RareVariantVis: Visualization of rare variants in whole genome sequencing data

Genomic variants can be analyzed and visualized using many tools. Unfortunately, number of tools for global interrogation of variants is limited. Package RareVariantVis aims to present genomic variants (especially rare ones) in a global, per chromosome way. Visualization is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases.

Author
Tomasz Stokowy
Date of publication
None
Maintainer
Tomasz Stokowy <tomasz.stokowy@k2.uib.no>
License
Artistic-2.0
Version
1.8.0

View on Bioconductor

Man pages

CentromeresHg19
Positions of centromeres on all chromosomes, human genome 19
chromosomeVis
Visualization of variants on the chromosome
FatherRareVariantsChr21
Annotated rare variants on the chromosome 21, human genome 19
MotherRareVariantsChr21
Annotated rare variants on the chromosome 21, human genome 19
movingAverage
Computation of moving average
multipleVis
Interactive visualization of rare variants on the chromosome,...
rareVariantVis
Interactive visualization of rare variants on the chromosome
SonRareVariantsChr21
Annotated rare variants on the chromosome 21, human genome...
trioVis
Interactive visualization of rare variants on the chromosome,...

Files in this package

RareVariantVis/DESCRIPTION
RareVariantVis/NAMESPACE
RareVariantVis/R
RareVariantVis/R/chromosomeVis.R
RareVariantVis/R/movingAverage.R
RareVariantVis/R/multipleVis.R
RareVariantVis/R/rareVariantVis.R
RareVariantVis/R/trioVis.R
RareVariantVis/build
RareVariantVis/build/vignette.rds
RareVariantVis/data
RareVariantVis/data/CentromeresHg19.txt
RareVariantVis/data/FatherRareVariantsChr21.txt
RareVariantVis/data/MotherRareVariantsChr21.txt
RareVariantVis/data/SonRareVariantsChr21.txt
RareVariantVis/inst
RareVariantVis/inst/doc
RareVariantVis/inst/doc/RareVariantsVis.R
RareVariantVis/inst/doc/RareVariantsVis.Rnw
RareVariantVis/inst/doc/RareVariantsVis.pdf
RareVariantVis/inst/extdata
RareVariantVis/man
RareVariantVis/man/CentromeresHg19.Rd
RareVariantVis/man/FatherRareVariantsChr21.Rd
RareVariantVis/man/MotherRareVariantsChr21.Rd
RareVariantVis/man/SonRareVariantsChr21.Rd
RareVariantVis/man/chromosomeVis.Rd
RareVariantVis/man/movingAverage.Rd
RareVariantVis/man/multipleVis.Rd
RareVariantVis/man/rareVariantVis.Rd
RareVariantVis/man/trioVis.Rd
RareVariantVis/tests
RareVariantVis/vignettes
RareVariantVis/vignettes/RareVariantsVis.Rnw