# Gitools

## What is Gitools ?

Gitools is a framework for analysis and visualization of genomic data. It's being developed by Biomedical Genomics Group at GRIB located at PRBB (Barcelona). It is in a very early stage of development and so there are still many things missing.

## What kind of analysis can I do ?

For the time being it has been implemented only a kind of enrichment analysis that allows to perform statistical tests for different conditions at the same time. There are many different tests you can choose from:

- For continuous data:
  - z-score of mean
  - z-score of median
- For binary data:
  - Binomial exact
  - Binomial with Normal aproximation
  - Binomial with Poisson aproximation
  - Fisher's exact
  - Chi square
  - Hipergeometric

It includes some filters that can transform continuous data to binary data in order to use the later analysis with continuous data.

For multiple test correction we implement Bonferroni (more restrictive) and Benjamini Hochberg False Discovery Rate (less restrictive).

It is planned to integrate some analysis available in R/Bioconductor as GOstats and GSEA, and q-values for FDR.

## How can I visualize the results ?

The results are shown in table using a color scale that allows to identify easily the tests with significant results from the one's that are not. When you click in a test you can view all the results obtained for that test in a convenient way. You can also do some things as filtering the results, sorting, changing visibility of rows and columns, and so on that allows you to better understand and interpret the results, and also to generate figures for your papers and presentations.

## How can I use Gitools ?

Gitools has a graphical interface that allows to perform analysis and browse and work with the results. It also contains a command line tool to perform analysis (useful when used with scripts). It is being developed with Java, so if you have installed the Java runtime you can download and start using it very easily. It requires at least the version 1.6 of Java.

## Home page

For more information and downloads visit: www.gitools.org

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