MiRKAT 1.2.1 – Microbiome Regression-Based Analysis Tests

MiRKAT 1.2.1

:: DESCRIPTION

MiRKAT is a package for testing microbiome and outcome association, adjusting for possible covariates.

::DEVELOPER

Hongzhe Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MiRKAT

:: MORE INFORMATION

Citation

Wilson N, Zhao N, Zhan X, Koh H, Fu W, Chen J, Li H, Wu MC, Plantinga AM.
MiRKAT: kernel machine regression-based global association tests for the microbiome.
Bioinformatics. 2021 Jul 12;37(11):1595-1597. doi: 10.1093/bioinformatics/btaa951. PMID: 33225342; PMCID: PMC8495888.

gNOMO – Host and Microbiome analysis of non-model Organisms

gNOMO

:: DESCRIPTION

gNOMO is a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.

::DEVELOPER

gNOMO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

gNOMO

:: MORE INFORMATION

Citation

Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, Piro VC, García-Ferris C, Latorre A, Renard BY, Muth T.
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.
NAR Genom Bioinform. 2020 Aug 5;2(3):lqaa058. doi: 10.1093/nargab/lqaa058. Erratum in: NAR Genom Bioinform. 2020 Oct 09;2(4):lqaa083. PMID: 33575609; PMCID: PMC7671378.

micropower – Power Estimation for Microbiome Studies

micropower

:: DESCRIPTION

The micropower package is designed to facilitate power estimation for microbiome studies that will be analyzed with pairwise distances (beta diversity) and PERMANOVA (a non-parametric extension of multivariate analysis of variance to a matrix of pairwise distances).

::DEVELOPER

Bushman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 micropower

:: MORE INFORMATION

Citation

Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA.
Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H.
Bioinformatics. 2015 Mar 29. pii: btv183.

phylogeo – Geographic Analysis and Visualization of Microbiome data

phylogeo

:: DESCRIPTION

The phylogeo package provides a convenient way to map microbiome-related information. phylogeo relies on the phyloseq package and provides methods for mappiin samples, drawing network diagrams, plotting phylogenetic trees and maps, and correlating physical distance with ecological distance.

::DEVELOPER

phylogeo team

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 phylogeo

:: MORE INFORMATION

Citation

phylogeo: an R package for geographic analysis and visualization of microbiome data.
Charlop-Powers Z, Brady SF.
Bioinformatics. 2015 Apr 25. pii: btv269.

DeepMicro – Deep Representation learning for Disease prediction based on Microbiome data

DeepMicro

:: DESCRIPTION

DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DeepMicro

:: MORE INFORMATION

Citation

Oh M, Zhang L.
DeepMicro: deep representation learning for disease prediction based on microbiome data.
Sci Rep. 2020 Apr 7;10(1):6026. doi: 10.1038/s41598-020-63159-5. PMID: 32265477; PMCID: PMC7138789.

Community-Analyzer – Microbiome Community Network Analysis

Community-Analyzer

:: DESCRIPTION

Community Analyzer is a GUI based Comparative Metagenomic Analysis platform that can be used to perform interactive ‘on the fly’ analysis of a given set of metagenomes on a PC/laptop with modest hardware configurations.

::DEVELOPER

Community-Analyzer team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

Community Analyzer

:: MORE INFORMATION

Citation

Kuntal BK, Ghosh TS, Mande SS.
Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.
Genomics. 2013 Oct;102(4):409-18. doi: 10.1016/j.ygeno.2013.08.004. Epub 2013 Aug 24. PMID: 23978768.

MetaQuery 1.0.4 – Annotation and Quantitative analysis of Genes in the human Gut Microbiome

MetaQuery 1.0.4

:: DESCRIPTION

MetaQuery is a web application for rapid and quantitative analysis of specific genes in the human gut microbiome.

::DEVELOPER

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaQuery

:: MORE INFORMATION

Citation

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.
Nayfach S, Fischbach MA, Pollard KS.
Bioinformatics. 2015 Jun 22. pii: btv382.

RevEcoR 0.99.3 / shiny-RevEcoR 0.1.1 – Reverse Ecology Analysis of Microbiomes

RevEcoR 0.99.3 / shiny-RevEcoR 0.1.1

:: DESCRIPTION

RevEcoR is an R package that implements the reverse ecology algorithm for determining microbe-microbe interactions in microbial communities.

shiny-RevEcoR is an interactive web application that provides a flexible graphical user interface (GUI) to the Reverse Ecology analysis package for R, called RevEcoR hosted on CRAN.

::DEVELOPER

Yang Cao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 RevEcoR , shiny-RevEcoR

:: MORE INFORMATION

Citation

RevEcoR: an R package for the reverse ecology analysis of microbiomes.
Cao Y, Wang Y, Zheng X, Li F, Bo X.
BMC Bioinformatics. 2016 Jul 29;17(1):294. doi: 10.1186/s12859-016-1088-4.

CowPI – A rumen microbiome focussed version of the PICRUSt Functional Inference software

CowPI

:: DESCRIPTION

CowPi consists of a set of pre-calculated files that can be used with an installation of PICRUSt to allow functional predictions to be made from 16S rRNA samples from the rumen microbiome.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Wilkinson, T.J., Huws, S.A., Edwards, J.E., Kingston-Smith, A., Siu Ting, K., Hughes, M., Rubino, F., Friedersdorff, M. and Creevey, C., 2018.
CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software.
Frontiers in Microbiology, 9, p.1095.

FishTaco 1.1.3 – Linking Taxonomic and Functional Shifts in the Microbiome

FishTaco 1.1.3

:: DESCRIPTION

FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework, aiming to identify the taxa that are driving the functional shifts we observe in microbiomes of different individuals or disease states.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

FishTaco

:: MORE INFORMATION

Citation

Cell Host Microbe. 2017 Feb 8;21(2):254-267. doi: 10.1016/j.chom.2016.12.014.
Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.
Manor O, Borenstein E.

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