microbiome-analysis

There are 10 repositories under microbiome-analysis topic.

microbiome / microbiome
microbiome R package
microbiome microbiology microbiome-analysis r phyloseq human-microbiome population-study hitchip hitchip-atlas
Language:R 272
opencobra / cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
cobra-toolbox reconstruction tutorial metabolic-models metabolic-reconstruction metabolic-engineering gap-filling strain-engineering omics-data-integration metabolomics transcriptomics cobra constraint-based-modeling human-metabolism microbiome-analysis
Language:MATLAB 237
YuLab-SMU / MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
microbiome microbiome-analysis microbiome-data rstats
Language:R 159
qiita-spots / qiita
Qiita - A multi-omics databasing effort
microbiome microbiome-analysis python
Language:Python 119
microsud / Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
microbiome-analysis microbial-communities microbiome-data amplicon-sequencing microbiota amplicon 16s-rrna metagenomics
Language:CSS 108
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 100
david-barnett / microViz
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
microbiome microbiome-analysis microbiota rstats r
Language:R 88
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.
microbiome microbiome-analysis
Language:R 67
Russel88 / MicEco
Various functions for analysis of microbial community data
amplicon-sequencing 16s microbiome microbiome-analysis null-model microbial-communities microbial-ecology
Language:R 39
microsud / microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
16s amplicon core-microbiome metagenomics microbial-communities microbiome microbiome-analysis qc-pipeline sequencing
Language:R 32
GPZ-Bioinfo / tmap
topological data analysis of population-scale microbiomes
microbiome-analysis topological-data-analysis
Language:Python 30
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 24
waldronlab / curatedMetagenomicDataAnalyses
Analyses in R and Python Using curatedMetagenomicData
r microbiome-analysis microbiome-data bioconductor
Language:Python 19
vallenderlab / MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
microbiome microbial-genomics microbiome-analysis phyloseq metacoder r rstats visualization color-palette bioinformatics permanova alpha-diversity beta-diversity pcoa comprehensive metagenomics microbiology
Language:R 18
mikemc / metacal
Metagenomics calibration R package
amplicon-sequencing marker-gene-analysis metagenomics microbiome-analysis r-package
Language:R 17
tmbuza / iMAP
iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline
16s-rrna metagenomic-analysis microbiome-analysis visualization
Language:HTML 13
itsmisterbrown / microfiltR
accessory functions for processing microbial community data
microbiome microbiome-analysis marker-gene-analysis 16s phyloseq 18s
Language:R 12
smdabdoub / phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
16s bioinformatics computational-biology cross-platform hpc microbial-genomics microbiome microbiome-analysis pbs phylogenetics python qiime slurm visualization
Language:Python 12
statdivlab / paramedic
Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations
microbiome-analysis statistical-inference bayesian-methods stan
Language:R 12
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).
bioinformatics containment-search genome-analysis genome-on-diet genomics large-scale metagenomic-analysis metagenomics microbiome-analysis minimap2 read-mapping sequence-alignment variant-calling wavefront-alignment
Language:Roff 11
guokai8 / microbial
Do microbiome analysis with dada2 and phyloseq object
microbiome-analysis microbiome
Language:R 11
wijerasa / bioinformatics-projects
A Collection of Bioinformatics Projects
16s microbiome-analysis r python
Language:Python 10
JelenaBanjac / microbiome-toolbox
Early Life Microbiome Toolbox
microbiome-analysis microbiome-trajectory microbiome microbiome-model data-analysis longitudinal-studies longitudinal-analysis microbiome-toolbox machine-learning python anomaly-detection
Language:Jupyter Notebook 8
tidytacos
LebeerLab / tidytacos
Functions to manipulate and visualize microbial community data
microbial-communities microbiome-analysis r tidy visualization
Language:R 7
liuyu8721 / csmd
A computational pipeline for high-resolution profiling of low abundance microbiome in clinical samples using whole genome shotgun sequencing
bioinformatics microbiome-analysis
Language:R 7
microbiome / miaViz
Microbiome Analysis Plotting and Visualization
bioconductor microbiome microbiome-analysis plotting visualization
Language:R 7
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
bioinformatics rrna microbiome-analysis open-source 16s
Language:Perl 6
pnnl / brislawn-2018-founders-species
🦠 📓 a microbiome paper
microbiome-analysis r research-paper science-research
Language:HTML 6
DanielSprockett / reltools
Microbiome Amplicon Analysis and Visualization
microbiome microbiome-analysis microbiology proteomics
Language:R 5
EmoryIntegratedComputationalCore / Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
qiime2 microbiome-analysis rna-seq-analysis rna-seq-pipeline deseq2 phyloseq ldm omics-experiments emory methods rna-seq bioconductor bayseq edger qvalue discovery-rates comparison-groups notebook analytical-processes
Language:R 5
jordiabante / biodive
A reference-free statistical approach to diversity-generating & mobile genetic element discovery
bioinformatics crispr-cas9 microbial-genomics microbiome-analysis mobile-genetic-elements
Language:Python 5
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.
metagenomics assembly contigs dna binning gene-classification ecology microbiome-analysis micobiome sequencing mapping
Language:Shell 5
biocorecrg / microbiome_procedures
Mothur procedures for 16S and ITS analysis
microbiome-analysis microbiome-workflow 16s its mothur phyloseq fungi
Language:R 4
meyermicrobiolab / Stony-Coral-Tissue-Loss-Disease-SCTLD-Project
R scripts used for the analysis of microbiomes associated with stony coral tissue loss disease (SCTLD) in the Florida Reef Tract
r phyloseq deseq2 microbiome-analysis
Language:R 4
northomics / pepFunk
Peptide-centric functional enrichment tool
shiny rstudio bioinformatics metaproteomics microbiome-analysis
Language:R 4
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

microbiome-analysis

microbiome / microbiome

opencobra / cobratoolbox

YuLab-SMU / MicrobiotaProcess

qiita-spots / qiita

microsud / Tools-Microbiome-Analysis

grimmlab / MicrobiomeBestPracticeReview

david-barnett / microViz

zoecastillo / microbiomeExplorer

Russel88 / MicEco

microsud / microbiomeutilities

GPZ-Bioinfo / tmap

cafferychen777 / MicrobiomeStat

waldronlab / curatedMetagenomicDataAnalyses

vallenderlab / MicrobiomeR

mikemc / metacal

tmbuza / iMAP

itsmisterbrown / microfiltR

smdabdoub / phylotoast

statdivlab / paramedic

CMU-SAFARI / Genome-on-Diet

guokai8 / microbial

wijerasa / bioinformatics-projects

JelenaBanjac / microbiome-toolbox

LebeerLab / tidytacos

liuyu8721 / csmd

microbiome / miaViz

carden24 / V-Xtractor

pnnl / brislawn-2018-founders-species

DanielSprockett / reltools

EmoryIntegratedComputationalCore / Methods

jordiabante / biodive

LeonDlugosch / MetaSeq-Toolkit

biocorecrg / microbiome_procedures

meyermicrobiolab / Stony-Coral-Tissue-Loss-Disease-SCTLD-Project

northomics / pepFunk

TomC-93 / Tree-Root-Microbiome-Project