microbiome-analysis
There are 11 repositories under microbiome-analysis topic.
microbiome / microbiome
microbiome R package
Language:R 277opencobra / cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Language:MATLAB 241YuLab-SMU / MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
Language:R 171- Language:Python 120
microsud / Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Language:CSS 108grimmlab / MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Language:Shell 107david-barnett / microViz
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
Language:R 94zoecastillo / 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.
Language:R 67- Language:R 41
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Language:R 32GPZ-Bioinfo / tmap
topological data analysis of population-scale microbiomes
Language:Python 31cafferychen777 / MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Language:R 30waldronlab / curatedMetagenomicDataAnalyses
Analyses in R and Python Using curatedMetagenomicData
Language:Python 20vallenderlab / MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
Language:R 18- Language:R 17
wijerasa / bioinformatics-projects
A Collection of Bioinformatics Projects
Language:Python 15- Language:HTML 14
smdabdoub / phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Language:Python 13itsmisterbrown / microfiltR
accessory functions for processing microbial community data
Language:R 12statdivlab / paramedic
Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations
Language:R 12CMU-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).
Language:Roff 11- Language:R 11
JelenaBanjac / microbiome-toolbox
Early Life Microbiome Toolbox
Language:Jupyter Notebook 11- tidytacosLanguage:R 9
Microbiome Analysis Plotting and Visualization
Language:R 9LeonDlugosch / 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.
Language:Shell 7liuyu8721 / csmd
A computational pipeline for high-resolution profiling of low abundance microbiome in clinical samples using whole genome shotgun sequencing
Language:R 7carden24 / 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
Language:Perl 6pnnl / brislawn-2018-founders-species
🦠 📓 a microbiome paper
Language:HTML 6biocorecrg / microbiome_procedures
Mothur procedures for 16S and ITS analysis
Language:R 5DanielSprockett / reltools
Microbiome Amplicon Analysis and Visualization
Language:R 5EmoryIntegratedComputationalCore / Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
Language:R 5jordiabante / biodive
A reference-free statistical approach to diversity-generating & mobile genetic element discovery
Language:Python 5MetaTrinity 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.
Language:HTML 4dib-lab / 2021-paper-ibd
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease
Language:HTML 4TomC-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.
Language:HTML 4
