

    Omero based integrated Workflow for annotating Microbes in the Cloud

    Language:Dockerfile4512

  • bioatmosphere/microbiome-drought-legacy

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

    Language:Jupyter Notebook3100

  • cguccione/NeutralEvolutionModeling

    Neutral evolution modeling of microbes.

    Language:Jupyter Notebook3201

  • TheJacksonLaboratory/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:Python2201

  • 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:Python1322

  • Gromulus-Romulus/Microbial-Metabolic-Network-Simulator

    Python simulation for visualizing the net geochemical outcomes of microbial metabolism - referred to here as "dead-end states." Poster presentation at Univ. Oregon Undergrad Symposium 2022.

    Language:Jupyter Notebook1100

  • 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:JavaScript1100

  • Asplund-Samuelsson/fitml

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

    Language:R0100
  • POUR

    CALeDNA/POUR

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  • jasoncr/Belly-Button-Biodiversity-Dashboard

    Javascript and D3 are used to create an interactive dashboard to explore a microbes on human subjects dataset.

    Language:JavaScript0200

  • kenan-erol/MicrobeClassification

    Classification model predicting the type of microbe from provided features

    Language:Jupyter Notebook0100

  • 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:JavaScript0100

  • 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:JavaScript0100

  • pbradleylab/phylogenize

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

    Language:HTML0280

  • ruthhinkle/belly-button-biodiversity

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

    Language:JavaScript0102

  • ArjunChakrawal/Stoichiometry-and-Thermodynamics

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

    Language:Python10

  • bioatmosphere/NM-GHGs

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

    10