FunSeq2 - A flexible framework to prioritize regulatory mutations from cancer genome sequencing

Overview

This tool is specialized to prioritize somatic variants from cancer whole genome sequencing. It contains two components : 1) building data context from various resources; 2) variants prioritization. We provide downloadable scripts for users to customize the data context (found under 'Downloads'). The variants prioritization step is downloadable, and also implemented as a web server (Right Panel), along with the pre-processed data context.

Instructions

✤ Input File - BED or VCF formatted. Click the "green" button to add multiple files. With multiple files, the tool will do recurrent analysis.(Note: for BED format, user can put variants from multiple genomes into one file, see Sample input file .)
✤ Recurrence DB - User can select particular cancer types from the database. The DB will continue to be updated with newly-available WGS data.
✤ Gene List - Option to analyze variants associated with a particular set of genes. Note: Please use Gene Symbols, with one row per gene.
✤ Differential Gene Expression Analysis - Option to detect differentially expressed genes in RNA-Seq data. Two files are needed: an expression file and a class label file. Please refer to Expression input files for instructions on how to prepare these files.

✤ Note: In addition to on-site calculation, we also provide scores for all possible noncoding SNVs of GRCh37/hg19 under 'Downloads' (without annotation and recurrence analysis).
Add a gene list (Optional)

Add differential gene expression analysis (Optional)
expression file

sample class
Copyright © 2013, GersteinLab@Yale