Category: Microbiology

SGAtools 20131030 – Web-based Analysis System for Designer Genetic Screens

SGAtools 20131030

:: DESCRIPTION

SGAtools offers a single stop solution for analysing data from genetic screens. There are three steps to the analysis pipeline, each of which can also be run separately from the rest. First, images of plates with colonies are processed to give quantified colony sizes for the screen. Next, the colony sizes are normalised and filtered within plates, taking into account position effects and other confounding factors.

::DEVELOPER

Boone lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 SGAtools

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul 1;41(Web Server issue):W591-6. doi: 10.1093/nar/gkt400. Epub 2013 May 15.
SGAtools: one-stop analysis and visualization of array-based genetic interaction screens.
Wagih O, Usaj M, Baryshnikova A, Vandersluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L.

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.

ZIBR v0.1 – Zero-Inflated Beta Random Effect model

ZIBR v0.1

:: DESCRIPTION

ZIBR is a package for fitting zero-inflated mixed-effects models for repeated measureed microbiome data.

::DEVELOPER

Hongzhe Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ZIBR

:: MORE INFORMATION

Citation

Chen EZ, Li H.
A two-part mixed-effects model for analyzing longitudinal microbiome compositional data.
Bioinformatics. 2016 Sep 1;32(17):2611-7. doi: 10.1093/bioinformatics/btw308. Epub 2016 May 14. PMID: 27187200; PMCID: PMC5860434.

PhysioFit 1.0.2 – Estimation of Extracellular Fluxes and Growth Rate

PhysioFit 1.0.2

:: DESCRIPTION

PhysioFit is a scientific tool designed to i) quantify exchange (production and consumption) fluxes and ii) cell growth rate during (batch) cultivations of microorganisms. Fluxes are estimated from time-course measurements of extracellular metabolites and biomass concentrations.

::DEVELOPER

MetaSys

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsx
  • R

:: DOWNLOAD

PhysioFit

:: MORE INFORMATION

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.