This package contains data which are used by functions of the abc package which implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit.

This package provides tools for the maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); it includes inference and basic methods.

This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both hcubature and pcubature routines in addition to a vector interface.

Namae (名前) is a parser for human names. It recognizes personal names of various cultural backgrounds and tries to split them into their component parts (e.g., given and family names, honorifics etc.).

Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.

This package provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

This package contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.

This package provides a header-only C++ library is provided with support for dates, time zones, ISO weeks, Julian dates, and Islamic dates. date offers extensive date and time functionality for the C++11, C++14 and C++17 standards. A slightly modified version has been accepted (along with tz.h) as part of C++20. This package regroups all header files from the upstream repository so that other R packages can use them in their C++ code.

RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.

Phylogenetic trees generally contain multiple components including nodes, edges, branches and associated data. This package provides an approach to convert tree objects to tidy data frames. It also provides tidy interfaces to manipulate tree data.

This package provides several analysis-related functions for the book entitled "R statistics and graph for medical articles" (written in Korean), version 1, by Keon-Woong Moon with Korean demographic data with several plot functions.

This package provides a collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.

This package provides Ruby support for the HOCON configuration file format. It supports parsing and modifying HOCON and JSON files, and rendering parsed objects back to a String.

Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.

This package is a r-ggplot2 extension that provides flipped components:

1. horizontal versions of r-ggplot2 stats and r-ggplot2 geoms;

2. vertical versions of r-ggplot2 positions.

This package provides distance-based parametric bootstrap tests for clustering with spatial neighborhood information. It implements some distance measures, clustering of presence-absence, abundance and multilocus genetical data for species delimitation, nearest neighbor based noise detection.

Full 64-bit resolution date and time functionality with nanosecond granularity is provided, with easy transition to and from the standard POSIXct type. Three additional classes offer interval, period and duration functionality for nanosecond-resolution timestamps.

This package provides integration of the Google Repo tool with emacs. It displays the output of the repo status command in a buffer and launches Magit from the status buffer for the project at point.

This package contains a MonadRef type class that abstracts over the details of manipulating references, allowing one to write code that can operate in either the ST monad or the IO monad.

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

This package provides tools for the identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

Query, set, and delete credentials from the git credential store. Manage GitHub tokens and other git credentials. This package is to be used by other packages that need to authenticate to GitHub and/or other git repositories.

This package manages the installation of CMake for building Bioconductor packages. This avoids the need for end-users to manually install CMake on their system. No action is performed if a suitable version of CMake is already available.