GenePattern

GenePattern

GenevPattern is a web interface for software. It was developed at the Broad Institute (Cambridge, USA). Genepattern contains a collection of tools, integrated under modules (currently 250), mainly for the analysis of high throughput genomics data.
There is a freely accessible server at the Broad Institute itself, but we also provide 4 VIB servers maintained by the VIB Bioinformatics Core. GenePattern can be installed local on Linux and MacOS (free to download).

Get it!

Mail to This email address is being protected from spambots. You need JavaScript enabled to view it. to request access to the GenePattern servers.

GenePattern at VIB

The VIB Bioinformatics Core maintains 4 GenePattern servers:
 VIB HQ (VIB members can obtain account)
 KU Leuven ICTS Tier-2 (KU Leuven/UHasselt members can obtain account)
 VIB Nucleomics Core (customized for managing local workflows)
 Test server (internal testing)

Next to the already excisting modules, there are new modules added for VIB: STAR NGS Aligner, HTSeq RNASeq Counter, CHROMIUM Single Cell NGS Manager,...
There are also dynamic lists for some modules pointing at anonymous ftp servers with data for 16 genomes studied at VIB.

GenePattern features
 Users can create pipelines that automatically execute a series of modules in succession
 Often output of modules can be given as input to another module
 Outputs are stored on the server for some days
 Users can upload data and keep them stored on the server
 Users with 'admin' rights can create and install new modules
 GenePattern Notebook (based on Jupyter) allows users to interleave text with GenePattern analysis

Additional Material

User guide at Broad Institute: GenePattern user guide

GenePattern