microbiome-workflow

There are 1 repository under microbiome-workflow topic.

grimmlab / MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
microbiome microbiome-analysis microbiome-workflow biomedical best-practices pipeline bioinformatics amplicon-sequencing assembly 16s-rrna metagenomics
Language:Shell 107
cafferychen777 / MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
16s-rrna amplicon-sequencing dada2 longitudinal-data metagenomes metagenomic-analysis microbiome microbiome-analysis microbiome-data phyloseq qiime2 statistics visualization microbiome-workflow omics omics-data-integration
Language:R 30
anwarMZ / CoMW
Comparative Metatranscriptomics Workflow
metatranscriptomics metagenomics omics benchmarking microbial-ecology bioinformatics microbiome-workflow
Language:Python 7
biocorecrg / microbiome_procedures
Mothur procedures for 16S and ITS analysis
microbiome-analysis microbiome-workflow 16s its mothur phyloseq fungi
Language:R 5
TomC-93 / Tree-Root-Microbiome-Project
The scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.
forest forestry ftir ftir-data-analysis microbiology microbiome microbiome-analysis microbiome-data microbiome-workflow soil soil-properties soil-science soil-survey spectroscopy tree
Language:HTML 4
Brochado-Kith / microbiome_analysis
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
16s alpha-diversity beta-diversity microbiome microbiome-analysis microbiome-workflow phyloseq rstudio shinny beta diversity metagenomic-pipeline
Language:R 3
cafferychen777 / MicrobiomeStat-Turtorial-Professional-Version
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
16s 16s-rrna 16s-seq analysis data-analysis metagenomes metagenomic-analysis metagenomic-pipeline metagenomics microbiome microbiome-analysis microbiome-analysis-pipelines microbiome-data microbiome-workflow omics omics-data omics-data-analysis omics-data-integration visualization
3
cafferychen777 / MicrobiomeStat-Shiny
A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.
longitudinal-data microbiome microbiome-analysis microbiome-data microbiome-workflow
Language:R 2
gone
DOieGYuan / gone
Use one command to perform genome-centric metagenomics using state-of-the-art methods
metagenomics bioinformatics microbiome microbiome-analysis-pipelines microbiome-workflow
Language:Shell 2
ahmedmoustafa / ALS
Analysis of the gut microbiome of Amyotrophic Lateral Sclerosis (ALS) patients using the DADA2 workflow
bioinformatics bioinformatics-analysis microbiome microbiome-analysis microbiome-workflow 16s-rrna amyotrophic-lateral-sclerosis
Language:Jupyter Notebook 1
EdwinMosesAppiah / Gastric-Microbiome-and-Gastric-Carcinogenesis
This repository contains all codes used in the "The Gastric Microbiome and Gastric Carcinogenesis: Bacterial Diversity, Co-occurrence Patterns and Predictive Models" projects
microbiome microbiome-analysis microbiome-analysis-pipelines microbiome-workflow r gastric-cancer
Language:R 1
natmurad / amplicon16S
Analysis for amplicon data
16s amplicon metagenomics microbiome-workflow phyloseq qiime2
Language:Jupyter Notebook 1
AlexUmbach / AOViz
short-read amplicon data visualization suite
microbiome-analysis microbiome-data microbiome-workflow amplicon-data-analysis amplicon-datasets amplicon-sequencing
Language:R 0
drothen15 / whitenose-project
Data analysis of a unique microbiome data set
microbiome-workflow data-analysis
Language:Shell 0
jjcolgan / Bodke-Script
Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2
r metagenomics microbiome-workflow dada2 phangorn
0
mschemmel / corrnet
Scripts to convert correlation and p-value matrices to edge list and network
network co-occurence correlation microbiome-workflow
Language:Python 0
glickmac / Microbiome_Demo
A repository containing a demo microbiome workflow for R and Python
16s-rrna dada2 jupyter-notebook microbiome microbiome-workflow qiime tutorial
Language:Jupyter Notebook