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R-bit64-0.9.7-2.lbn25.x86_64: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support interactive data exploration and manipulation and optionally leverage caching.

R-bit-1.1.12-2.lbn25.x86_64: bitmapped vectors of booleans (no NAs), coercion from and to logicals, integers and integer subscripts; fast boolean operators and fast summary statistics. With 'bit' vectors you can store true binary booleans {FALSE,TRUE} at the expense of 1 bit only, on a 32 bit architecture this means factor 32 less RAM and ~ factor 32 more speed on boolean operations. Due to overhead of R calls, actual speed gain depends on the size of the vector: expect gains for vectors of size > 10000 elements. Even for one-time boolean operations it can pay-off to convert to bit, the pay-off is obvious, when such components are used more than once. Reading from and writing to bit is approximately as fast as accessing standard logicals - mostly due to R's time for memory allocation. The package allows to work with pre-allocated memory for return values by calling .Call() directly: when evaluating the speed of C-access with pre-allocated vector memory, coping from bit to logical requires only 70% of the time for copying from logical to logical; and copying from logical to bit comes at a performance penalty of 150%. the package now contains further classes for representing logical selections: 'bitwhich' for very skewed selections and 'ri' for selecting ranges of values for chunked processing. All three index classes can be used for subsetting 'ff' objects (ff-2.1-0 and higher).

R-bindrcpp-0.2.2-1.lbn25.x86_64: Provides an easy way to fill an environment with active bindings that call a C++ function.

R-bindr-0.1.1-1.lbn25.noarch: Provides a simple interface for creating active bindings where the bound function accepts additional arguments.

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.

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