Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Last revision Both sides next revision
cbase [2017/10/12 01:34]
dweghorn
cbase [2017/10/29 22:01]
dweghorn
Line 1: Line 1:
 +~~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>​
Line 14: Line 14:
 </​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]].
  
 +===== Contact =====
  
 +[[dweghorn@research.bwh.harvard.edu|Donate Weghorn]]