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Search results for bioinformatics microbiome
bioinformatics
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microbiome
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43 search results found
Vsearch
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605
Versatile open-source tool for microbiome analysis
Dada2
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428
Accurate sample inference from amplicon data with single nucleotide resolution
Dram
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214
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Metagem
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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
Pandora
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127
PANDORA Advanced Machine Learning for Data Integration, Analysis, and Insightful Discoveries in Health and Disease 💻
Decontam
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122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Swarm
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110
A robust and fast clustering method for amplicon-based studies
Taxprofiler
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78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Ganon
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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
Deepmicrobes
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61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Woltka
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58
Woltka: a versatile meta'omic data classifier
Emperor
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52
Emperor a tool for the analysis and visualization of large microbial ecology datasets
Flashweave.jl
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52
Inference of microbial interaction networks from large-scale heterogeneous abundance data
Microbiomebestpracticereview
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45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Redbiom
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42
Sample search by metadata and features
Panphlan
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38
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
Rdptools
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36
Collection of commonly used RDP Tools for easy building
Empress
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33
A fast and scalable phylogenetic tree viewer for microbiome data analysis
Mmlong2
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26
An all-in-one genome-centric metagenomics workflow using long reads
Qurro
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23
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
Ghost Tree
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23
creating hybrid-gene phylogenetic trees for diversity analyses
Calour
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23
exploratory and interactive microbiome analyses based on heatmaps
Mitre
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22
The Microbiome Interpretable Temporal Rule Engine
Birdman
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21
Bayesian Inferential Regression for Differential Microbiome Analysis
Super Focus
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19
A tool for agile functional analysis of shotgun metagenomic data
Amon
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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
Microbiomer
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17
A comprehensive R package for microbiome analysis.
Metasub_cap
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16
A comprehensive pipeline for short read metagenomic data
Qadabra
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13
Snakemake workflow for comparison of differential abundance ranks
Taxor
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13
Fast and space-efficient taxonomic classification of long reads
Phylotoast
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12
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Microbial Bioinformatics Introductory Course Material 2018
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12
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
Ng Meta Profiler
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10
Profiler for metagenomics based on NGLess
Mtd
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8
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Famli
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8
Functional Analysis of Metagenomes by Likelihood Inference
16s Rdna V3 V4
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8
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Qupid
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7
Case-control matching for microbiome data
Microbiomeanalysis.jl
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5
Functions and workflows for the analysis of microbiome data.
Metasequencing
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5
A metagenomics pipeline using the CGAT framework.
Focus
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5
FOCUS: An Agile Profiler for Metagenomic Data
Flint
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5
Main repository of the Flint project for Spark and Amazon EMR.
Microbiome
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5
The standardized analysis pipeline used for analyzing 16S and metagenome data.
Xebec
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5
Snakemake pipeline for microbiome diversity effect size benchmarking
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1-43 of 43 search results
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