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Last data update: 2014.03.03

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Results 1 - 5 of 5 found.
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traseR : GWAS trait-associated SNP enrichment analyses in genomic intervals

Package: traseR
Type: Package
Title: GWAS trait-associated SNP enrichment analyses in genomic
intervals
Version: 1.2.0
Depends: R (>= 3.2.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19
Suggests: BiocStyle, RUnit, BiocGenerics
Date: 2015-11-20
Author: Li Chen, Zhaohui S.Qin
Maintainer: li chen<li.chen@emory.edu>
Description: traseR performs GWAS trait-associated SNP enrichment
analyses in genomic intervals using different hypothesis
testing approaches, also provides various functionalities to
explore and visualize the results.
License: GPL
LazyLoad: yes
biocViews: Genetics,Sequencing, Coverage, Alignment, QualityControl,
DataImport
NeedsCompilation: no
Packaged: 2016-05-04 06:24:56 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Alignment, Coverage, DataImport, Genetics, QualityControl, Sequencing
● 4 images, 9 functions, 0 datasets
● Reverse Depends: 0

CODEX : A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Package: CODEX
Type: Package
Title: A Normalization and Copy Number Variation Detection Method for
Whole Exome Sequencing
Version: 1.4.0
Author: Yuchao Jiang, Nancy R. Zhang
Maintainer: Yuchao Jiang <yuchaoj@wharton.upenn.edu>
Description: A normalization and copy number variation calling procedure for
whole exome DNA sequencing data. CODEX relies on the availability of
multiple samples processed using the same sequencing pipeline for
normalization, and does not require matched controls. The normalization
model in CODEX includes terms that specifically remove biases due to GC
content, exon length and targeting and amplification efficiency, and latent
systemic artifacts. CODEX also includes a Poisson likelihood-based recursive
segmentation procedure that explicitly models the count-based exome
sequencing data.
License: GPL-2
Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings
Suggests: WES.1KG.WUGSC
biocViews: ExomeSeq, Normalization, QualityControl, CopyNumberVariation
LazyData: yes
NeedsCompilation: no
Packaged: 2016-05-04 06:01:34 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: CopyNumberVariation, ExomeSeq, Normalization, QualityControl
● 0 images, 10 functions, 8 datasets
● Reverse Depends: 0

BSgenome.Hsapiens.UCSC.hg19.masked : Full masked genome sequences for Homo sapiens (UCSC version hg19)

Package: BSgenome.Hsapiens.UCSC.hg19.masked
Title: Full masked genome sequences for Homo sapiens (UCSC version
hg19)
Description: Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Version: 1.3.99
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
Depends: BSgenome (>= 1.31.8), BSgenome.Hsapiens.UCSC.hg19
Imports: BSgenome, BSgenome.Hsapiens.UCSC.hg19
License: Artistic-2.0
organism: Homo sapiens
species: Human
provider: UCSC
provider_version: hg19
release_date: Feb. 2009
release_name: Genome Reference Consortium GRCh37
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
biocViews: AnnotationData, Genetics, BSgenome, Homo_sapiens
Packaged: 2014-01-08 20:13:51 UTC; hpages

● Data Source: BioConductor
● BiocViews: AnnotationData, BSgenome, Genetics, Homo_sapiens
● 0 images, 1 functions, 0 datasets
● Reverse Depends: 0

motifRG : A package for discriminative motif discovery, designed for high throughput sequencing dataset

Package: motifRG
Title: A package for discriminative motif discovery, designed for high
throughput sequencing dataset
Version: 1.16.0
Date: 2012-03-23
Author: Zizhen Yao
Description: Tools for discriminative motif discovery using regression methods
Imports:
Biostrings,IRanges,seqLogo,parallel,methods,grid,graphics,XVector
Maintainer: Zizhen Yao <yzizhen@fhcrc.org>
License: Artistic-2.0
LazyLoad: yes
biocViews: Transcription,MotifDiscovery
Packaged: 2016-05-04 04:36:10 UTC; biocbuild
Depends: R (>= 2.15), Biostrings (>= 2.26), IRanges, seqLogo, parallel,
methods, grid, graphics, BSgenome, XVector,
BSgenome.Hsapiens.UCSC.hg19
NeedsCompilation: no

● Data Source: BioConductor
● BiocViews: MotifDiscovery, Transcription
● 7 images, 10 functions, 3 datasets
● Reverse Depends: 0

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