gkmSVM: an R package for gapped-kmer SVM #MMPMID27153639
Ghandi M; Mohammad-Noori M; Ghareghani N; Lee D; Garraway L; Beer MA
Bioinformatics 2016[Jul]; 32 (14): 2205-7 PMID27153639show ga
Summary: We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorithm. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.Availability and Implementation: gkmSVM package is freely available through the Comprehensive R Archive Network (CRAN), for Linux, Mac OS and Windows platforms. The C?++?implementation is available at www.beerlab.org/gkmsvmContact:mghandi@gmail.com or mbeer@jhu.eduSupplementary information:Supplementary data are available at Bioinformatics online.