Seed – Exploring and Visualizing Microbial Community Data

Seed

:: DESCRIPTION

Seed (Simple Exploration of Ecological Datasets) is an R/Shiny package for visualizing ecological data. It provides a visual interface for generating a wide variety of plots, including histograms, scatterplots, bar plots, stacked bar plots, PCoA plots, cluster dendrograms, and heatmaps.

::DEVELOPER

Daniel Beck , Christopher Dennis at christozoan@gmail.com.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 Seed

:: MORE INFORMATION

Citation

Seed: a user-friendly tool for exploring and visualizing microbial community data.
Beck D, Dennis C, Foster JA.
Bioinformatics. 2014 Oct 20. pii: btu693.

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.

mcaGUI 1.37.0 – Microbial Community Analysis Graphical User Interface

mcaGUI 1.37.0

:: DESCRIPTION

mcaGUI is a microbial community analysis GUI for R using gWidgets.

::DEVELOPER

Wade K. Copeland

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 mcaGUI

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 15;28(16):2198-9. doi: 10.1093/bioinformatics/bts338. Epub 2012 Jun 12.
mcaGUI: microbial community analysis R-Graphical User Interface (GUI).
Copeland WK1, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z.

MycPermCheck 1.1 – Mycobacterium Tuberculosis Permeability Prediction tool for small Molecules

MycPermCheck 1.1

:: DESCRIPTION

MycPermCheck, given the current lack of precise molecular criteria determining mycobacterial permeability, represents an unprecedented prediction tool intended to support antimycobacterial drug discovery.

::DEVELOPER

the Research Group of Prof. Sotriffer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Perl

:: DOWNLOAD

MycPermCheck

:: MORE INFORMATION

Citation

Merget et al. (2013)
MycPermCheck: The Mycobacterium tuberculosis permeability prediction tool for small molecules,
Bioinformatics, 29(1): 62-68.

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.

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.

BioAtlas – Location-specific analysis of Microbial profiles

BioAtlas

:: DESCRIPTION

BioAtlas is a web service, primarily designed for biologists to explore where 16S rRNA strains classified from bacteria and/or archaea taxonomy are found, whether it be geographical and/or host-oriented locations.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Interactive microbial distribution analysis using BioAtlas.
Lund JB, List M, Baumbach J.
Nucleic Acids Res. 2017 Jul 3;45(W1):W509-W513. doi: 10.1093/nar/gkx304.

BURRITO – Visualization Tool for Exploratory Data Analysis of Metagenomic data

BURRITO

:: DESCRIPTION

BURRITO is a web-based tool for interactive exploration of metagenomic datasets, linking taxonomic and functional microbiome profiles

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

BURRITO

:: MORE INFORMATION

Citation

Front Microbiol. 2018 Mar 1;9:365. doi: 10.3389/fmicb.2018.00365. eCollection 2018.
BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data.
McNally CP, Eng A, Noecker C, Gagne-Maynard WC, Borenstein E.

CoMiDA v1.0.0 – Designing Minimal Microbial Communities with specified Metabolic Functions

CoMiDA v1.0.0

:: DESCRIPTION

CoMiDA is an algorithm for designing simple communities with some predefined metabolic capacities.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CoMiDA

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Jul 1;32(13):2008-16. doi: 10.1093/bioinformatics/btw107.
An algorithm for designing minimal microbial communities with desired metabolic capacities.
Eng A, Borenstein E.

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.