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Cancer Bayesian Selection Estimation (CBaSE)

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Usage

Running CBaSE

python 

Input file format

Gene symbolMutation 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 here.

CBaSE web tool

The CBaSE web tool can be found here.