~~NOTOC~~
====== Cancer Bayesian Selection Estimation (CBaSE) ======
 
===== Download =====

{{ :cbase_v1.0.gzip | CBaSE v1.0 }}

===== Usage =====

=== Running CBaSE ===

<code>
python 
</code>

=== Input file format ===

^Gene symbol^Mutation effect       ^Mutated nucleotide       ^Context index^
|ECE1	|coding-synon	|C	|26|
|SAMD11	|missense	|A	|53|
|TNFRSF4	|nonsense	|A	|52|


(1) **Gene symbol** -- corresponds to the official gene symbol as used in the UCSC knownGene track.\\
(2) **Mutation effect** -- one of ["missense", "nonsense", "coding-synon", "utr-3", "utr-5"].\\
(3) **Mutated nucleotide** -- one of [A, C, G, T].\\
(4) **Context index** -- 0-based indices of tri- or pentanucleotide contexts can be looked up [[pagename|here]].

===== CBaSE web tool =====

The CBaSE web tool can be found [[http://genetics.bwh.harvard.edu/cbase/index.html|here]].

===== How to cite =====

Please cite

Contact: [[dweghorn@research.bwh.harvard.edu|Donate Weghorn]]