microbes

There are 3 repositories under microbes topic.

• innit

  micutio / innit

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

  dnagamegame-enginegeneticsinnitmicro-organismsmicrobesroguelikeroguelike-gameroguelikedevrust
  Language:Rust 45

• YuLab-SMU / MMINP

  Microbe-Metabolite INteractions-based metabolic profiles Predictor

  microbesmetabolitesmetabolite-prediction
  Language:R 12
• 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

  rnasequnmapped-ngs-datacontaminating-sequencesdecontaminer-pipelinengsdecontaminercontaminationcontamination-detectioninvestigationmicrobesinfectionssequencingbioinformaticsrna-seqvirusbacteriafungusvirusscancanceromics
  Language:Perl 8

• joshualiuxu / qcmi

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

  ecologymicrobesr
  Language:HTML 7

• SysBioChalmers / ecFactory

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

  cell-factoryenzyme-constraintsmetabolic-modelsmicrobes
  Language:MATLAB 7

• hip-satomi / microbeSEG

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

  cell-segmentationmicrobesnucleus-segmentationdeep-learningomerosegmentationtime-lapse-imaging
  Language:Python 6

• BCCDC-PHL / fluflo

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

  nextflowphylogeneticstreesauspicenextstrainmicrobes
  Language:Nextflow 4

• BCCDC-PHL / WasteFlow

  Nextflow pipeline for pathogen surveillance in wastewater

  nextflowfreyjamicrobessars-cov-2surveillancewastewater
  Language:Nextflow 4

• hip-satomi / ObiWan-Microbi

  Omero based integrated Workflow for annotating Microbes in the Cloud

  annotation-toolcell-segmentationdata-managementdeep-learningdockerhuman-in-the-loopomeroplatform-independentmicrobes
  Language:Dockerfile 4

• bioatmosphere / microbiome-drought-legacy

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

  microbesbacteriamicrobiomecommunityecologydroughtcarbonsoilsystemslegacyenzymeosmolytedementpydementmemorytradeoff
  Language:Jupyter Notebook 3

• cguccione / NeutralEvolutionModeling

  Neutral evolution modeling of microbes.

  microbesneutral-evolution
  Language:Jupyter Notebook 3

• 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.

  bioinformaticspipelinegenomeprobesequencemicrobiomencbi-blasttargetedmicrobesannotationpredictors
  Language:Python 2

• 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.

  probebioinformaticspipelinetargetedsequencencbi-blastmicrobiomegenomemicrobespredictorsannotation
  Language:Python 1

• 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.

  metabolismmicrobesode-solverpythonsimulation
  Language:Jupyter Notebook 1

• Asplund-Samuelsson / fitml

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

  microbessvm-classifier
  Language:R 0
• POUR

  CALeDNA / POUR

  biodiversitylosangelesriverenvironmentaldnadnametabarcodingmicrobesplantsanimalsprotistsalgaefungibacteriaarchaeavertebratesinvertebrates
  0

• jasoncr / Belly-Button-Biodiversity-Dashboard

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

  belly-buttondashboardmicrobes
  Language:JavaScript 0

• kenan-erol / MicrobeClassification

  Classification model predicting the type of microbe from provided features

  antibiotic-resistanceartificial-intelligencebacteriadata-sciencegenomesmicrobes
  Language:Jupyter Notebook 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.

  gauge-chartdashboard-pagebelly-buttonsmicrobesplotlyd3js
  Language:JavaScript 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.

  bootstrapd3dashboardjavascriptmicrobesotusplotly
  Language:JavaScript 0

• ruthhinkle / belly-button-biodiversity

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

  dashboardmicrobesmicrobial-speciesplotly
  Language:JavaScript 0

• ArjunChakrawal / Stoichiometry-and-Thermodynamics

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

  energeticsstoichiometrysoilmicrobesmodel
  Language:Python

• bioatmosphere / NM-GHGs

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

  biogeochemistryclimateenzymegreenhouse-gasesmicrobessoil-organic-mattersomabioticnon-microbialnm-ghgs

• pbradleylab / phylogenize

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

  evolutionary-genomicsmicrobesmicrobiologyphylogeneticspopulation-geneticsr-package
  Language:HTML