R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 15 found.
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cummeRbund : Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Package: cummeRbund
Title: Analysis, exploration, manipulation, and visualization of
Cufflinks high-throughput sequencing data.
Version: 2.14.0
Date: 2013-04-22
Author: L. Goff, C. Trapnell, D. Kelley
Description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2,
reshape2, fastcluster, rtracklayer, Gviz
Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
Maintainer: Loyal A. Goff <lgoff@csail.mit.edu>
License: Artistic-2.0
Collate: AllGenerics.R AllClasses.R database-setup.R methods-CuffSet.R
methods-CuffData.R methods-CuffDist.R methods-CuffGeneSet.R
methods-CuffFeatureSet.R methods-CuffGene.R
methods-CuffFeature.R tools.R
LazyLoad: yes
biocViews: HighThroughputSequencing, HighThroughputSequencingData,
RNAseq, RNAseqData, GeneExpression, DifferentialExpression,
Infrastructure, DataImport, DataRepresentation, Visualization,
Bioinformatics, Clustering, MultipleComparisons, QualityControl
NeedsCompilation: no
Packaged: 2016-05-04 04:17:08 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Bioinformatics, Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, MultipleComparisons, QualityControl, RNAseq, RNAseqData, Visualization
● 18 images, 54 functions, 5 datasets
● Reverse Depends: 2

regioneR : Association analysis of genomic regions based on permutation tests

Package: regioneR
Type: Package
Title: Association analysis of genomic regions based on permutation
tests
Version: 1.4.2
Date: 2016-04-06
Author: Anna Diez-Villanueva <adiez@imppc.org>, Roberto Malinverni
<rmalinverni@carrerasresearch.org> and Bernat Gel <bgel@imppc.org>
Maintainer: Bernat Gel <bgel@imppc.org>
Description: regioneR offers a statistical framework based on
customizable permutation tests to assess the association
between genomic region sets and other genomic features.
License: Artistic-2.0
Depends: memoise, GenomicRanges, BSgenome, rtracklayer, parallel
Imports: memoise, GenomicRanges, BSgenome, rtracklayer, parallel,
graphics, stats, utils, GenomeInfoDb, IRanges
Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19.masked,
testthat
VignetteBuilder: knitr
biocViews: Genetics, ChIPSeq, DNASeq, MethylSeq, CopyNumberVariation
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:22:11 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: ChIPSeq, CopyNumberVariation, DNASeq, Genetics, MethylSeq
● 29 images, 40 functions, 0 datasets
● Reverse Depends: 0

spliceR : Classification of alternative splicing and prediction of coding potential from RNA-seq data.

Package: spliceR
Version: 1.14.0
Date: 2014/04/29
Title: Classification of alternative splicing and prediction of coding
potential from RNA-seq data.
Author: Johannes Waage <johannes.waage@gmail.com>, Kristoffer
Vitting-Seerup <k.vitting.seerup@gmail.com>
Maintainer: Johannes Waage <johannes.waage@gmail.com>, Kristoffer
Vitting-Seerup <k.vitting.seerup@gmail.com>
Imports: GenomicRanges, IRanges
Depends: R (>= 2.15.0), methods, cummeRbund, rtracklayer, VennDiagram,
RColorBrewer, plyr
Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome
Description: An R package for classification of alternative splicing
and prediction of coding potential from RNA-seq data.
License: GPL (>=2)
biocViews: GeneExpression, Transcription, AlternativeSplicing,
DifferentialExpression, DifferentialSplicing, Sequencing,
Visualization
NeedsCompilation: yes
Packaged: 2016-05-04 05:00:59 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, Sequencing, Transcription, Visualization
● 2 images, 15 functions, 0 datasets
● Reverse Depends: 0

r3Cseq : Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

Package: r3Cseq
Version: 1.18.0
Title: Analysis of Chromosome Conformation Capture and Next-generation
Sequencing (3C-seq)
Author: Supat Thongjuea, MRC Molecular Haematology Unit, Weatherall
Institute of Molecular Medicine, University of Oxford, UK
<supat.thongjuea@ndcls.ox.ac.uk>
Maintainer: Supat Thongjuea <supat.thongjuea@ndcls.ox.ac.uk>
Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf,
RColorBrewer
Suggests: BSgenome.Mmusculus.UCSC.mm9.masked,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Hsapiens.UCSC.hg18.masked,
BSgenome.Hsapiens.UCSC.hg19.masked,
BSgenome.Rnorvegicus.UCSC.rn5.masked
Description: This package is an implementation of data analysis for the
long-range interactions from 3C-seq assay.
License: GPL-3
URL: http://r3cseq.genereg.net
Collate: AllClasses.R AllGenerics.R Export.R FunctionInCommon.R
FunctionsForBatchAnalysis.R RestrictionEnzymeFunctions.R
FunctionsForNoReplicationAnalysis.R Report.R Visualize3Cseq.R
Annotation.R
biocViews: Preprocessing, Sequencing
NeedsCompilation: no
Packaged: 2016-05-04 04:17:49 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Preprocessing, Sequencing
● 0 images, 37 functions, 8 datasets
● Reverse Depends: 0

GenomicFiles : Distributed computing by file or by range

Package: GenomicFiles
Title: Distributed computing by file or by range
Description: This package provides infrastructure for parallel
computations distributed 'by file' or 'by range'. User
defined MAPPER and REDUCER functions provide added
flexibility for data combination and manipulation.
Version: 1.8.0
Author: Valerie Obenchain, Michael Love, Martin Morgan
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, Coverage
Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges
(>= 1.23.21), SummarizedExperiment, BiocParallel (>= 1.1.0),
Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3)
Imports: GenomicAlignments (>= 1.7.7), Biobase, IRanges, S4Vectors (>=
0.9.25), VariantAnnotation, GenomeInfoDb
Suggests: BiocStyle, RUnit, genefilter, deepSNV,
RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
License: Artistic-2.0
Collate: GenomicFiles-class.R VcfStack-class.R reduceByFile-methods.R
reduceByRange-methods.R reduceFiles.R reduceRanges.R
reduceByYield.R pack-methods.R unpack-methods.R registry.R
zzz.R
Video: https://www.youtube.com/watch?v=3PK_jx44QTs
NeedsCompilation: no
Packaged: 2016-05-04 05:27:40 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Coverage, DataImport, Genetics, Infrastructure, Sequencing
● 0 images, 7 functions, 0 datasets
● Reverse Depends: 0

Guitar : Guitar

Package: Guitar
Type: Package
Title: Guitar
Version: 1.10.0
Date: 2016-4-15
Author: Jia Meng
Maintainer: Jia Meng <jia.meng@xjtlu.edu.cn>
Description: The package is designed for visualization
of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e.,
transcription starting site, start codon, stop codon and transcription ending site.
License: GPL-2
Depends: Rsamtools, GenomicFeatures, rtracklayer, GenomicAlignments,
GenomicRanges, ggplot2, grid, IRanges
biocViews: Sequencing, SplicedAlignment, Alignment, DataImport, RNASeq,
MethylSeq, QualityControl, Transcription, Coverage
NeedsCompilation: no
Packaged: 2016-05-04 06:34:21 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Alignment, Coverage, DataImport, MethylSeq, QualityControl, RNASeq, Sequencing, SplicedAlignment, Transcription
● 2 images, 7 functions, 0 datasets
● Reverse Depends: 0

IdeoViz : Plots data (continuous/discrete) along chromosomal ideogram

Package: IdeoViz
Type: Package
Title: Plots data (continuous/discrete) along chromosomal ideogram
Version: 1.6.0
Date: 2014-09-08
Author: Shraddha Pai <shraddha.pai@utoronto.ca>, Jingliang Ren
Maintainer: Shraddha Pai <shraddha.pai@utoronto.ca>
Depends: Biobase, IRanges, GenomicRanges, RColorBrewer,
rtracklayer, graphics, GenomeInfoDb
biocViews: Visualization,Microarray
Description: Plots data associated with arbitrary genomic intervals
along chromosomal ideogram.
License: GPL-2
NeedsCompilation: no
Packaged: 2016-05-04 05:49:25 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Microarray, Visualization
● 2 images, 6 functions, 8 datasets
● Reverse Depends: 0

ChIPComp : Quantitative comparison of multiple ChIP-seq datasets

Package: ChIPComp
Type: Package
Title: Quantitative comparison of multiple ChIP-seq datasets
Version: 1.2.0
Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang
Maintainer: Li Chen <li.chen@emory.edu>
Depends: R (>=
3.2.0), GenomicRanges, IRanges, rtracklayer, GenomeInfoDb, S4Vectors
Imports: Rsamtools, limma, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm9, BiocGenerics
Suggests: BiocStyle, RUnit
Description: ChIPComp detects differentially bound sharp binding sites
across multiple conditions considering matching control.
License: GPL
LazyLoad: yes
biocViews: ChIPSeq, Sequencing, Transcription, Genetics,Coverage,
MultipleComparison, DataImport
NeedsCompilation: yes
Packaged: 2016-05-04 06:29:01 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: ChIPSeq, Coverage, DataImport, Genetics, MultipleComparison, Sequencing, Transcription
● 1 images, 6 functions, 1 datasets
● Reverse Depends: 0

CoverageView : Coverage visualization package for R

Package: CoverageView
Type: Package
Title: Coverage visualization package for R
Version: 1.8.0
Date: 2016-01-17
Author: Ernesto Lowy
Maintainer: Ernesto Lowy <ernestolowy@gmail.com>
Description: This package provides a framework for the visualization of
genome coverage profiles. It can be used for ChIP-seq
experiments, but it can be also used for genome-wide nucleosome
positioning experiments or other experiment types where it is
important to have a framework in order to inspect how the
coverage distributed across the genome
biocViews: Visualization,RNASeq,ChIPSeq,Sequencing,Technology,Software
License: Artistic-2.0
Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer
Imports: S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges,
GenomicAlignments, parallel, tools
NeedsCompilation: no
Packaged: 2016-05-04 05:24:39 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: ChIPSeq, RNASeq, Sequencing, Software, Technology, Visualization
● 0 images, 12 functions, 6 datasets
● Reverse Depends: 0

RIPSeeker : RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

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

● Data Source: BioConductor
● BiocViews: RIPSeq, Sequencing
● 7 images, 39 functions, 0 datasets
● Reverse Depends: 1