## try http:// if https:// URLs are not supported source("//www.anjoumacpherson.com/biocLite.R") biocLite("GenomicAlignments")

DOI:10.18129/B9.bioc.GenomicAlignments

Representation and manipulation of short genomic alignments

Bioconductor version: Release (3.5)

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Author: Hervé Pagès, Valerie Obenchain, Martin Morgan

Maintainer: Bioconductor Package Maintainer

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported source("//www.anjoumacpherson.com/biocLite.R") biocLite("GenomicAlignments")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicAlignments")

PDF	R Script	An Introduction to the GenomicAlignments Package
PDF	R Script	Counting reads with summarizeOverlaps
PDF	R Script	Overlap encodings
PDF	R Script	Working with aligned nucleotides
PDF		Reference Manual
Text		NEWS
Video		Reading from a BAM file - Part 1
Video		Reading from a BAM file - Part 2

Details

biocViews	Alignment,Coverage,DataImport,Genetics,Infrastructure,RNASeq,SNP,Sequencing,Software
Version	1.12.2
In Bioconductor since	BioC 2.14 (R-3.1) (3.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods,BiocGenerics(>= 0.15.3),S4Vectors(>= 0.13.13),IRanges(>= 2.5.36),GenomeInfoDb(>= 1.11.5),GenomicRanges(>= 1.27.19),SummarizedExperiment(>= 1.5.3),Biostrings(>= 2.37.1),Rsamtools(>= 1.21.4)
Imports	methods, utils, stats,BiocGenerics,S4Vectors,IRanges,GenomicRanges,Biostrings,Rsamtools,BiocParallel
LinkingTo	S4Vectors,IRanges
Suggests	ShortRead,rtracklayer,BSgenome,GenomicFeatures,RNAseqData.HNRNPC.bam.chr14,pasillaBamSubset,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Dmelanogaster.UCSC.dm3.ensGene,BSgenome.Dmelanogaster.UCSC.dm3,BSgenome.Hsapiens.UCSC.hg19,DESeq2,edgeR,RUnit,BiocStyle
SystemRequirements
Enhances
URL
Depends On Me	AllelicImbalance,Basic4Cseq,BasicSTARRseq,chimera,ChIPexoQual,exomePeak,GoogleGenomics,groHMM,Guitar,HelloRanges,hiReadsProcessor,prebs,recoup,RIPSeeker,rnaSeqMap,ShortRead,SplicingGraphs
Imports Me	alpine,AneuFinder,ASpli,ATACseqQC,BaalChIP,biovizBase,chimeraviz,ChIPpeakAnno,ChIPQC,chromstaR,CNEr,contiBAIT,CopywriteR,CoverageView,CrispRVariants,customProDB,derfinder,DiffBind,easyRNASeq,FourCSeq,FunChIP,gcapc,GenoGAM,genomation,GenomicFiles,ggbio,gmapR,GreyListChIP,GUIDEseq,Gviz,HTSeqGenie,IMAS,INSPEcT,IntEREst,leeBamViews,MADSEQ,metagene,methylPipe,mosaics,msgbsR,NADfinder,PICS,QuasR,ramwas,Rcade,Repitools,RiboProfiling,RNAprobR,roar,Rqc,rtracklayer,seqplots,SGSeq,soGGi,SplicingGraphs,SPLINTER,TarSeqQC,TCseq,trackViewer,transcriptR,TSRchitect
Suggests Me	alpineData,BiocParallel,gage,GenomeInfoDb,GenomicDataCommons,GenomicFeatures,GenomicRanges,IRanges,oneChannelGUI,parathyroidSE,RNAseqData.HNRNPC.bam.chr14,RnaSeqTutorial,Rsamtools,similaRpeak,Streamer
Build Report

Package Archives

Followbob 体育网址 指示在R会话中使用这个包.

Source Package	GenomicAlignments_1.12.2.tar.gz
Windows Binary	GenomicAlignments_1.12.2.zip(32- & 64-bit)
Mac OS X 10.11 (El Capitan)	GenomicAlignments_1.12.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomicAlignments
Package Short Url	//www.anjoumacpherson.com/packages/GenomicAlignments/
Package Downloads Report	Download Stats