intansv: Integrative analysis of structural variations

This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.

Author
Wen Yao <ywhzau@gmail.com>
Date of publication
None
Maintainer
Wen Yao <ywhzau@gmail.com>
License
Artistic-2.0
Version
1.12.0

View on Bioconductor

Man pages

geneAnnotation
Annotation of genes affected by structural variations
methodsMerge
Integrate structural variations predicted by different...
plotChromosome
Display the chromosome distribution of structural variations
plotRegion
Display structural variations in a specific genomic region
readBreakDancer
Read in the structural variations predicted by breakDancer
readCnvnator
Read in the structural variations predicted by CNVnator
readDelly
Read in the structural variations predicted by DELLY
readLumpy
Read in the structural variations predicted by Lumpy
readPindel
Read in the structural variations predicted by Pindel
readSoftSearch
Read in the structural variations predicted by SoftSearch
readSvseq
Read in the structural variations predicted by SVseq2
svAnnotation
Annotation of structural variations

Files in this package

intansv/DESCRIPTION
intansv/NAMESPACE
intansv/NEWS
intansv/R
intansv/R/geneAnnotation.R
intansv/R/methodsMerge.R
intansv/R/plotChromosome.R
intansv/R/plotRegion.R
intansv/R/readBreakDancer.R
intansv/R/readCnvnator.R
intansv/R/readDelly.R
intansv/R/readLumpy.R
intansv/R/readPindel.R
intansv/R/readSoftSearch.R
intansv/R/readSvseq.R
intansv/R/svAnnotation.R
intansv/README.md
intansv/build
intansv/build/vignette.rds
intansv/inst
intansv/inst/doc
intansv/inst/doc/intansvOverview.R
intansv/inst/doc/intansvOverview.Rnw
intansv/inst/doc/intansvOverview.pdf
intansv/inst/extdata
intansv/inst/extdata/ZS97.breakdancer.sv
intansv/inst/extdata/ZS97.lumpy.pesr.bedpe
intansv/inst/extdata/ZS97.softsearch
intansv/inst/extdata/chr05_chr10.gff3
intansv/inst/extdata/cnvnator
intansv/inst/extdata/cnvnator/ZS97.chr05.out
intansv/inst/extdata/cnvnator/ZS97.chr10.out
intansv/inst/extdata/delly
intansv/inst/extdata/delly/ZS97.bam.del.vcf
intansv/inst/extdata/delly/ZS97.bam.dup.vcf
intansv/inst/extdata/delly/ZS97.bam.inv.vcf
intansv/inst/extdata/genome.anno.RData
intansv/inst/extdata/pindel
intansv/inst/extdata/pindel/ZS97.chr05_D
intansv/inst/extdata/pindel/ZS97.chr05_INV
intansv/inst/extdata/pindel/ZS97.chr05_TD
intansv/inst/extdata/pindel/ZS97.chr10_D
intansv/inst/extdata/pindel/ZS97.chr10_INV
intansv/inst/extdata/pindel/ZS97.chr10_TD
intansv/inst/extdata/svseq2
intansv/inst/extdata/svseq2/ZS97.bam.chr10.svseq.del
intansv/man
intansv/man/geneAnnotation.Rd
intansv/man/methodsMerge.Rd
intansv/man/plotChromosome.Rd
intansv/man/plotRegion.Rd
intansv/man/readBreakDancer.Rd
intansv/man/readCnvnator.Rd
intansv/man/readDelly.Rd
intansv/man/readLumpy.Rd
intansv/man/readPindel.Rd
intansv/man/readSoftSearch.Rd
intansv/man/readSvseq.Rd
intansv/man/svAnnotation.Rd
intansv/vignettes
intansv/vignettes/intansvOverview.Rnw
intansv/vignettes/intansvOverview.bib