MSIseq: Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations

A decision tree classifier for detecting microsatellite instability (MSI) in somatic mutation data from whole exome sequencing. MSI is detected based on different mutation rates in all sites as well as in simple sequence repeats. This mechanism can also be applied to sequence data of targeted gene panels with shorter sequence length.

AuthorMini Huang
Date of publication2015-06-15 16:26:10
MaintainerMini Huang <mini.huang@nus.edu.sg>
LicenseGPL (>= 2)
Version1.0.0

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Files

MSIseq
MSIseq/inst
MSIseq/inst/doc
MSIseq/inst/doc/MSIseq.pdf
MSIseq/NAMESPACE
MSIseq/data
MSIseq/data/test.mutationNum.rda
MSIseq/data/NGStraindata.rda
MSIseq/data/NGStraintype.rda
MSIseq/data/train.mutationNum.rda
MSIseq/data/NGStesttype.rda
MSIseq/data/NGStrainclass.rda
MSIseq/data/NGStestdata.rda
MSIseq/data/datalist
MSIseq/data/NGStestseqLen.rda
MSIseq/data/NGStrainseqLen.rda
MSIseq/R
MSIseq/R/Compute.input.variables.R MSIseq/R/MSIseq.train.R
MSIseq/R/sysdata.rda
MSIseq/R/find.mono.R MSIseq/R/MSIseq.classify.R
MSIseq/vignettes
MSIseq/vignettes/MSIseq.Rnw
MSIseq/MD5
MSIseq/DESCRIPTION
MSIseq/man
MSIseq/man/find.mono.repeats.Rd MSIseq/man/MSIseq.train.Rd MSIseq/man/Compute.input.variables.Rd MSIseq/man/read.fasta.Rd MSIseq/man/NGStestdata.Rd MSIseq/man/train.mutationNum.Rd MSIseq/man/MSIseq.classify.Rd MSIseq/man/test.mutationNum.Rd MSIseq/man/NGStestseqLen.Rd MSIseq/man/NGStraintype.Rd MSIseq/man/NGStraindata.Rd MSIseq/man/MSIseq-package.Rd MSIseq/man/NGStesttype.Rd MSIseq/man/NGStrainclass.Rd MSIseq/man/NGStrainseqLen.Rd

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