Package: GenomicFeatures
Title: Tools for making and manipulating transcript centric annotations
Version: 1.24.3
Encoding: UTF-8
Author: M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan,
D. Sarkar, M. Lawrence
License: Artistic-2.0
Description: A set of tools and methods for making and manipulating
transcript centric annotations. With these tools the user can
easily download the genomic locations of the transcripts, exons
and cds of a given organism, from either the UCSC Genome
Browser or a BioMart database (more sources will be supported
in the future). This information is then stored in a local
database that keeps track of the relationship between
transcripts, exons, cds and genes. Flexible methods are
provided for extracting the desired features in a convenient
format.
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.47), IRanges (>=
2.3.21), GenomeInfoDb (>= 1.5.16), GenomicRanges (>= 1.21.32), AnnotationDbi (>= 1.33.15)
Imports: methods, utils, stats, tools, DBI, RSQLite, RCurl, XVector, Biostrings (>= 2.23.3), rtracklayer (>= 1.29.24), biomaRt (>=
2.17.1), Biobase (>= 2.15.1)
Suggests: org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>=
1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP141.GRCh38, Rsamtools, pasillaBamSubset
(>= 0.0.5), GenomicAlignments, RUnit, BiocStyle, knitr
Collate: utils.R TxDb-SELECT-helpers.R Ensembl.utils.R
findCompatibleMarts.R TxDb-class.R FeatureDb-class.R makeTxDb.R
makeTxDbFromUCSC.R makeTxDbFromBiomart.R makeTxDbFromGRanges.R
makeTxDbFromGFF.R makeFeatureDbFromUCSC.R mapIdsToRanges.R
id2name.R transcripts.R transcriptsBy.R transcriptsByOverlaps.R
transcriptLengths.R disjointExons.R features.R microRNAs.R
extractTranscriptSeqs.R extractUpstreamSeqs.R
getPromoterSeq-methods.R makeTxDbPackage.R select-methods.R
nearest-methods.R transcriptLocs2refLocs.R
coordinate-mapping-methods.R coverageByTranscript.R zzz.R
VignetteBuilder: knitr
biocViews: Genetics, Infrastructure, Annotation, Sequencing,
GenomeAnnotation
NeedsCompilation: no
Packaged: 2016-06-21 02:07:09 UTC; biocbuild
Package: GenomicRanges
Title: Representation and manipulation of genomic intervals and
variables defined along a genome
Description: The ability to efficiently represent and manipulate genomic
annotations and alignments is playing a central role when it comes
to analyzing high-throughput sequencing data (a.k.a. NGS data).
The GenomicRanges package defines general purpose containers for
storing and manipulating genomic intervals and variables defined along
a genome. More specialized containers for representing and manipulating
short alignments against a reference genome, or a matrix-like
summarization of an experiment, are defined in the GenomicAlignments
and SummarizedExperiment packages respectively. Both packages build
on top of the GenomicRanges infrastructure.
Version: 1.24.2
Encoding: UTF-8
Author: P. Aboyoun, H. Pagès, and M. Lawrence
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
GenomeAnnotation
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.17.5), S4Vectors (>=
0.9.47), IRanges (>= 2.5.36), GenomeInfoDb (>= 1.1.20)
Imports: utils, stats, XVector
LinkingTo: S4Vectors, IRanges
Suggests: Biobase, AnnotationDbi (>= 1.21.1), annotate, Biostrings (>=
2.25.3), Rsamtools (>= 1.13.53), SummarizedExperiment (>=
0.1.5), Matrix, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db, pasilla, pasillaBamSubset, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene
License: Artistic-2.0
Collate: utils.R phicoef.R transcript-utils.R constraint.R
strand-utils.R range-squeezers.R GenomicRanges-class.R
GenomicRanges-comparison.R GRanges-class.R GPos-class.R
DelegatingGenomicRanges-class.R GNCList-class.R
GenomicRangesList-class.R GRangesList-class.R
makeGRangesFromDataFrame.R RangedData-methods.R
findOverlaps-methods.R intra-range-methods.R
inter-range-methods.R coverage-methods.R setops-methods.R
nearest-methods.R absoluteRanges.R tileGenome.R tile-methods.R
genomicvars.R zzz.R
NeedsCompilation: yes
Packaged: 2016-06-15 02:21:39 UTC; biocbuild
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
Package: CSAR
Type: Package
Title: Statistical tools for the analysis of ChIP-seq data
Version: 1.24.0
Date: 2009-11-09
Author: Jose M Muino
Description: Statistical tools for ChIP-seq data analysis. The package
includes the statistical method described in Kaufmann et al.
(2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average
DNA fragment size subjected to sequencing into account, the
software calculates genomic single-nucleotide read-enrichment
values. After normalization, sample and control are compared
using a test based on the Poisson distribution. Test statistic
thresholds to control the false discovery rate are obtained
through random permutation.
Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
Maintainer: Jose M Muino <jose.muino@wur.nl>
Suggests: ShortRead, Biostrings
Imports: stats, utils
License: Artistic-2.0
LazyLoad: yes
LazyData: yes
biocViews: ChIPSeq, Transcription, Genetics
NeedsCompilation: yes
Packaged: 2016-05-04 03:23:30 UTC; biocbuild
Package: SNPlocs.Hsapiens.dbSNP142.GRCh37
Title: SNP locations for Homo sapiens (dbSNP Build 142)
Description: SNP locations and alleles for Homo sapiens extracted from
NCBI dbSNP Build 142. The source data files used for this
package were created by NCBI on October 14, 2014, and contain
SNPs mapped to reference genome GRCh37.p13.
WARNING: Note that the GRCh37.p13 genome is a patched version of
GRCh37 but the patch doesn't alter chromosomes 1-22, X, Y, MT.
GRCh37 itself is the same as the hg19 genome from UCSC *except*
for the mitochondrion chromosome. Therefore, the SNPs in this
package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they
will land at the correct location but this injection will exclude
chrM (i.e. nothing will be injected in that sequence).
Version: 0.99.5
Author: Herv'e Pag`es
Maintainer: Simon Coetzee <simon.coetzee@cshs.org>
Depends: R (>= 2.10), IRanges, GenomeInfoDb, GenomicRanges, BSgenome
(>= 1.25.6)
Imports: methods, utils, IRanges, GenomeInfoDb, GenomicRanges, BSgenome
Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked (>= 1.3.19)
License: Artistic-2.0
organism: Homo sapiens
species: Human
provider: dbSNP
provider_version: 20141014
release_date: October 14, 2014
release_name: Build 142
reference_genome: GRCh37.p13
download_url:
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/ASN1_flat/
download_date: April 10, 2015
biocViews: AnnotationData, Genetics, Homo_sapiens
NeedsCompilation: no
Packaged: 2015-05-01 00:10:59 UTC; hpages
providing 
.