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: systemPipeR
Type: Package
Title: systemPipeR: NGS workflow and report generation environment
Version: 1.6.2
Date: 2016-02-26
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
RiboSeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,
GeneSetEnrichment, Alignment, QualityControl
Description: R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. Instructions for using systemPipeR are given in the Overview Vignette (HTML). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.
Depends: Rsamtools, Biostrings, ShortRead, methods
Imports: BiocGenerics, GenomicRanges, GenomicFeatures, SummarizedExperiment, VariantAnnotation, rjson, ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, BatchJobs
Suggests: ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel
VignetteBuilder: knitr
SystemRequirements: systemPipeR can be used to run external
command-line software (e.g. short read aligners), but the
corresponding tool needs to be installed on a system.
License: Artistic-2.0
URL: https://github.com/tgirke/systemPipeR
NeedsCompilation: no
Packaged: 2016-05-16 04:51:50 UTC; biocbuild
Package: rSFFreader
Type: Package
Title: rSFFreader reads in sff files generated by Roche 454 and Life
Sciences Ion Torrent sequencers
Version: 0.20.0
Date: 2011-10-02
Author: Matt Settles <mattsettles@gmail.com>, Sam Hunter, Brice Sarver,
Ilia Zhbannikov, Kyu-Chul Cho
Maintainer: Matt Settles <mattsettles@gmail.com>
Description: rSFFreader reads sequence, qualities and clip point values
from sff files generated by Roche 454 and Life Sciences Ion
Torrent sequencers into similar classes as are present for fastq files.
License: Artistic-2.0
Depends: ShortRead (>= 1.23.17)
Imports: methods, Biostrings, IRanges
Suggests: xtable
LinkingTo: S4Vectors, IRanges, XVector, Biostrings
Collate: allClasses.R allGenerics.R methods-Misc.R methods-SffHeader.R
methods-SffReads.R methods-SffReadsQ.R readSFF.R
biocViews: DataImport, Sequencing
NeedsCompilation: yes
Packaged: 2016-05-04 04:46:02 UTC; biocbuild
Package: OTUbase
Type: Package
Title: Provides structure and functions for the analysis of OTU data
Description: Provides a platform for Operational Taxonomic Unit based
analysis
Version: 1.22.0
Date: 2010-09-10
Author: Daniel Beck, Matt Settles, and James A. Foster
Maintainer: Daniel Beck <danlbek@gmail.com>
Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>=
1.23.15), Biobase, vegan
Imports: Biostrings
License: Artistic-2.0
LazyLoad: yes
biocViews: Sequencing, DataImport
NeedsCompilation: no
Packaged: 2016-05-04 03:44:52 UTC; biocbuild
providing 
.