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Differential abundant analysis software tools | Shotgun metagenomic sequencing data analysis

The analysis of differential abundance for features (e.g. species or genes) can provide us with a better understanding of microbial communities, thus increasing our comprehension and understanding of the behaviors of microbial communitiesSource…
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DESeq
Desktop

DESeq

A method for differential analysis of RNA-sequencing count data, using…

A method for differential analysis of RNA-sequencing count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a…

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MEGAN
Desktop

MEGAN MEtaGenome ANalyzer

Allows to interactively explore and analyze, both taxonomically and…

Allows to interactively explore and analyze, both taxonomically and functionally, large-scale microbiome sequencing data. MEGAN is a comprehensive microbiome analysis toolbox for metagenome,…

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STAMP
Desktop

STAMP Statistical Analysis of Metagenomic Profiles

A graphical software package that provides statistical hypothesis tests and…

A graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles. It supports tests for comparing pairs of samples or…

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metagenomeSeq
Desktop

metagenomeSeq

A package for differential abundance analysis in sparse high-throughput marker…

A package for differential abundance analysis in sparse high-throughput marker gene survey data. metagnomeSeq relies on a normalization technique and a statistical model that accounts for…

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METAREP
Web
Desktop

METAREP

Helps scientists to analyze and compare annotated metagenomics datasets.…

Helps scientists to analyze and compare annotated metagenomics datasets. METAREP provides a suite of web based tools and allows to compare multiple datasets at various functional and taxonomic levels…

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OMiAT
Desktop

OMiAT Optimal Microbiome-based Association Test

Provides a method for microbial association. OMiAT offers a data-driven…

Provides a method for microbial association. OMiAT offers a data-driven approach which aims to help in discovering significant association signals from multiple underlying association patterns. The…

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Myrna
Desktop

Myrna

A cloud computing tool for calculating differential gene expression in large…

A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization,…

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RADs
Desktop

RADs Rank Abundance Distributions

Compares communities in many areas of biology. RADs enables novel quantitative…

Compares communities in many areas of biology. RADs enables novel quantitative approaches that help to understand structures and dynamics of complex generalize communities. The tool can be applied to…

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MiCAM
Desktop

MiCAM Microbiome Comprehensive Association Mapping

Provides a microbial taxa discovery framework. MiCAM allows users to test…

Provides a microbial taxa discovery framework. MiCAM allows users to test possible associations between microbial compositions among multiple microbial taxa throughout all taxonomic ranks. Besides,…

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ShinyMB
Web

ShinyMB

Explores the power/sample sizes behaviour in microbiome case-control studies…

Explores the power/sample sizes behaviour in microbiome case-control studies with or without stratification. ShinyMB calculates a recoded version of the two-sample generalized Wald test of the…

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MMiRKAT
Desktop
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Rhea
Desktop

Rhea

Encodes a series of well documented choices for the downstream analysis of…

Encodes a series of well documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic…

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ShotgunFunction…
Desktop

ShotgunFunctionalizeR

An R-package for functional comparison of metagenomes. The package contains…

An R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualising metagenomic data produced by shotgun high-throughput sequencing.…

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StructFDR
Desktop

StructFDR

Performs powerful false discovery rate (FDR) control for microbiome data,…

Performs powerful false discovery rate (FDR) control for microbiome data, taking into account the prior phylogenetic relationship among bacteria species. StructFDR was implemented in an R package…

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HirBin
Desktop

HirBin

Extends the standard supervised binning with an unsupervised clustering step,…

Extends the standard supervised binning with an unsupervised clustering step, which enables quantification of metagenomes at a sub-bin level. HirBin is a method for gene-centric analysis of…

cydar
Desktop

cydar

Detects ‘differentially abundant’ populations between samples and groups in…

Detects ‘differentially abundant’ populations between samples and groups in mass cytometry data. Cydar is a computational strategy to perform differentially abundant (DA) analyses of mass…

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DiTASiC
Desktop

DiTASiC Differential Taxa Abundance including Similarity Correction

Provides a new generalized linear model (GLM) framework for the resolution of…

Provides a new generalized linear model (GLM) framework for the resolution of shared read counts. DiTASiC integrates abundance variances for differential testing sensitive to strain level. It relies…

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metaDprof
Desktop

metaDprof

Detects metagenomic features differentially abundant between biological/medical…

Detects metagenomic features differentially abundant between biological/medical conditions. metaDprof consists two stages: 1) global detection of features and 2) time interval detection of…

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MicrobeCensus
Desktop

MicrobeCensus

A fast and easy to use pipeline for estimating the average genome size (AGS) of…

A fast and easy to use pipeline for estimating the average genome size (AGS) of a microbial community from metagenomic data. In short, AGS is estimated by aligning reads to a set of universal…

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myPhyloDB
Desktop

myPhyloDB

A user-friendly personal database with a browser-interface designed to…

A user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files,…

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NMIT
Desktop

NMIT Non-parametric Microbial Interdependence Test

Provides a method, based on a multivariate distance-based nonparametric test…

Provides a method, based on a multivariate distance-based nonparametric test that allows users to estimate associations between microbial interdependence and phenotypic variables. NMIT compares…

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RegLRSD
Desktop

RegLRSD Regularized Low Rank-Sparse Decomposition

Detects biomarkers by using a matrix. RegLRSD models the abundance profiles of…

Detects biomarkers by using a matrix. RegLRSD models the abundance profiles of relevant and irrelevant microbes as sparse and low-rank matrices, respectively. It constrains the low rank matrix to be…

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MicrobiomeDDA
Desktop

MicrobiomeDDA

Helps in differential distribution analysis of microbiome sequencing data.…

Helps in differential distribution analysis of microbiome sequencing data. MicrobiomeDDA is a robust framework of differential analysis of microbiome data based on a zero-inflated negative binomial…

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FastViromeExplo…
Desktop

FastViromeExplorer

Identifies and quantifies the abundance of viruses in metagenomics data.…

Identifies and quantifies the abundance of viruses in metagenomics data. FastViromeExplorer is a stand-alone pipeline that uses kallisto to map short reads to a reference virus database and then…

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MetaComp
Desktop

MetaComp

Allows comparison of metagenomics and other meta-omics data. MetaComp is a…

Allows comparison of metagenomics and other meta-omics data. MetaComp is a graphical software that incorporates metagenomics, metatranscriptomics, metaproteomics and metabolomics data. The software…

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COMMET
Desktop

COMMET COmpare Multiple METagenomes

Provides a global similarity overview between all datasets of a metagenomic…

Provides a global similarity overview between all datasets of a metagenomic project. COMMET is able to (1) filter reads, given user-defined parameters, (2) compare all-against-all read sets, and (3)…

MicrobiomeAnaly…
Web

MicrobiomeAnalyst

Integrates recent progress in statistics and visualization techniques.…

Integrates recent progress in statistics and visualization techniques. MicrobiomeAnalyst provides an analysis of common data outputs produced from microbiome studies. It gives support for diversity…

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mcaGUI
Desktop

mcaGUI Microbial Community Analysis GUI

Provides an interface to access a set of statistical tools to summarize and…

Provides an interface to access a set of statistical tools to summarize and analyze microbial community data such as principal component analysis (PCA), cluster analysis and others. mcaGUI is a…

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ENNB
Desktop

ENNB

A two-stage statistical procedure for selecting informative features and…

A two-stage statistical procedure for selecting informative features and identifying differentially abundant features between two or more groups of microbial communities. In the functional analysis…

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RAIDA
Desktop

RAIDA Ratio Approach for Identifying Differential Abundance

An R package for robustly identifying differential abundant features across…

An R package for robustly identifying differential abundant features across microbial conditions. RAIDA utilizes the ratio between features in a modified zero-inflated lognormal model. RAIDA removes…

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LEfSe
Web

LEfSe

A method for metagenomic biomarker discovery by way of class comparison, tests…

A method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or…

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MetaBoot
Desktop

MetaBoot

Allows feature selection from microbial community samples. MetaBoot is based on…

Allows feature selection from microbial community samples. MetaBoot is based on taxonomical profiles generated from the microbial community’s 16S rRNA gene sequences. It is composed of four steps:…

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METAGENassist
Web

METAGENassist

A freely accessible, easy-to-use web server for comparative metagenomic…

A freely accessible, easy-to-use web server for comparative metagenomic analysis. Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA…

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MetaPath
Desktop

MetaPath

Identifies differentially abundant metabolic pathways in metagenomic datasets,…

Identifies differentially abundant metabolic pathways in metagenomic datasets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge (from KEGG). Compared with…

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biojs-io-biom
Desktop

biojs-io-biom

Provides a unified interface to read, modify, and write BIOM (Biological…

Provides a unified interface to read, modify, and write BIOM (Biological Observation Matrix) data. Biojs-io-biom can be readily used as a library by applications that need to handle BIOM data for…

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Fizzy
Desktop

Fizzy

A Python command line tool, which is compatible with the widely adopted BIOM…

A Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data…

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FCMM
Desktop

FCMM

A pipeline for top-k based functional characterization of multiple metagenome…

A pipeline for top-k based functional characterization of multiple metagenome samples to infer the major functions as well as their quantitative scores in a comparative metagenomics manner. The…

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edgeR
Desktop

edgeR empirical analysis of DGE in R

Allows differential expression analysis of digital gene expression data. edgeR…

Allows differential expression analysis of digital gene expression data. edgeR implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes…

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Metastats
Web

Metastats

Employs the false discovery rate to improve specificity in high-complexity…

Employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher's exact test. While designed for…

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Community-analy…
Desktop

Community-analyzer

A GUI-based comparative metagenomic analysis application which implements a…

A GUI-based comparative metagenomic analysis application which implements a correlation-based graph layout algorithm that not only facilitates a quick visualization of the differences in the analyzed…

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OMiSA
Desktop

OMiSA Optimal Microbiome-based Survival Analysis

Provides an R package dealing with microbiome association. OMiSA is composed of…

Provides an R package dealing with microbiome association. OMiSA is composed of three main components: (i) OMiSA for examines microbial composition/survival association influence on health and…

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MALINA
Web

MALINA

A web-based tool for comparative analysis and statistical visualization of…

A web-based tool for comparative analysis and statistical visualization of human gut metagenomic samples. MALINA provides researchers with visual and intuitive tools for comparing samples, as well as…

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MetaRank
Desktop

MetaRank

Employs a series of statistical hypothesis tests to compare abundances within a…

Employs a series of statistical hypothesis tests to compare abundances within a microbial community and determine their ranks. MetaRank can reduce the effects of sampling biases and clarify the…

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