LncFinder has been included in CRAN (Comprehensive R Archive Network). This package can be installed simply by entering command install.packages("LncFinder") in R, and an appropriate version with all dependencies will be installed automatically.

If users try to identify transcripts with secondary structure information, software RNAfold from ViennaRNA Package is required.

Additional models for other species can be downloaded from GitHub.

Identify Sequences
result_1 <- LncFinder::lnc_finder(yourFile, SS.features = FALSE, format = "DNA", frequencies.file = "human", svm.model = "human")

result_2 <- LncFinder::lnc_finder(Sequences, SS.features = TRUE, format = "SS", frequencies.file = "mouse", svm.model = "mouse")

Build New Model
myFile <- LncFinder::make_frequencies(cds.seq, mRNA.seq, lncRNA.seq, SS.features = TRUE, cds.format = "DNA", lnc.format = "SS")

myModel <- LncFinder::build_model(mRNA.seq, lncRNA.seq = SS.Seq, frequencies.file = myFile, SS.features = TRUE, lncRNA.format = "SS", mRNA.format = "SS", parallel.cores = -1, folds.num = 10)

Compute/Import Secondary Structure Information
SS_Seq_1 <- LncFinder::run_RNAfold(Seq, RNAfold.path = "RNAfold", parallel.cores = 2)

SS_Seq_2 <- LncFinder::read_SS(oneFile.loc = yourFile, separateFile = FALSE, withMFE = TRUE)

Perform SVM Parameter Tuning
tuneSVM <- LncFinder::svm_tune(dataset = Dataset, positive.class = "NonCoding", folds.num = 5, seed = 1, gamma.range = (2^seq(-5, -1, 0)), cost.range = (2^seq(0, 5, 1)), return.model = TRUE, parallel.cores = -1)