Package that implements the COSNet classification algorithm. The algorithm predicts node labels in partially labeled graphs where few positives are available for the class being predicted.

Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput data with ordered conditions.

The parody package provides routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

This package provides routines for parsing Affymetrix data files based upon file format information. The primary focus is on accessing the CEL and CDF file formats.

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

This package converts the output of the Sailfish and Salmon RNA-seq quantification tools so that it can be used with the Sleuth differential analysis package.

randfold computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

This package provides density, distribution, quantile and hazard functions of a stable variate, as well as generalized regression models for the parameters of a stable distribution.

This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.

This package implements targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality.

This package implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.

This package implements the Simulating Optimal FUNctioning framework for site-scale simulations of ecosystem processes, including model calibration. It contains Fortran 90 modules for the P-model (Stocker et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH (Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>) and BiomeE (Weng et al. (2015) <doi:10.5194/bg-12-2655-2015>).

This package provides functions to compute recentered influence functions (RIF) of a distributional variable at the mean, quantiles, variance, gini or any custom functional of interest. The package allows to regress the RIF on any number of covariates. Generic print, plot and summary functions are also provided. Reference: Firpo, Sergio, Nicole M. Fortin, and Thomas Lemieux. (2009) <doi:10.3982/ECTA6822>. "Unconditional Quantile Regressions.".

This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly oaDOI, a service finding free full-texts of academic papers by linking DOIs with open access journals and repositories. It provides unified access to various data sources for open access full-text links including Crossref and the Directory of Open Access Journals (DOAJ). API usage is free and no registration is required.

Create Tables for Reporting Clinical Trials. Calculates descriptive statistics and hypothesis tests, arranges the results in a table ready for reporting with LaTeX, HTML or Word.

Play casino games in the R console, including poker, blackjack, and a slot machine. Try to build your fortune before you succumb to the gambler's ruin!

Fast functions for effective sample size, weighted multivariate mean, variance, and quantile computation, and weight diagnostic plot for generic importance sampling type or other probability weighted samples.

This package contains functions to perform copula estimation by the non-parametric Bayesian method, Dirichlet-based Polya Tree. See Ning (2018) <doi:10.1080/00949655.2017.1421194>.

Create a grid-based graphviz using the following functions: 1 - Creating the data.frame where the nodes are; 2 - Adding and editing nodes; 3 - Plotting these nodes.

Package for Genetic Epidemiologic Methods Developed at MSKCC. It contains functions to calculate haplotype specific odds ratio and the power of two stage design for GWAS studies.

This package provides functions to compute generalized eigenvalues and eigenvectors, the generalized Schur decomposition and the generalized Singular Value Decomposition of a matrix pair, using Lapack routines.

This package provides methods to perform and analyse I-prior regression models. Estimation is done either via direct optimisation of the log-likelihood or an EM algorithm.

One-way and two-way analysis of variance for replicated point patterns, grouped by one or two classification factors, on the basis of the corresponding K-functions.

Interact with LaminDB'. LaminDB is an open-source data framework for biology. This package allows you to query and download data from LaminDB instances.