Package: prebs
Title: Probe region expression estimation for RNA-seq data for improved
microarray comparability
Description: The prebs package aims at making RNA-sequencing (RNA-seq)
data more comparable to microarray data. The comparability is
achieved by summarizing sequencing-based expressions of probe
regions using a modified version of RMA algorithm. The pipeline
takes mapped reads in BAM format as an input and produces
either gene expressions or original microarray probe set
expressions as an output.
Version: 1.12.0
Author: Karolis Uziela and Antti Honkela
Maintainer: Karolis Uziela <karolis.uziela@scilifelab.se>
Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA
Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, GenomeInfoDb, S4Vectors
Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe
License: Artistic-2.0
Collate: 'PREBS.R'
biocViews: Microarray, RNASeq, Sequencing, GeneExpression,
Preprocessing
NeedsCompilation: no
Packaged: 2016-05-04 04:59:04 UTC; biocbuild
Package: RIPSeeker
Type: Package
Title: RIPSeeker: a statistical package for identifying
protein-associated transcripts from RIP-seq experiments
Version: 1.12.0
Date: 2013-Apr-13
Author: Yue Li
Maintainer: Yue Li <yueli@cs.toronto.edu>
Description: Infer and discriminate RIP peaks from RIP-seq alignments
using two-state HMM with negative binomial emission
probability. While RIPSeeker is specifically tailored for
RIP-seq data analysis, it also provides a suite of
bioinformatics tools integrated within this self-contained
software package comprehensively addressing issues ranging from
post-alignments processing to visualization and annotation.
Depends: R (>= 2.15), methods, S4Vectors (>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment, Rsamtools, GenomicAlignments, rtracklayer
Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures
License: GPL-2
URL: http://www.cs.utoronto.ca/~yueli/software.html
Lazyload: yes
Packaged: 2016-05-04 04:46:29 UTC; biocbuild
biocViews: Sequencing, RIPSeq
NeedsCompilation: no
Package: ShortRead
Type: Package
Title: FASTQ input and manipulation
Version: 1.30.0
Author: Martin Morgan, Michael Lawrence, Simon Anders
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
Description: This package implements sampling, iteration, and input of
FASTQ files. The package includes functions for filtering and
trimming reads, and for generating a quality assessment report.
Data are represented as DNAStringSet-derived objects, and
easily manipulated for a diversity of purposes. The package
also contains legacy support for early single-end, ungapped
alignment formats.
License: Artistic-2.0
LazyLoad: yes
Depends: BiocGenerics (>= 0.11.3), BiocParallel, Biostrings (>=
2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4)
Imports: Biobase, S4Vectors (>= 0.7.1), IRanges (>= 2.3.7), GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.21.6), hwriter, methods, zlibbioc, lattice, latticeExtra,
Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
LinkingTo: S4Vectors, IRanges, XVector, Biostrings
biocViews: DataImport, Sequencing, QualityControl
NeedsCompilation: yes
Packaged: 2016-05-04 03:09:08 UTC; biocbuild
Package: SplicingGraphs
Title: Create, manipulate, visualize splicing graphs, and assign
RNA-seq reads to them
Version: 1.12.0
Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
License: Artistic-2.0
Description: This package allows the user to create, manipulate, and visualize
splicing graphs and their bubbles based on a gene model for a given
organism. Additionally it allows the user to assign RNA-seq reads to
the edges of a set of splicing graphs, and to summarize them in
different ways.
Maintainer: H. Pages <hpages@fredhutch.org>
Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7)
Imports: methods, utils, igraph, BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 2.3.21), GenomeInfoDb, GenomicRanges (>= 1.23.21), GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz
Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit
Collate: utils.R igraph-utils.R SplicingGraphs-class.R
plotTranscripts-methods.R sgedgesByGene-methods.R
txpath-methods.R sgedges-methods.R sgraph-methods.R
rsgedgesByGene-methods.R bubbles-methods.R assignReads.R
countReads-methods.R toy_data.R zzz.R
biocViews: Genetics, Annotation, DataRepresentation, Visualization,
Sequencing, RNASeq, GeneExpression, AlternativeSplicing,
Transcription
NeedsCompilation: no
Packaged: 2016-05-04 04:58:04 UTC; biocbuild
Package: Basic4Cseq
Type: Package
Title: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Version: 1.8.0
Date: 2015-08-24
Author: Carolin Walter
Maintainer: Carolin Walter <carolin.walter@uni-muenster.de>
Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805
Depends: R (>= 3.0.0), Biostrings, GenomicAlignments, caTools, GenomicRanges
Suggests: BSgenome.Hsapiens.UCSC.hg19
Description: Basic4Cseq is an R/Bioconductor package for basic
filtering, analysis and subsequent visualization of 4C-seq
data. Virtual fragment libraries can be created for any
BSGenome package, and filter functions for both reads and
fragments and basic quality controls are included. Fragment
data in the vicinity of the experiment's viewpoint can be
visualized as a coverage plot based on a running median
approach and a multi-scale contact profile.
License: LGPL-3
biocViews: Visualization, QualityControl
NeedsCompilation: no
Packaged: 2016-05-04 05:21:03 UTC; biocbuild
providing 
.