GPTCM - Generalized Promotion Time Cure Model with Bayesian Shrinkage Priors
Generalized promotion time cure model (GPTCM) via Bayesian hierarchical modeling for multiscale data integration (Zhao et al. (2025) <doi:10.48550/arXiv.2509.01001>). The Bayesian GPTCMs are applicable for both low- and high-dimensional data.
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bayesian-inferencecell-populationsmultiscale-dataomics-data-integrationsurvival-analysistumor-heterogeneitytumor-microenvironmentvariable-selectionopenblascppopenmp
4.85 score 5 scripts 127 downloadsBayesSurvive - Bayesian Survival Models for High-Dimensional Data
An implementation of Bayesian survival models with graph-structured selection priors for sparse identification of omics features predictive of survival (Madjar et al., 2021 <doi:10.1186/s12859-021-04483-z>) and its extension to use a fixed graph via a Markov Random Field (MRF) prior for capturing known structure of omics features, e.g. disease-specific pathways from the Kyoto Encyclopedia of Genes and Genomes database (Hermansen et al., 2025 <doi:10.48550/arXiv.2503.13078>).
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bayesian-cox-modelsbayesian-variable-selectiongraph-learninghigh-dimensional-statisticsomics-data-integrationsurvival-analysisopenblascppopenmp
4.78 score 4 stars 1 scripts 269 downloadsDIscBIO - A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
An open, multi-algorithmic pipeline for easy, fast and efficient analysis of cellular sub-populations and the molecular signatures that characterize them. The pipeline consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification. More details on Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements extensions of the work published by Ghannoum et. al. (2019) <doi:10.1101/700989>.
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biomarker-discoveryjupyter-notebookscrna-seqsingle-cell-analysistranscriptomicsopenjdk
4.75 score 14 stars 5 scripts 487 downloadscellmigRation - Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.
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cellbiologydatarepresentationdataimportbioconductor-packagecell-trackingshinytrajectory-analysis
4.60 score 1 stars 6 scripts 328 downloadspsbcSpeedUp - Penalized Semiparametric Bayesian Cox Models
Algorithms to speed up the Bayesian Lasso Cox model (Lee et al., Int J Biostat, 2011 <doi:10.2202/1557-4679.1301>) and the Bayesian Lasso Cox with mandatory variables (Zucknick et al. Biometrical J, 2015 <doi:10.1002/bimj.201400160>).
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bayesian-cox-modelsbayesian-lassoomics-datasurvival-analysisopenblascppopenmp
4.48 score 3 stars 267 downloadsBayesSUR - Bayesian Seemingly Unrelated Regression Models in High-Dimensional Settings
Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, the software paper is in Zhao et al. (2021) <doi:10.18637/jss.v100.i11>, and the model with random effects is described in Zhao et al. (2024) <doi:10.1093/jrsssc/qlad102>.
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linear-regressionmultivariate-analysisopenblascppopenmp
4.08 score 3 scripts 419 downloads
TruncExpFam - Truncated Exponential Family
Handles truncated members from the exponential family of probability distributions. Contains functions such as rtruncnorm() and dtruncpois(), which are truncated versions of rnorm() and dpois() from the stats package that also offer richer output containing, for example, the distribution parameters. It also provides functions to retrieve the original distribution parameters from a truncated sample by maximum-likelihood estimation.
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truncated-distribution
3.70 score 8 scripts 281 downloadspermChacko - Chacko Test for Order-Restriction with Permutation
Implements an extension of the Chacko chi-square test for ordered vectors (Chacko, 1966, <https://www.jstor.org/stable/25051572>). Our extension brings the Chacko test to the computer age by implementing a permutation test to offer a numeric estimate of the p-value, which is particularly useful when the analytic solution is not available.
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3.70 score 3 scripts 165 downloads
contingencytables - Statistical Analysis of Contingency Tables
Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
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contingency-table
3.62 score 6 stars 14 scripts 454 downloadsmatlab2r - Translation Layer from MATLAB to R
Allows users familiar with MATLAB to use MATLAB-named functions in R. Several basic MATLAB functions are written in this package to mimic the behavior of their original counterparts, with more to come as this package grows.
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matlab
3.48 score 2 stars 1 dependents 149 downloads