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cbase [2017/10/12 01:34]
dweghorn
cbase [2017/10/29 22:22]
dweghorn
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 +~~NOTOC~~
 ====== Cancer Bayesian Selection Estimation (CBaSE) ====== ====== Cancer Bayesian Selection Estimation (CBaSE) ======
- 
-[[http://​www.nature.com/​ng/​journal/​vaop/​ncurrent/​full/​ng.3795.html|Chun et al. 2017]] 
    
 ===== Download ===== ===== Download =====
-{{ :​jlim-1.0.2.tar.gz | JLIM release v1.0.2 }} 
  
-===== How to install =====+{{ :​cbase_v1.0.gzip | CBaSE v1.0 }}
  
-**getopt**+===== Usage ===== 
 + 
 +=== Running CBaSE ===
  
 <​code>​ <​code>​
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 </​code>​ </​code>​
  
-==== Example data ====+=== 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]]