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Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, and BigWig built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Query the main 'R' 'SVN' repository to find the versions 'r-release' and 'r-oldrel' refer to, and also all previous 'R' versions and their release
Wrappers around the 'xml2' and 'httr' packages to make it easy to download, then manipulate, HTML and XML.
Plots a three dimensional (3D) point cloud.
Translates a CSS3 selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package 'cssselect' (<https://cssselect.readthedocs.io/>).
Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich, some of which were ported from S-plus in the 1990's. For graphics, have pretty (Log-scale) axes, an enhanced Tukey-Anscombe plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()', pretty arrows, etc. For robustness, have a robust F test and robust range(). For system support, notably on Linux, provides 'Sys.*()' functions with more access to system and CPU information. Finally, miscellaneous utilities such as simple efficient prime numbers, integer codes, Duplicated(), toLatex.numeric() and is.whole().
Tools for the reading and tokenization of R code. The 'sourcetools' package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.
Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary,
Various statistical modeling functions including growth curve comparisons, limiting dilution analysis, mixed linear models, heteroscedastic regression, Tweedie family generalized linear models, the inverse-Gaussian distribution and Gauss quadrature.
Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.