Package: PINSPlus 2.0.7

Van-Dung Pham

PINSPlus: Clustering Algorithm for Data Integration and Disease Subtyping

Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et al. (2019) <doi:10.1093/bioinformatics/bty1049>, Nguyen et al. (2017)<doi:10.1101/gr.215129.116>, Nguyen et al. (2021)<doi:10.3389/fonc.2021.725133>).

Authors:Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen

PINSPlus_2.0.7.tar.gz
PINSPlus_2.0.7.tar.gz(r-4.5-noble)PINSPlus_2.0.7.tar.gz(r-4.4-noble)
PINSPlus_2.0.7.tgz(r-4.4-emscripten)PINSPlus_2.0.7.tgz(r-4.3-emscripten)
PINSPlus.pdf |PINSPlus.html✨
PINSPlus/json (API)

# Install 'PINSPlus' in R:
install.packages('PINSPlus', repos = 'https://cloud.r-project.org')
Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • AML2004 - Acute myelogenous leukemia dataset
  • KIRC - Kidney renal clear cell carcinoma dataset

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblascpp

2.95 score 1 packages 352 downloads 3 mentions 2 exports 16 dependencies

Last updated 12 months agofrom:2b48b77780. Checks:2 OK, 1 NOTE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKApr 01 2025
R-4.5-linux-x86_64NOTEApr 01 2025
R-4.4-linux-x86_64OKApr 01 2025

Exports:PerturbationClusteringSubtypingOmicsData

Dependencies:clustercodetoolsdoParallelentropyFNNforeachimputeirlbaiteratorslatticeMatrixmatrixStatsmclustRcppRcppArmadilloRcppParallel

PINSPlus: Clustering Algorithm for Data Integration and Disease Subtyping

| Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen$^*$ | Department of Computer Science and Engineering | University of Nevada, Reno, NV 89557

Rendered fromPINSPlus.Rmdusingknitr::knitron Apr 01 2025.

Last update: 2021-12-14
Started: 2018-03-16

Citation

Nguyen T, Tagett R, Diaz D, Draghici S (2017). “A novel approach for data integration and disease subtyping.” Genome Research.

Nguyen H, Shrestha S, Draghici S, Nguyen T (2018). “PINSPlus: A tool for tumor subtype discovery in integrated genomic data.” Bioinformatics.

Nguyen H, Tran D, Tran B, Roy M, Cassell A, Dascalu S, Draghici S, Nguyen T (2021). “SMRT: Randomized Data Transformation for Cancer Subtyping and Big Data Analysis.” Frontiers in oncology.

Corresponding BibTeX entries: 

  @Article{nguyen2017novel,
    title = {A novel approach for data integration and disease
      subtyping},
    author = {Tin Nguyen and Rebecca Tagett and Diana Diaz and Sorin
      Draghici},
    journal = {Genome Research},
    year = {2017},
    date = {2017-10-24},
  }

  @Article{nguyen2018pinsplus,
    title = {PINSPlus: A tool for tumor subtype discovery in integrated
      genomic data},
    author = {Hung Nguyen and Sangam Shrestha and Sorin Draghici and
      Tin Nguyen},
    journal = {Bioinformatics},
    year = {2018},
    date = {2018-12-24},
  }

  @Article{nguyen2021smrt,
    title = {SMRT: Randomized Data Transformation for Cancer Subtyping
      and Big Data Analysis},
    author = {Hung Nguyen and Duc Tran and Bang Tran and Monikrishna
      Roy and Adam Cassell and Sergiu Dascalu and Sorin Draghici and
      Tin Nguyen},
    journal = {Frontiers in oncology},
    year = {2021},
    date = {2021-10-20},
  }