TVTB
This is the development version of TVTB; for the stable release version, see TVTB.
TVTB: The VCF Tool Box
Bioconductor version: Development (3.24)
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("TVTB")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("TVTB")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TVTB")| Introduction to TVTB | HTML | R Script |
| The Shiny Variant Explorer | HTML | R Script |
| VCF filter rules | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), methods, utils, stats |
| Imports | AnnotationFilter, BiocGenerics(>= 0.25.1), BiocParallel, Biostrings, ensembldb, Seqinfo, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges(>= 2.21.6), reshape2, Rsamtools, S4Vectors(>= 0.25.14), SummarizedExperiment, VariantAnnotation(>= 1.19.9) |
| System Requirements | |
| URL | https://github.com/kevinrue/TVTB |
| Bug Reports | https://github.com/kevinrue/TVTB/issues |
See More
| Suggests | EnsDb.Hsapiens.v75(>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle(>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TVTB_1.39.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | TVTB_1.39.0.tgz |
| macOS Binary (sonoma-arm64) | TVTB_1.39.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TVTB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TVTB |
| Bioc Package Browser | https://code.bioconductor.org/browse/TVTB/ |
| Package Short Url | https://bioconductor.org/packages/TVTB/ |
| Package Downloads Report | Download Stats |