Statistical Software Packages:

1. fact: Factor analysis via correlation thresholding.
2. scorelingam: Learning topological ordering of non-Gaussian linear DAGs.
3. phsl: Partitioned hybrid structure learning.
4. EAinference: Estimator augmentation and simulation-based inference.
5. sparsebn: Learning sparse Bayesian networks from high-dimensional data.
6. discretecdAlgorithm: Learning discrete Bayesian networks by coordinate descent.
7. ccdr: Concave penalized learning of Bayesian networks.
8. SPClustering: Solution path clustering via concave penalization.

Computational Biology Software:

1. TFKFunctions: Decting clustering and ordering binding patterns among transcription factors.
2. CMF: Contrast motif finder that finds motifs with differential enrichment between two datasets.
3. HtBackground: Building a heterogeneous background model for DNA multiple alignments.
4. MultiScan: Motif scan in multiple alignments with background built from HtBackground.
5. MultiModule: Motif-module discovery in multiple species by coupling hidden Markov models.
6. CisModule: De novo motif-module discovery algorithm based on a hierarchical mixture model.
7. CisModScan: Scanning for cis-regulatory modules given PWMs.
8. GMS-MP: Gibbs motif sampler for pare correlation model.