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cbase [2017/10/29 22:22] (current) – created - external edit 127.0.0.1
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 +~~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]]