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.
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see TVTB.
Bioconductor version: 3.4
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("TVTB")
HTML | R Script | Introduction to TVTB |
HTML | R Script | The Shiny Variant Explorer |
HTML | R Script | VCF filter rules |
Reference Manual | ||
Text | NEWS |
biocViews | Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome |
Version | 1.0.2 |
In Bioconductor since | BioC 3.4 (R-3.3) (0.5 years) |
License | Artistic-2.0 |
Depends | R (>= 3.3), methods, utils, stats |
Imports | BiocGenerics(>= 0.19.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, ggplot2, 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 |
SystemRequirements | |
Enhances | |
URL | https://github.com/kevinrue/TVTB |
BugReports | https://github.com/kevinrue/TVTB/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | TVTB_1.0.2.tar.gz |
Windows Binary | |
Mac OS X 10.9 (Mavericks) | TVTB_1.0.2.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/TVTB/tree/release-3.4 |
Package Short Url | http://bioconductor.org/packages/TVTB/ |
Package Downloads Report | Download Stats |
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