Tools

Linear aggregation analysis

This tool performs the linear aggregation analysis from Scolari et al. Molecular BioSystems 7, 878-888 2011.

Perform the linear aggregation cluster analysis

Multifun ontology enrichment test

(To be written)

Perform the functional classification enrichment test

Multiple sliding window histogram

This tool compares the spatial distribution of two or more data sets by superimposing the plots of their sliding window histogram along the chromosome with a user-prescribed window-size.

Plot multiple sliding-window histograms

Local Pearson correlation

This tool compares the spatial distribution of two data sets by plotting the local Pearson correlation coefficient between their sliding-window histograms along the chromosome with a prescribed window size.

Plot the local Pearson correlation

Operations with data sets

Intersection of multiple data sets and hypergeometric test

This tool tests the statistical significance of the intersection between two data sets. It also creates a new data set as an intersection betwen two existing ones.

Intersect data sets

Merge lists

This tool creates a new data set by merging two already existing ones.

Merge data sets

Load a list of genes from file

This tool allows to load a personal data set as a gene list.

Load a data set from file

List of genes from list of binding sites (or chromosomal loci)

This tool implements a simple algorithm that generates a gene list out of a list of binding sites or chromosomal loci. For example, it can be used to apply the linear aggregation analysis to CHiP-Chip or Chip-seq binding site data.

Generate a gene list from a list of loci

List of genes from known regulons (RegulonDB)

(To be written)

Generate a data set as the list of genes controlled by specified transcription factors

List of genes from functional categories (MultiFUN)

(To be written)

Generate a data set from the genes belonging to specified functional categories