Tag: Microbial Ecology

TEXMEX 0.3 – Treatment Effect eXplorer for Microbial Ecology eXperiments

TEXMEX 0.3

:: DESCRIPTION

Texmex is designed to normalize OTU count data and correct for community composition changes that are common to a control and experimental unit.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python
  • R

:: DOWNLOAD

TEXMEX

:: MORE INFORMATION

Citation

Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodríguez J, Hazen TC, Alm EJ.
A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.
PLoS One. 2016 May 6;11(5):e0154804. doi: 10.1371/journal.pone.0154804. PMID: 27152415; PMCID: PMC4859510.

TIME – Temporal Insights into Microbial Ecology

TIME

:: DESCRIPTION

TIME is a web application which enables microbiome researchers to visually explore, make logical inferences, and gather insights from time series microbiome datasets.

::DEVELOPER

TIME team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Baksi KD, Kuntal BK, Mande SS.
‘TIME’: A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.
Front Microbiol. 2018 Jan 24;9:36. doi: 10.3389/fmicb.2018.00036. Erratum in: Front Microbiol. 2020 Nov 11;11:605295. PMID: 29416530; PMCID: PMC5787560.

EMPeror 1.0.0-beta.20 – Analysis of High Throughput Microbial Ecology datasets

EMPeror 1.0.0-beta.20

:: DESCRIPTION

Emperor is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

 EMPeror

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • Numpy
  • qcli

:: DOWNLOAD

 EMPeror

 :: MORE INFORMATION

Citation

EMPeror: a tool for visualizing high-throughput microbial community data.
Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R.
Gigascience. 2013 Nov 26;2(1):16. doi: 10.1186/2047-217X-2-16.