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The SummarizedExperiment container contains one or more assays, each represented by a marix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Data for other R packages.
An R interface to V8: Google's open source JavaScript and WebAssembly engine.
Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an XPath "interpreter".
Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).
Combine multi-dimensional arrays. This is a generalization of cbind and rbind. Takes a sequence of vectors, matrices, or arrays and produces a single array of the same or higher dimension.
ACE and AVAS (additivity and variance stabilization) are used to estimate transformations for regression.
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Utilities for secure password hashing via the argon2 algorithm. It is a relatively new hashing algorithm and is believed to be very secure. The 'argon2' implementation included in the package is the reference implementation. The package also includes some utilities that should be useful for digest authentication, including a wrapper of 'blake2b'. For similar R packages, see sodium and 'bcrypt'. See <https://en.wikipedia.org/wiki/Argon2> or <https://eprint.iacr.org/2015/430.pdf> for more information.
Coerce R object to asciidoc, txt2tags, restructuredText, org, textile or pandoc syntax. Package comes with a set of drivers for Sweave.