- RITHMS: An advanced stochastic framework for the simulation of transgenerational hologenomic data
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- betaHMM: A hidden Markov model to identify differential methylation sites and regions from beta-valued methylation data
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- betaclust: A Family of Beta Mixture Models for Clustering Beta-Valued DNA Methylation Data
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- BayesRCO: Bayesian genomic prediction models for overlapping annotations
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- rpl: Randomized pairwise likelihood method for complex statistical inferences
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- padma: Pathway deviation scores using multiple factor analysis
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- maskmeans: Multi-view aggregation/splitting K-means clustering algorithm
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- coseq: Co-expression analysis of sequencing data
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- ICAL: Model selection for model based clustering of annotated data
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- metaRNASeq: Meta-analysis of RNA-seq data
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- HTSDiff: Differential analysis for RNA-seq data
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- HTSFilter: Filter for replicated high-throughput sequencing data
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- HTSCluster: Clustering high-throughput sequencing data with Poisson mixture models
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- ebdbNet: Empirical Bayes estimation for dynamic Bayesian networks
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