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cbase [2017/10/12 01:33]
dweghorn created
cbase [2017/10/12 17:42]
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>​
-Rscript -e '​install.packages("​getopt",​ repos="​http://​cran.r-project.org"​)' ​+python ​
 </​code>​ </​code>​
  
-==== Example data ====+=== Input file format ​=== 
 + 
 +^Gene symbol^Mutation effect ​      ​^Mutated nucleotide ​      ​^Context index^ 
 +|ECE1 |coding-synon |C |38| 
 +|SAMD11 |missense |A |29| 
 +|TNFRSF4 |nonsense |A |28| 
 + 
 + 
 +(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",​ "​intron",​ "​utr-3",​ "​utr-5",​ "​IGR"​] ("​intron"​ and "​IGR"​ mutations are discarded). 
 +(3) Mutated nucleotide 
 +    One of [A, C, G, T]. 
 +(4) Context index 
 +    0-based indices of trinucleotide contexts can be looked up here.
  
 +===== CBaSE tool =====
  
 +You can also find a web-based user interface for CBaSE here: http://​genetics.bwh.harvard.edu/​cbase/​index.html