Name Function Features Language paper documentation
ClusterMine Identify sample clusters based on gene expression data Knowledge integrated; identify gene sets/functions that may underlie cluster R PDF web
iREAD intron retention detection from RNA-seq only suitable for polyA RNA-seq Python/Perl PDF web
GTFtools Analyze various modes of gene models in GTF format python PDF web
MIL Multiple instance learning (MIL) algorithms for learning instance label based on instance-level features and bag-level labels. An application in bioinformatics is to predict splice isoform functions based on gene function annotations python web
libPLS a library for building PLS regression and classification models Methods on cross validation,outlier detection and feature selection integrated; Model Population Analysis approaches. Matlab PDF web
Random Frog feature selection/variable selection Especially suitable for high dimensional data; Reversible Jump Markov Chain Monte Carlo(RJMCMC)-like Matlab PDF web