This package facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R, a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file. It also may be converted into other popular R objects. This package provides a link between VCF data and familiar R software.

This package supports the analysis of count data exhibiting autoregressive properties, using the Autoregressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003).

This package allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g. via regular expressions), random string generation, string collation, transliteration, concatenation, date-time formatting and parsing, etc.

This package implements density, distribution functions, quantile functions and random generation functions for a large number of univariate and multivariate distributions.

This package provides a number of methods for creating and augmenting Latin Hypercube Samples.

Dunn's test computes stochastic dominance & reports pairwise comparisons. This is done following a Kruskal-Wallis test (Kruskal and Wallis, 1952). It employs Dunn's z-test-statistic approximations for rank statistics, conducting k(k-1)/2 comparisons. The null hypothesis assumes that the probability of a randomly selected value from the first group being larger than one from the second group is one half, similar to the Wilcoxon-Mann-Whitney test. Dunn's test serves as a test for median difference and takes into account tied ranks.

This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

This package provides methods for calculating accurate numerical first and second order derivatives.

This package contains the program ttf2pt1, for use with the extrafont package.

This package extends the mlr3 package with cluster analysis.

This package provides an interface to use SPARQL to pose SELECT or UPDATE queries to an end-point.

The fit.models function and its associated methods (coefficients, print, summary, plot, etc.) were originally provided in the robust package to compare robustly and classically fitted model objects. The aim of the fit.models package is to separate this fitted model object comparison functionality from the robust package and to extend it to support fitting methods (e.g., classical, robust, Bayesian, regularized, etc.) more generally.

Download and install R packages stored in GitHub, BitBucket, or plain subversion or git repositories. This package is a lightweight replacement of the install_* functions in the devtools package. Indeed most of the code was copied over from devtools.

This package provides some functions for sample classification in microarrays.

This package provides chronological R objects which can handle dates and times.

Miscellaneous functions commonly used by YuLab-SMU, such as install_zip_gh to install R packages from Github ZIP files.

This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.

This package provides an object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided.

The revgeo procedure allows you to use the Photon geocoder for OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with minimal hassle.

This package implements an opinionated framework for building a production- ready Shiny application. Golem contains a series of tools like dependency management, version management, easy installation and deployment or documentation management.

Designed to enable simultaneous substitution in strings in a safe fashion. Safe means it does not rely on placeholders (which can cause errors in same length matches).

This package provides an interface to Amazon Web Services developer tools services, including version control, continuous integration and deployment, and more.

This package is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted.

This package contains a number of common astronomy conversion routines, particularly the HMS and degrees schemes, which can be fiddly to convert between on mass due to the textural nature of the former. It allows users to coordinate match datasets quickly. It also contains functions for various cosmological calculations.