Modified items

All recently modified items, latest first.

R-biglm-0.9.1-12.lbn25.x86_64: Regression for data too large to fit in memory.

R-biglm-0.9.1-12.lbn25.x86_64: Regression for data too large to fit in memory.

R-base64enc-0.1.3-2.lbn25.x86_64: This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.

R-backports-1.1.2-2.lbn25.x86_64: Implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.

R-assertthat-0.2.0-2.lbn25.noarch: assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what they've done wrong.

R-ascii-2.1-1.lbn25.noarch: Coerce R object to asciidoc, txt2tags, restructuredText, org, textile or pandoc syntax. Package comes with a set of drivers for Sweave.

R-argon2-0.2.0-1.lbn25.x86_64: 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.

R-ape-5.0-1.lbn25.x86_64: 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.

R-affyio-1.46.0-3.lbn25.x86_64: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.

R-affy-1.54.0-3.lbn25.x86_64: The package contains functions for exploratory oligonucleotide array analysis. The dependancy to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

R-acepack-1.4.1-6.lbn25.x86_64: ACE and AVAS (additivity and variance stabilization) are used to estimate transformations for regression.

R-XVector-0.16.0-3.lbn25.x86_64: Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).

R-XML-3.98.1.7-3.lbn25.x86_64: This package provides many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath "interpreter".

R-V8-1.5-4.lbn25.x86_64: An R interface to Google's open source JavaScript engine. V8 is written in C++ and implements ECMAScript as specified in ECMA-262, 5th edition. In addition, this package implements typed arrays as specified in ECMA 6 used for high-performance computing and libraries compiled with 'emscripten'.

R-S4Vectors-0.16.0-1.lbn25.x86_64: The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

R-Rsolid-0.9.31-22.lbn25.x86_64: Rsolid is an R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles. Under the random DNA fragmentation assumption, these proportions should be equal across sequencing cycles and proportional to the dinucleotide frequencies of the sample. Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors. Results show that after normalization, the total number of mappable reads increases by around 5%, and number of perfectly mapped reads increases by 10%. Moreover a 2-5% reduction in overall error rates is observed, with a 2-6% reduction in the rate of valid adjacent color mis-matches. The latter is important, since it leads to a decrease in false-positive SNP calls. The normalization algorithm is computationally efficient. In a test we are able to process 300 million reads in 2 hours using 10 computer cluster nodes. The engine functions of the package are written in C for better performance.

R-Rsamtools-1.28.0-3.lbn25.x86_64: This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

R-Rmpfr-0.7.0-1.lbn25.x86_64: Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.

R-RcppCCTZ-0.2.3-2.lbn25.x86_64: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone.

R-Rcpp-0.12.16-1.lbn25.x86_64: The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer). See citation("Rcpp") for details on the last two.


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