Packages for Network Analysis:

NET

  • Description: Computationally efficient tests of network effects for weighted direct network with statistical guarantee
  • Reference: W. Du, Y. Zhang, and W. Zhou (2024). Optimal Nonparametric Inference on Network Effects with Dependent Edges (ArXiv).
  • Download link: Github (Maintainer : W. Du)

Packages for Genomics and Bioinformatics:

PARSE

  • Description: Simultaneous clustering-DE analysis for scRNA-Seq to identify HVG without double dipping 
  • Reference: L. Zhang, X. Tang, W. Zhou, and L. Wang (2024). High-resolutional feature identification on data heterogeneity in high-dimensional clustering, preprint
  • Download link: CRAN, Github (Maintainer : L. Zhang)

CESME

  • Description: scRNA-Seq clustering that is robust against server data heavy tailedness and asymmetricity, normalization-free approach.
  • Reference: L. Zhang, B. Wang, W. Zhou, L. Wang, and H. Zou (2024). High-dimensional latent semiparametric mixture model for clustering large non-Gaussian data, preprint
  • Download link: CRAN (Maintainer : L. Zhang)

HDtest

  • Reference:
    • J. Chang, W. Zhou, L. Wang, and W.-X. Zhou (2017). Comparing large covariance matrices under weak conditions on the dependence structure and its application to gene clustering, Biometrics 2017, 73(1), 31-41. (website)
    • J. Chang, C. Zheng, W.-X. Zhou, and W. Zhou (2017). Simulation-based hypothesis testing of high dimensional means under covariance heterogeneity, Biometrics 2017, 73(4), 1300-1310. (website)
    • J. Chang, Q. Yao, and W. Zhou (2017). Testing for high-dimensional white noise using maximum cross correlations, Biometrika2017, 104(1), 111-127. (website)
  • Download link: CRAN, Github (updated 08/22/2018, Maintainer : M. Cao)

MAPTest

  • Description: scRNA-Seq or bulk-Seq DE analysis for longitudinal studies
  • Reference: M. Cao, W. Zhou, F.J. Breidt, and G. Peers (2019). Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis, Biometrics 2020, 76(1), 9-22 (website)
  • Download link: Github (Maintainer : M. Cao)

Packages for High-Dimensional Statistics:

FILTER

  • Reference: Y. Lin, W. Zhou, J. Yin, Z. Gang, and G. Xiao (2021). Fused logistic threshold regression for identifying genetic heterogeneity and therapy effectiveness prediction. (with Y. Lin, Z. Geng, G. Xiao, and J. Yin, ArXiv, 2021)
  • Download link: Github (Maintainer : Y, Lin)