To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TVTB")
In most cases, you don't need to download the package archive at all.
TVTB
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TVTB: The VCF Tool Box
Bioconductor version: Release (3.5)
The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).
Author: Kevin Rue-Albrecht [aut, cre]
Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>
Citation (from within R,
enter citation("TVTB")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TVTB")
Documentation
| HTML | R Script | Introduction to TVTB |
| HTML | R Script | The Shiny Variant Explorer |
| HTML | R Script | VCF filter rules |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (1 year) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), methods, utils, stats |
| Imports | AnnotationFilter, BiocGenerics(>= 0.19.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges(>= 2.7.1), reshape2, Rsamtools, S4Vectors(>= 0.11.11), SummarizedExperiment, VariantAnnotation(>= 1.19.9) |
| LinkingTo | |
| Suggests | EnsDb.Hsapiens.v75(>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle(>= 2.1.23), knitr (>= 1.12), rmarkdown, testthat, covr, pander |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/kevinrue/TVTB |
| BugReports | https://github.com/kevinrue/TVTB/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TVTB_1.2.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | TVTB_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TVTB |
| Package Short Url | http://bioconductor.org/packages/TVTB/ |
| Package Downloads Report | Download Stats |
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