microbiome-analysis
There are 135 repositories under microbiome-analysis topic.
microbiome/microbiome
microbiome R package
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
YuLab-SMU/MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
qiita-spots/qiita
Qiita - A multi-omics databasing effort
microsud/Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
grimmlab/MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
david-barnett/microViz
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
zoecastillo/microbiomeExplorer
The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.
Russel88/MicEco
Various functions for analysis of microbial community data
microsud/microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
GPZ-Bioinfo/tmap
topological data analysis of population-scale microbiomes
cafferychen777/MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
waldronlab/curatedMetagenomicDataAnalyses
Analyses in R and Python Using curatedMetagenomicData
vallenderlab/MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
mikemc/metacal
Metagenomics calibration R package
tmbuza/iMAP
iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline
smdabdoub/phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
itsmisterbrown/microfiltR
accessory functions for processing microbial community data
statdivlab/paramedic
Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations
wijerasa/bioinformatics-projects
A Collection of Bioinformatics Projects
CMU-SAFARI/Genome-on-Diet
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
guokai8/microbial
Do microbiome analysis with dada2 and phyloseq object
JelenaBanjac/microbiome-toolbox
Early Life Microbiome Toolbox
microbiome/miaViz
Microbiome Analysis Plotting and Visualization
LebeerLab/tidytacos
Functions to manipulate and visualize microbial community data
liuyu8721/csmd
A computational pipeline for high-resolution profiling of low abundance microbiome in clinical samples using whole genome shotgun sequencing
carden24/V-Xtractor
Repository for V-Xtractor an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences
LeonDlugosch/MetaSeq-Toolkit
This pipeline is intended to be a convenient way to work though large sets of metagenomic or metatranscriptiomic datasets while also retaining high analytical flexibility due to retained intermediate results that might be useful outside of the intended purpose.
pnnl/brislawn-2018-founders-species
🦠 📓 a microbiome paper
biocorecrg/microbiome_procedures
Mothur procedures for 16S and ITS analysis
DanielSprockett/reltools
Microbiome Amplicon Analysis and Visualization
EmoryIntegratedComputationalCore/Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
jordiabante/biodive
A reference-free statistical approach to diversity-generating & mobile genetic element discovery
CMU-SAFARI/MetaTrinity
MetaTrinity is a novel metagenomic analysis tool employing efficient containment search techniques and heuristics for read mapping to achieve significant speedup while maintaining high accuracy. This positions MetaTrinity as an efficient solution, optimally balancing speed and precision in metagenomic analysis.
dib-lab/2021-paper-ibd
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease
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.