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


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 provided downloadable scripts for users to customize the data context (found under 'Downloads'). The variants prioritization step is downloadable, and also implemented as web server (Right Panel), with pre-processed data context.


✤ 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: This online web server is based on Funseq2 v2.10. In addition to on-site calculation, we also provide latest updates, 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
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