|
r-ipflasso
|
public |
The core of the package is cvr2.ipflasso(), an extension of glmnet to be used when the (large) set of available predictors is partitioned into several modalities which potentially differ with respect to their information content in terms of prediction. For example, in biomedical applications patient outcome such as survival time or response to therapy may have to be predicted based on, say, mRNA data, miRNA data, methylation data, CNV data, clinical data, etc. The clinical predictors are on average often much more important for outcome prediction than the mRNA data. The ipflasso method takes this problem into account by using different penalty parameters for predictors from different modalities. The ratio between the different penalty parameters can be chosen by cross-validation.
|
2025-09-23 |
|
r-paireddata
|
public |
Many datasets and a set of graphics (based on ggplot2), statistics, effect sizes and hypothesis tests are provided for analysing paired data with S4 class.
|
2025-09-23 |
|
r-goric
|
public |
Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate linear models and generalised linear models.
|
2025-09-23 |
|
coded-flows
|
public |
Various utilities for Coded Flows
|
2025-09-23 |
|
r-reactlog
|
public |
Building interactive web applications with R is incredibly easy with 'shiny'. Behind the scenes, 'shiny' builds a reactive graph that can quickly become intertwined and difficult to debug. 'reactlog' (Schloerke 2019) <doi:10.5281/zenodo.2591517> provides a visual insight into that black box of 'shiny' reactivity by constructing a directed dependency graph of the application's reactive state at any time point in a reactive recording.
|
2025-09-23 |
|
arm_pyart
|
public |
Python ARM Radar Toolkit
|
2025-09-23 |
|
r-liqueuer
|
public |
Provides three classes: Queue, PriorityQueue and Stack. Queue is just a "plain vanilla" FIFO queue; PriorityQueue orders items according to priority. Stack implements LIFO.
|
2025-09-23 |
|
r-nls2
|
public |
Adds brute force and multiple starting values to nls.
|
2025-09-23 |
|
r-effects
|
public |
Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.
|
2025-09-23 |
|
r-frictionless
|
public |
Read and write Frictionless Data Packages. A 'Data Package' (<https://specs.frictionlessdata.io/data-package/>) is a simple container format and standard to describe and package a collection of (tabular) data. It is typically used to publish FAIR (<https://www.go-fair.org/fair-principles/>) and open datasets.
|
2025-09-23 |
|
r-treetools
|
public |
Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
|
2025-09-23 |
|
geotexxx
|
public |
Package om geotechnisch grondonderzoek te verwerken
|
2025-09-23 |
|
folly
|
public |
Facebook Open-source Library
|
2025-09-23 |
|
r-ggsci
|
public |
A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.
|
2025-09-23 |
|
pyjuliapkg
|
public |
Julia version manager and package manager
|
2025-09-23 |
|
rslib
|
public |
The Rsbuild-based library development tool.
|
2025-09-23 |
|
intel-media-driver
|
public |
Intel(R) Media Driver for VAAPI
|
2025-09-23 |
|
r-vbsr
|
public |
Efficient algorithm for solving ultra-sparse regularized regression models using a variational Bayes algorithm with a spike (l0) prior. Algorithm is solved on a path, with coordinate updates, and is capable of generating very sparse models. There are very general model diagnostics for controling type-1 error included in this package.
|
2025-09-23 |
|
stopt
|
public |
Library for stochastic control
|
2025-09-23 |
|
tranche
|
public |
ConfigParser with layered precedence, provenance, and safe expressions
|
2025-09-23 |
|
r-getip
|
public |
A micro-package for getting your 'IP' address, either the local/internal or the public/external one. Currently only 'IPv4' addresses are supported.
|
2025-09-23 |
|
r-rworkflows
|
public |
Reproducibility is essential to the progress of research, yet achieving it remains elusive even in computational fields. Continuous Integration (CI) platforms offer a powerful way to launch automated workflows to check and document code, but often require considerable time, effort, and technical expertise to setup. We therefore developed the rworkflows suite to make robust CI workflows easy and freely accessible to all R package developers. rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template, 2) an R package to quickly implement a standardised workflow, and 3) a centrally maintained GitHub Action.
|
2025-09-23 |
|
r-remacor
|
public |
Meta-analysis is widely used to summarize estimated effects sizes across multiple statistical tests. Standard fixed and random effect meta-analysis methods assume that the estimated of the effect sizes are statistically independent. Here we relax this assumption and enable meta-analysis when the correlation matrix between effect size estimates is known. Fixed effect meta-analysis uses the method of Lin and Sullivan (2009) <doi:10.1016/j.ajhg.2009.11.001>, and random effects meta-analysis uses the method of Han, et al. <doi:10.1093/hmg/ddw049>.
|
2025-09-23 |
|
r-omicnavigator
|
public |
A tool for interactive exploration of the results from 'omics' experiments to facilitate novel discoveries from high-throughput biology. The software includes R functions for the 'bioinformatician' to deposit study metadata and the outputs from statistical analyses (e.g. differential expression, enrichment). These results are then exported to an interactive JavaScript dashboard that can be interrogated on the user's local machine or deployed online to be explored by collaborators. The dashboard includes 'sortable' tables, interactive plots including network visualization, and fine-grained filtering based on statistical significance.
|
2025-09-23 |
|
r-pdtoolkit
|
public |
The goal of this package is to cover the most common steps in probability of default (PD) rating model development and validation. The main procedures available are those that refer to univariate, bivariate, multivariate analysis, calibration and validation. Along with accompanied 'monobin' and 'monobinShiny' packages, 'PDtoolkit' provides functions which are suitable for different data transformation and modeling tasks such as: imputations, monotonic binning of numeric risk factors, binning of categorical risk factors, weights of evidence (WoE) and information value (IV) calculations, WoE coding (replacement of risk factors modalities with WoE values), risk factor clustering, area under curve (AUC) calculation and others. Additionally, package provides set of validation functions for testing homogeneity, heterogeneity, discriminatory and predictive power of the model.
|
2025-09-23 |
