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This is the development version of TVTB; for the stable release version, see TVTB.
Bioconductor version: Development (3.18)
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 (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("TVTB")
For older versions of R, please refer to the appropriate Bioconductor release.
Reference Manual |
biocViews | Alignment, Coverage, DNASeq, DataImport, DataRepresentation, GUI, GeneticVariability, Genetics, GenomicVariation, MultipleComparison, SequenceMatching, Sequencing, Software, VariantAnnotation, Visualization, WholeGenome |
Version | 1.27.0 |
In Bioconductor since | BioC 3.4 (R-3.3) (7 years) |
License | Artistic-2.0 |
Depends | R (>= 3.4), methods, utils, stats |
Imports | AnnotationFilter, BiocGenerics(>= 0.25.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges(>= 2.21.6), reshape2, Rsamtools, S4Vectors(>= 0.25.14), SummarizedExperiment, VariantAnnotation(>= 1.19.9) |
LinkingTo | |
Suggests | EnsDb.Hsapiens.v75(>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle(>= 2.5.19), 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 | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | |
Windows Binary | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/TVTB |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TVTB |
Package Short Url | https://bioconductor.org/packages/TVTB/ |
Package Downloads Report | Download Stats |
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