Modified items

All recently modified items, latest first.

R-SummarizedExperiment-1.2.3-1.lbn19.noarch: The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

R-S4Vectors-0.10.3-1.lbn19.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-0.9.31-18.lbn19.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-1.24.0-1.lbn19.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-Rcpp-0.12.6-1.lbn19.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.

R-Rcompression-0.93.2-13.lbn19.x86_64: This package is a basic R interface to the zlib and bzip2 facilities for compressing and uncompressing data that are in memory rather than in files.

R-RUnit-0.4.26-11.lbn19.noarch: R functions implementing a standard Unit Testing framework, with additional code inspection and report generation tools

R-RSQLite-0.11.4-5.lbn19.x86_64: A SQLite database interface definition for communication between R and SQLite databases.

R-RM2-0.0-16.lbn19.noarch: RM2 is a simple package that implements functions used in revenue management and pricing environments.

R-RInside-0.2.13-3.lbn19.x86_64: The RInside packages makes it easier to have "R inside" your C++ application by providing a C++ wrapper class providing the R interpreter.

R-RCurl-1.95.4.1-6.lbn19.x86_64: The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

R-R6-2.1.3-1.lbn19.noarch: The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.

R-IRkernel-0.6.1-1.git659435f.lbn19.noarch: Per default IRkernel::installspec() will install a kernel with the name “ir” and a display name of “R”. Multiple calls will overwrite the kernel with a kernel spec pointing to the last R interpreter you called that commands from. You can install kernels for multiple versions of R by supplying a name and displayname argument to the installspec() call

R-IRdisplay-0.4.4-1.lbn19.noarch: An interface to the rich display capabilities of 'Jupyter' front-ends (e.g. 'Jupyter Notebook') <https://jupyter.org>. Designed to be used from a running 'IRkernel' session

R-IRanges-2.6.1-1.lbn19.x86_64: The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions.

R-GenomicRanges-1.24.2-1.lbn19.x86_64: The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

R-GenomicFeatures-1.24.5-1.lbn19.noarch: A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.


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