Package: epigenomix
Type: Package
Title: Epigenetic and gene transcription data normalization and
integration with mixture models
Version: 1.12.0
Date: 2016-02-08
Author: Hans-Ulrich Klein, Martin Schaefer
Maintainer: Hans-Ulrich Klein <h.klein@uni-muenster.de>
Depends: R (>= 3.2.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment
Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray
Description: A package for the integrative analysis of RNA-seq or
microarray based gene transcription and histone modification
data obtained by ChIP-seq. The package provides methods for
data preprocessing and matching as well as methods for fitting
bayesian mixture models in order to detect genes with
differences in both data types.
License: LGPL-3
biocViews: ChIPSeq, GeneExpression, DifferentialExpression,
Classification
NeedsCompilation: no
Packaged: 2016-05-04 04:53:55 UTC; biocbuild
Package: segmentSeq
Type: Package
Title: Methods for identifying small RNA loci from high-throughput
sequencing data
Version: 2.6.0
Date: 2010-01-20
Author: Thomas J. Hardcastle
Maintainer: Thomas J. Hardcastle <tjh48@cam.ac.uk>
Description: High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.
License: GPL-3
LazyLoad: yes
Depends: R (>= 2.3.0), methods, baySeq (>= 1.99.0), ShortRead, GenomicRanges, IRanges, S4Vectors
Suggests: BiocStyle, BiocGenerics
Imports: graphics, grDevices, utils
biocViews: MultipleComparison, Sequencing, Alignment,
DifferentialExpression, QualityControl, DataImport
Packaged: 2016-05-04 04:02:57 UTC; biocbuild
NeedsCompilation: no
Package: triplex
Type: Package
Title: Search and visualize intramolecular triplex-forming sequences in
DNA
Version: 1.12.0
Date: 2013-09-28
Authors@R: c(person("Jiri", "Hon", role = c("aut", "cre"),
email = "jiri.hon@gmail.com"),
person("Matej", "Lexa", role = "aut",
email = "lexa@fi.muni.cz"),
person("Tomas", "Martinek", role = "aut",
email = "martinto@fit.vutbr.cz"),
person("Kamil", "Rajdl", role = "aut"),
person("Daniel", "Kopecek", role = "ctb"))
Author: Jiri Hon, Matej Lexa, Tomas Martinek and Kamil Rajdl with contributions from Daniel Kopecek
Maintainer: Jiri Hon <jiri.hon@gmail.com>
Description: This package provides functions for identification and
visualization of potential intramolecular triplex patterns in DNA sequence.
The main functionality is to detect the positions of subsequences capable of
folding into an intramolecular triplex (H-DNA) in a much larger sequence.
The potential H-DNA (triplexes) should be made of as many cannonical
nucleotide triplets as possible. The package includes visualization showing
the exact base-pairing in 1D, 2D or 3D.
License: BSD_2_clause + file LICENSE
URL: http://www.fi.muni.cz/~lexa/triplex/
biocViews: SequenceMatching, GeneRegulation
Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10)
Imports: methods, grid, GenomicRanges
Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs
LinkingTo: S4Vectors, IRanges, XVector, Biostrings
NeedsCompilation: yes
Packaged: 2016-05-05 03:50:37 UTC; biocbuild
providing 
.