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Version 1.18

We have been releasing smaller patches more often recently, but majority of these updates targeted the internal structure of the system to improve stability and code quality. Since the last version we published an update about (1.8), we have implemented: Complete rewrite of our REST API – see our interactive documentation Speed improvements in page loading times. […]

Version 1.18

We have been releasing smaller patches more often recently, but majority of these updates targeted the internal structure of the system to improve stability and code quality. Since the last version we published an update about (1.8), we have implemented:

  • Complete rewrite of our REST API – see our interactive documentation
  • Speed improvements in page loading times.
  • Small improvements to the UI all across the website.
  • Changes in our admin tools and improved UI for our data-curation team.
  • Fixes to many bugs of various magnitude.

You can visit our GitHub project for a more detailed list of implemented features and bugfixes, or to report an issue yourself.

Overview

Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize coexpression and differential expression results. Some of Gemma's key features:

  • Gemma re-annotates expression platforms as the sequence level to allow more consistent cross-platform comparisons.
  • Gemma supports a variety of expression technologies, including Affymetrix, Illumina and other oligonucleotide arrays, one channel and ratiometric cDNA arrays. Support for RNA-seq data is incomplete but in the works.
  • Gemma provides manual and automated annotations of data sets to enhance usability of the data.
  • Gemma can provide external sites with processed data, web services, software and other means of including Gemma tools and data in other systems.
  • Gemma allows users to securely upload their own data, to be shared either "privately" with users of their choice. Gemma also allows users to create and save gene or data set groups for use in queries.

Go to Gemma tool.

Zoubarev, A., et al., Gemma: A resource for the re-use, sharing and meta-analysis of expression profiling data. Bioinformatics, 2012. (link)