cafferychen777/ggpicrust2

Make Picrust2 Output Analysis and Visualization Easier

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micom-dev/micom

Python package to study microbial communities using metabolic modeling.

Language: Python - Size: 49 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 100 - Forks: 18

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: R - Size: 58 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 3 - Forks: 0

microsud/Tools-Microbiome-Analysis

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

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Elisseeff-Lab/etbf_fbr_stromal_bulkseq

Bulk RNAseq analysis of stromal cells from peri-implant fibrosis of mice with and without ETBF infection

Language: R - Size: 6.41 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

david-barnett/microViz

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

Language: R - Size: 439 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 114 - Forks: 12

microsud/dysbiosisR

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

Language: R - Size: 13.8 MB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 0

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.

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FabbriniMarco/microbAIDeR

An ensemble of functions for easier and quicker preliminary microbiome analyses

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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, Dräger 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: Python - Size: 34.9 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

Gabriele-Conti/KEGGSearch

Comprehensive KEGG Data Retrieval Using Multiple Sources

Language: R - Size: 40 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

oliverdesa/Clustering_Metagenomics

This directory contains many scripts delving into the downstream analysis of shotgun metagenomic sequencing data from colorectal cancer patient, ICI patients and some IBD patients. This directory is not finished or meant to be copied and used by others. simply to provide examples of code currently being written and worked on.

Language: Jupyter Notebook - Size: 142 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

ycl6/dada2 Fork of benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

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ep142/Metaolive

Scripts and data for the METAolive project

Language: R - Size: 1.23 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

oschakoory/RiboTaxa

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

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barbarahelena/vsearchpipeline

VSEARCH pipeline for ASV inference of 16S seq data

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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: R - Size: 27.8 MB - Last synced at: 6 months ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 5

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: R - Size: 309 KB - Last synced at: 6 months ago - Pushed at: almost 4 years ago - Stars: 33 - Forks: 18

erictleung/phyloseq-cheatsheet

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

Size: 504 KB - Last synced at: about 2 months ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 0

hsp-microbiology/HSP-Phageome-ECCMID2024

ECCMID 2024 Abstract #04375. Code used to perform the analysis and figures.

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danielpodlesny/fmt_rcdi

Notebooks and files necessary to replicate the graphs and analyses presented in the Preprint, doi: 10.1101/2020.09.29.20203638

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gioche96/milk_microbiota

Repository for pipelines and scripts to analyse microbiota

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HuaZou/MicrobiomeAnalysis_book

Tutorial for MicrobiomeAnalysis R package

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SchlossLab/Sze_CRCMetaAnalysis_mBio_2018

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SchlossLab/Sze_FollowUps_Microbiome_2017

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munozalexander/Cervicovaginal-Microbiome-Temporal-Dynamics

This repo models the temporal dynamics of the cervicovaginal microbiome to identify targets that promote reproductive health

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bdaisley/BEExact

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

Size: 406 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 2

nezapajek/proteus-skin-microbiome

Amplicon sequencing data analysis of skin microbiota in the black olm subspecies using Qiime2

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

Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

Language: R - Size: 121 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 25 - Forks: 21

Zubair2021/16S_Microbiome_Analysis

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

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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: R - Size: 4.9 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

HuaZou/MetaAnalysis_CRC

Meta-analysis on human gut microbiota in Colorectal cancer

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llrs/Rhea Fork of Lagkouvardos/Rhea

A set of R scripts for the analysis of microbial profiles

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HuaZou/ML_microbiota_CRC

Machine Learning on gut microbiota of patients with Colorectal cancer

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mvictoriabuss/Protein_Structure_Prediction

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

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ASaiM/framework

Open-source opinionated Galaxy-based framework for microbiota analysis

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Chloe-Perrais/Microbiota

Master 1 project of 4 students at Institut Agro Montpellier in collaboration with a research lab for population biology and management (CBGP) in Montpellier

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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.

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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"

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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: R - Size: 9.17 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

microsud/Indian-gut-microbiota

Data and analysis code for the Indian gut microbiota study

Language: R - Size: 483 KB - Last synced at: 12 days ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 1

jjmpal/rrgutbiota

Association Between Gut Microbiota and Hypertension

Language: R - Size: 1.01 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

DariiaVyshenska/IBDteam1

MB599 class, spring 2018, group1, stomach microbiota in IBD

Language: R - Size: 1.57 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

microsud/Gut-microbiota-Celiac-disease

R scripts used for analysis of data reported in Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls

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