Awesome Open Source
Search
Programming Languages
Languages
All Categories
Categories
About
Search results for microbiome
microbiome
x
106 search results found
Vsearch
⭐
605
Versatile open-source tool for microbiome analysis
Dada2
⭐
428
Accurate sample inference from amplicon data with single nucleotide resolution
Qiime
⭐
275
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Microbiome
⭐
257
microbiome R package
Dram
⭐
214
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Metagem
⭐
155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Microbiomemarker
⭐
151
R package for microbiome biomarker discovery
Microbiotaprocess
⭐
150
🦠 A comprehensive R package for deep mining microbiome
Humanmicrobiome
⭐
146
Human Microbiome wiki
Ampliseq
⭐
141
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Pandora
⭐
127
PANDORA Advanced Machine Learning for Data Integration, Analysis, and Insightful Discoveries in Health and Disease 💻
Decontam
⭐
122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Qiita
⭐
118
Qiita - A multi-omics databasing effort
Swarm
⭐
110
A robust and fast clustering method for amplicon-based studies
Ancombc
⭐
87
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
Maaslin2
⭐
86
MaAsLin2: Microbiome Multivariate Association with Linear Models
Microviz
⭐
80
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
Taxprofiler
⭐
78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Micom
⭐
73
Python package to study microbial communities using metabolic modeling.
Ganon
⭐
73
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
Oma
⭐
69
Orchestrating Microbiome Analysis
Deepmicrobes
⭐
61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Ancientmetagenomedir
⭐
61
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Gemelli
⭐
60
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
Ggpicrust2
⭐
59
Make Picrust2 Output Analysis and Visualization Easier
Woltka
⭐
58
Woltka: a versatile meta'omic data classifier
Hulk
⭐
57
Histosketching Using Little Kmers
Emperor
⭐
52
Emperor a tool for the analysis and visualization of large microbial ecology datasets
Flashweave.jl
⭐
52
Inference of microbial interaction networks from large-scale heterogeneous abundance data
Ancom Code Archive
⭐
47
R functions for Analysis of Composition of Microbiomes (ANCOM).
Microbiomebestpracticereview
⭐
45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Microbiomeexplorer
⭐
44
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.
Redbiom
⭐
42
Sample search by metadata and features
Mia
⭐
42
Microbiome analysis
Microbiome.jl
⭐
42
For analysis of microbiome and microbial community data
Microbiomehd
⭐
40
Cross-disease comparison of case-control gut microbiome studies
Panphlan
⭐
39
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
Sccomp
⭐
37
Robust differential composition and variability analysis for single-cell data
Microbiomeviz
⭐
36
Visualize microbiome data with black magic ggtree
Rdptools
⭐
36
Collection of commonly used RDP Tools for easy building
Datest
⭐
34
Compare different differential abundance and expression methods
Empress
⭐
33
A fast and scalable phylogenetic tree viewer for microbiome data analysis
Microbiomeutilities
⭐
29
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Miceco
⭐
28
Various functions for analysis of microbial community data
Schtools
⭐
26
Schloss Lab Tools for Reproducible Microbiome Research 💩
Mmlong2
⭐
26
An all-in-one genome-centric metagenomics workflow using long reads
Q2 Qemistree
⭐
24
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Melonnpan
⭐
24
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Tweedieverse
⭐
24
Differential analysis of multi-omics data based on the Tweedie distribution
Stag Mwc
⭐
24
StaG Metagenomic Workflow Collaboration
Qurro
⭐
23
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
Nmdc Schema
⭐
23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
Calour
⭐
23
exploratory and interactive microbiome analyses based on heatmaps
Ghost Tree
⭐
23
creating hybrid-gene phylogenetic trees for diversity analyses
Mitre
⭐
22
The Microbiome Interpretable Temporal Rule Engine
Isb_course_2022
⭐
22
Materials and presentation for the 2022 ISB Microbiome course.
Birdman
⭐
21
Bayesian Inferential Regression for Differential Microbiome Analysis
Super Focus
⭐
19
A tool for agile functional analysis of shotgun metagenomic data
Microbiomestat
⭐
18
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Microbiomer
⭐
17
A comprehensive R package for microbiome analysis.
Microbiome Analysis Using R
⭐
17
Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
Amon
⭐
17
Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data
Microbiome Mvib
⭐
16
Microbiome-based disease prediction with multimodal variational information bottlenecks, Grazioli et al., PLOS Computational Biology 2022
Rcm
⭐
16
A model-based visualization method for microbiome data
Metasub_cap
⭐
16
A comprehensive pipeline for short read metagenomic data
Micone
⭐
15
The Microbial Co-occurrence Network Explorer
Fantaxtic
⭐
14
Fantaxtic - Nested Bar Plots for Phyloseq Data
Qadabra
⭐
13
Snakemake workflow for comparison of differential abundance ranks
Taxor
⭐
13
Fast and space-efficient taxonomic classification of long reads
Phylotoast
⭐
12
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Ancom Bc Code Archive
⭐
12
Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction"
Microbial Bioinformatics Introductory Course Material 2018
⭐
12
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
Agora
⭐
11
The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.
Snakemake Workflow Qiime2
⭐
11
Snakemake pipeline for 16S, 18S and ITS metagenomics using qiime2
Sze_obesity_mbio_2016
⭐
11
Isb_course_2023
⭐
10
Materials and presentation for the 2023 ISB Microbiome course.
Microbiome
⭐
10
scripts for microbiome analysis
Ng Meta Profiler
⭐
10
Profiler for metagenomics based on NGLess
16s Rdna V3 V4
⭐
8
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Dementpy
⭐
8
A spatially explicit trait- and individual-based microbial systems modelling framework
Specificity
⭐
8
R package for calculating specificity in ecological data
Dogs
⭐
8
Companion notebooks for "Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks"
Hannigan_crcvirome_mbio_2018
⭐
8
Investigating the gut virus communities associated with colon cancer.
Mtd
⭐
8
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Famli
⭐
8
Functional Analysis of Metagenomes by Likelihood Inference
Microbiome Toolbox
⭐
8
Early Life Microbiome Toolbox
Qupid
⭐
7
Case-control matching for microbiome data
Mdpbiome
⭐
7
microbiome engineering through prescriptive perturbations
Miaviz
⭐
7
Microbiome Analysis Plotting and Visualization
Microbiomedatasets
⭐
6
Experiment Hub based microbiome datasets
Localhgt
⭐
6
Detect complete HGT event rapidly and accurately from complex metagenomics data
Microbial
⭐
6
Do microbiome analysis with dada2 and phyloseq object
Tofu Maapo
⭐
6
Nextflow pipeline for the analysis of metagenomic short reads.
Focus
⭐
5
FOCUS: An Agile Profiler for Metagenomic Data
Microberx
⭐
5
MicrobeRX
Flint
⭐
5
Main repository of the Flint project for Spark and Amazon EMR.
Microbiomeanalysis.jl
⭐
5
Functions and workflows for the analysis of microbiome data.
Benchdamic
⭐
5
Benchmark of differential abundance methods on microbiome data
Sample Annotator
⭐
5
NMDC Sample Annotator
Grimer
⭐
5
GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
1-100 of 106 search results
Next >
Privacy
|
About
|
Terms
|
Follow Us On Twitter
Copyright 2018-2024 Awesome Open Source. All rights reserved.