BayesMallows - Bayesian Preference Learning with the Mallows Rank Model

An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>; Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>; Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).

Last updated 3 days ago

mallows-modelopenblascppopenmp

8.09 score 21 stars 1 dependents 36 scripts 619 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.

Last updated 4 months ago

truncated-distribution

4.90 score 6 scripts 216 downloads

BayesSurvive - 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.

Last updated 4 months ago

bayesian-cox-modelsbayesian-variable-selectiongraph-learninghigh-dimensional-statisticsomics-data-integrationsurvival-analysiscpp

4.70 score 1 stars 1 scripts 195 downloads

psbcSpeedUp - 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>).

Last updated 7 months ago

bayesian-cox-modelsomics-datasurvival-analysisopenblascppopenmp

4.65 score 3 stars 163 downloads

cellmigRation - 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.

Last updated 3 months ago

cellbiologydatarepresentationdataimportbioconductor-packagecell-trackingshinytrajectory-analysis

4.60 score 4 scripts 130 downloads

EnrichIntersect - Enrichment Analysis and Intersecting Sankey Diagram

A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al., 2022 <doi:10.1016/j.isci.2022.104767>) or similar methods.

Last updated 10 months ago

4.60 score 4 stars 300 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>.

Last updated 5 months ago

contingency-table

4.43 score 3 stars 1 dependents 7 scripts 393 downloads

permChacko - 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.

Last updated 4 months ago

4.40 score 3 scripts 162 downloads

DIscBIO - 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>.

Last updated 1 years ago

biomarker-discoveryjupyter-notebookscrna-seqsingle-cell-analysistranscriptomicsopenjdk

4.38 score 12 stars 5 scripts 249 downloads

matlab2r - 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.

Last updated 1 years ago

matlab

3.48 score 2 stars 1 dependents 192 downloads