microbiota

There are 49 repositories under microbiota topic.

  • ggpicrust2

    cafferychen777/ggpicrust2

    Make Picrust2 Output Analysis and Visualization Easier

    Language:R120211916

  • david-barnett/microViz

    R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

    Language:R113510511

  • microsud/Tools-Microbiome-Analysis

    A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

    Language:CSS11312546

  • micom-dev/micom

    Python package to study microbial communities using metabolic modeling.

    Language:Python9754318

  • ycl6/16S-rDNA-V3-V4

    16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

    Language:R334718

  • mibwurrepo/Microbial-bioinformatics-introductory-course-Material-2018

    Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

    Language:R288720

  • ASaiM/framework

    Open-source opinionated Galaxy-based framework for microbiota analysis

    Language:HTML14607

  • microsud/dysbiosisR

    The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures

    Language:R14320

  • oschakoory/RiboTaxa

    RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

    Language:Shell8150

  • SchlossLab/Sze_CRCMetaAnalysis_mBio_2018

    Language:R7483

  • bdaisley/BEExact

    Improved bee microbiota characterization using routine 16S rRNA gene sequencing 🐝🧬

    6312

  • erictleung/phyloseq-cheatsheet

    :notebook: Minimal cheatsheet for functions in the phyloseq R package

    6100

  • HuaZou/MetaAnalysis_CRC

    Meta-analysis on human gut microbiota in Colorectal cancer

    Language:HTML5102

  • ycl6/16S-Demo

    Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output

    Language:R5205

  • Gabriele-Conti/KEGGSearch

    Comprehensive KEGG Data Retrieval Using Multiple Sources

    Language:R4100

  • microsud/Indian-gut-microbiota

    Data and analysis code for the Indian gut microbiota study

    Language:R4201

  • Headonpillow/16S_analysis

    A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

    Language:R3100

  • RIVM-IIV-Microbiome/biomeUtils

    biomeUtils is Module-01 of the RIVM-ToolBox. R pkg with common utilities for microbiome research done at the RIVM.

    Language:R3270

  • vaxherra/MicrobiomeSLE

    Microbiome Study of Lupus Patients

    Language:HTML3200

  • yanxianl/Li_AqFl2-Microbiota_ASM_2020

    Code for reproducing results in the paper: "Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon"

    Language:HTML3012

  • gletroadec/Projet_5.1

    Les études de métagénomiques mettent en évidence la présence et l'absence de différentes souches dans un microbiome. Pour résumer les abondances, on peut établir des graphes de co-occurence via : Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data, Janko Tackmann, Joao Frederico Matias Rodrigues, Christian von Mering. bioRxiv 390195; doi : https://doi.org/10.1101/390195 Cependant, ces techniques reposent sur des corrélations et non sur des causalités. Elles ne permettent pas de comprendre les interactions entre organismes. Pour cela, il est important d'intégrer une autre dimension comme les informations contenues dans les réseaux métaboliques des bactéries. Pour cela, certaines bases de données existent : Brunk E, Sahoo S, Zielinski DC, Altunkaya A, DrÀger A, Mih N, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. Nature Publishing Group; 2018 Mar;36(3):272-81 https://github.com/cdanielmachado/carveme/tree/master/carveme Ce projet vise à proposer une stratégie pour détecter les interactions via les échanges de métabolites via Flux Variability Analysis. La stratégie sera a tester sur des données de microbiotes intestinales fournies par le projet HMP.

    Language:Python2100

  • JerryPan2718/Microbiome-PTR

    Calculate Peak-to-Trough Ratio (PTR), plot coverage graph, and perform quality control over contigs in a single pipeline integrating Glimmer3, Bowtie2, Sickle, and algorithms in R.

    Language:C2100

  • LeandroD94/Papers

    Papers in which I have been involved as data scientist. For the title, info and and/or the DOI of each one of them, check the corrispective "Paper_title_and_info" txt file

    Language:R2110

  • llrs/Rhea

    A set of R scripts for the analysis of microbial profiles

    Language:R2301

  • Zubair2021/16S_Microbiome_Analysis

    This repository provides scripts for the 16S microbiome analysis and metagenome prediction using linux and R-Studio

    Language:Shell2101

  • Constellab/gws_ubiome

    Constellab brick for microbiome data analysic

    Language:Python1100
  • microbAIDeR

    FabbriniMarco/microbAIDeR

    An ensemble of functions for easier and quicker preliminary microbiome analyses

    Language:R1100

  • HuaZou/ML_microbiota_CRC

    Machine Learning on gut microbiota of patients with Colorectal cancer

    Language:Jupyter Notebook1100

  • mvictoriabuss/Protein_Structure_Prediction

    Repository with scripts and data generated during my internship at Institut Pasteur of Paris

    Language:Python1100

  • RIVM-IIV-Microbiome/biomeViz

    biomeViz is Module-03 of the RIVM-ToolBox. R pkg with data visualization tools for microbiome research done at the RIVM. . Development Phase: Active Development

    Language:R1310

  • SchlossLab/Sze_FollowUps_Microbiome_2017

    Language:HTML1473

  • ycl6/dada2

    Accurate sample inference from amplicon data with single nucleotide resolution

    Language:R110

  • zhangyang2017/2017_XN_16S

    Repository for 16S paper

    1001

  • barbarahelena/rodam

    Analyses Pros-RODAM microbiota data

    Language:R0100

  • barbarahelena/vsearchpipeline

    VSEARCH pipeline for ASV inference of 16S seq data

    Language:Nextflow0101

  • ep142/Metaolive

    Scripts and data for the METAolive project

    Language:R0100