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Last data update: 2014.03.03

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Results 1 - 6 of 6 found.
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erma : epigenomic road map adventures

Package: erma
Title: epigenomic road map adventures
Version: 0.4.2
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: Software and data to support
epigenomic road map adventures.
Suggests: rmarkdown, BiocStyle, knitr, GO.db, BiocParallel, png, DT,
doParallel
Depends: R (>= 3.1), methods, Homo.sapiens
Imports: GenomicFiles (>= 1.5.2), rtracklayer, S4Vectors, BiocGenerics,
GenomicRanges, SummarizedExperiment, ggplot2, Biobase, shiny,
foreach, AnnotationDbi
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
LazyLoad: yes
BiocViews: epigenetics, panomics, annotation, chipseq
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-16 05:31:06 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: annotation, chipseq, epigenetics, panomics
● 2 images, 5 functions, 1 datasets
● Reverse Depends: 0

yriMulti : support for expression, methylation, DHS for YRI

Package: yriMulti
Title: support for expression, methylation, DHS for YRI
Version: 0.0.9
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: expression, methylation, DHS for YRI
Suggests: erma, BiocStyle, knitr, rmarkdown
Depends: gQTLBase, SummarizedExperiment, GenomicRanges, Homo.sapiens,
dsQTL, geuvPack
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
LazyLoad: yes
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-02-03 16:48:27 UTC; biocbuild

● Data Source: BioConductor
● 0 images, 1 functions, 0 datasets
● Reverse Depends: 0

ELMER : Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Package: ELMER
Title: Inferring Regulatory Element Landscapes and Transcription Factor
Networks Using Cancer Methylomes
Version: 1.4.2
Authors@R: c(person("Lijing", "Yao", role = c("cre", "aut"),
email = "lijingya@usc.edu"),
person("Ben", "Berman", role = "aut"),
person("Peggy", "Farnham", role = "aut"),
person("Hui", "Shen", role = "ctb"),
person("Peter", "Laird", role = "ctb"),
person("Simon","Coetzee", role = "ctb"))
Description:
ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.
Depends: R (>= 3.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
Homo.sapiens, ELMER.data
License: GPL-3
LazyData: true
VignetteBuilder: knitr
Imports:
methods,BiocGenerics,S4Vectors,IRanges,GenomeInfoDb,GenomicRanges,ggplot2,reshape,grid,gridExtra,minfi,GenomicFeatures
Suggests: parallel, snow, BiocStyle, knitr, R.utils, downloader
biocViews: DNAMethylation, GeneExpression, MotifAnnotation, Software,
GeneRegulation
NeedsCompilation: no
Packaged: 2016-05-16 05:29:23 UTC; biocbuild
Author: Lijing Yao [cre, aut],
Ben Berman [aut],
Peggy Farnham [aut],
Hui Shen [ctb],
Peter Laird [ctb],
Simon Coetzee [ctb]
Maintainer: Lijing Yao <lijingya@usc.edu>

● Data Source: BioConductor
● BiocViews: DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Software
● 6 images, 30 functions, 0 datasets
● Reverse Depends: 0

GGtools : software and data for analyses in genetics of gene expression

Package: GGtools
Title: software and data for analyses in genetics of gene expression
Version: 5.8.0
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: software and data for analyses in genetics of gene expression
and/or DNA methylation
Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37,
multtest, aod, rmeta
Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel,
Homo.sapiens
Imports: methods, utils, stats, BiocGenerics, snpStats, ff, Rsamtools,
AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin,
rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges,
GenomeInfoDb, GenomicRanges, iterators, Biostrings, ROCR,
biglm, ggplot2, reshape2
Enhances: MatrixEQTL, foreach, doParallel, gwascat
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
biocViews: Genetics, GeneExpression, GeneticVariability, SNP
LazyLoad: yes
Packaged: 2016-05-04 02:57:50 UTC; biocbuild
Collate: AllClasses.R AllGenerics.R eqtlTests.R managers.R topFeats.R
gwSnpTests.R snpsCisToGenes.R relocate.R topSnps.R
snplocsDefault.R transutils.R vcfutils.R eqtlEstimates.R
alleq.R meta.R eqME.R meta.all.R best.trans.eQTLs.R
meta.transScores.R summInfra.R bindmaf.R fdr.all.cis.R pifdr.R
getFDR.R cisConfig.R thinclass.R harvest.R scoredist.R binqq.R
gffprocess.R cisEqTools.R modutils.R seqinfo.R pureSensSoft.R
cisa.R scan.R basicappraise.R Eqappr.R
NeedsCompilation: no

● Data Source: BioConductor
● BiocViews: GeneExpression, GeneticVariability, Genetics, SNP
● 3 images, 38 functions, 4 datasets
● Reverse Depends: 3

chimera : A package for secondary analysis of fusion products

Package: chimera
Type: Package
Title: A package for secondary analysis of fusion products
Version: 1.14.0
Date: 31 March 2015
Author: Raffaele A Calogero, Matteo Carrara, Marco Beccuti, Francesca Cordero
Maintainer: Raffaele A Calogero <raffaele.calogero@unito.it>
Depends: Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1),
GenomicAlignments, methods, AnnotationDbi,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Homo.sapiens
Suggests: BiocParallel, geneplotter
Enhances: Rsubread, BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus,
BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene
Description: This package facilitates the characterisation of fusion products events. It allows to import fusion data results from the following fusion finders: chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher.
biocViews: Infrastructure
SystemRequirements: STAR, TopHat, bowtie and samtools are required for
some functionalities
License: Artistic-2.0
NeedsCompilation: yes
Packaged: 2016-05-04 04:52:34 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Infrastructure
● 3 images, 32 functions, 0 datasets
● Reverse Depends: 1

gwascat : representing and modeling data in the EMBL-EBI GWAS catalog

Package: gwascat
Title: representing and modeling data in the EMBL-EBI GWAS catalog
Version: 2.4.2
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: Represent and model data in the EMBL-EBI GWAS catalog.
Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37
Depends: R (>= 3.0.0), Homo.sapiens
Imports: methods, BiocGenerics, S4Vectors (>= 0.9.25), IRanges,
GenomeInfoDb, GenomicRanges, snpStats, Biostrings, Rsamtools,
rtracklayer, gQTLstats, Gviz, VariantAnnotation, AnnotationHub,
AnnotationDbi, GenomicFeatures, graph, ggbio, ggplot2,
SummarizedExperiment
Suggests: DO.db, DT, utils, knitr, RBGL, RUnit, GGtools
VignetteBuilder: utils, knitr
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
LazyData: no
biocViews: Genetics
NeedsCompilation: no
Packaged: 2016-05-16 03:16:36 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Genetics
● 2 images, 10 functions, 3 datasets
● Reverse Depends: 1