This package provides a package for quantifying, profiling and removing cell free mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments.

This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.

This package implements asymptotic methods related to maximally selected statistics, with applications to single-nucleotide polymorphism (SNP) data.

This package provides lots of plotting, various labeling, axis and color scaling functions for R.

This package provides a set of predicates and assertions for checking the properties of code. This is mainly for use by other package developers who want to include run-time testing features in their own packages.

This package provides tools to compute marginal effects from statistical models and return the result as tidy data frames. These data frames are ready to use with the ggplot2 package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are ggpredict() and ggeffect(). There is a generic plot() method to plot the results using ggplot2.

The smurf package contains the implementation of the Sparse Multi-type Regularized Feature (SMuRF) modeling algorithm to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood. Next to the fitting procedure, following functionality is available:

• Selection of the regularization tuning parameter lambda using three different approaches: in-sample, out-of-sample or using cross-validation.

• S3 methods to handle the fitted object including visualization of the coefficients and a model summary.

This package provides functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.

The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. This package also supports rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.

NbClust provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.

This package provides a parallel estimation of the mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks.

This package provides a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.

This is a package for interactive Reingold-Tilford tree diagrams created using D3.js, where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame.

This package provides various R programming tools for model fitting.

Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System.

This package performs Bayesian calibration of computer models as per Kennedy and O'Hagan 2001. The package includes routines to find the hyperparameters and parameters; see the help page for stage1() for a worked example using the toy dataset. A tutorial is provided in the calex.Rnw vignette; and a suite of especially simple one dimensional examples appears in inst/doc/one.dim/.

The R package data.table is an extension of data.frame providing functions for fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group, column listing and fast file reading.

Functions to help implement the extraction / subsetting / indexing function [ and replacement function [<- of custom matrix-like types (based on S3, S4, etc.), modeled as closely to the base matrix class as possible (with tests to prove it).

This package provides an implementation of scale functions for setting axis breaks of a ggplot.

The biglm package lets you create a linear model object that uses only codep^2 memory for p variables. It can be updated with more data using update. This allows linear regression on data sets larger than memory.

Given a protein multiple sequence alignment, it is a daunting task to assess the effects of substitutions along sequence length. The aaSEA package is intended to help researchers to rapidly analyze property changes caused by single, multiple and correlated amino acid substitutions in proteins.

oai provides a general purpose client to work with any Open Archives Initiative Protocol for 'Metadata' Harvesting (OAI-PMH) service. Functions are provided to work with the OAI-PMH verbs: GetRecord, Identify, ListIdentifiers, ListMetadataFormats, ListRecords, and ListSets.

This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.

This package provides functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.