Data

Tools

Indexes

Applications

Experiments

Open Source Science

TVTB

The VCF Tool Box

https://github.com/kevinrue/tvtb

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.4%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioconductor bioinformatics functional-similarity gene gene-sets pathway-analysis similarity similarity-measurement mirror
Last synced: 11 months ago · JSON representation

Repository

The VCF Tool Box

Basic Info
  • Host: GitHub
  • Owner: kevinrue
  • Language: R
  • Default Branch: devel
  • Size: 1.61 MB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created almost 9 years ago · Last pushed 12 months ago
Metadata Files
Readme

README.md

logo.png

The VCF Tool Box (TVTB)

R build status Codecov.io coverage status <!-- badges: end -->

Bioconductor release status

| Branch | R CMD check | Last updated | |:----------------:|:----------------:|:------------:| | devel | Bioconductor-devel Build Status | | | release | Bioconductor-release Build Status | |

Description

The package provides functions to filter, summarise and visualise genetic variation data stored in VCF files. Functionalities are also demonstrated in a Shiny web-application.

Motivation

The VCF file format encodes a plethora of useful information, including optional predictions using the Ensembl Variant Effect Predictor (VEP) that can be parsed using expert packages such as VariantAnnotation and formatted into VCF objects. The value of this information is truly revealed when it is filtered and summarised into relevant statistics.

This package offers methods:

  • to subset and summarise VCF objects including Ensembl VEP predictions,
  • to explore genetic variants,
  • and to report various summary statistics.

Installation

Instructions to install the latest release of TVTB are available at: http://bioconductor.org/packages/release/bioc/html/TVTB.html

Using devtools, versions more recent than the official releases can be obtained:

install.packages("devtools")

The latest version pushed to Bioconductor release (may be more recent than the official release in the absence of version bump) :

devtools::install_github("Bioconductor-mirror/TVTB", ref="release-3.4")

The latest version pushed to Bioconductor devel (as above):

devtools::install_github("Bioconductor-mirror/TVTB", ref="master")

Original GitHub development repository:

devtools::install_github("kevinrue/TVTB")

Specific commit:

devtools::install_github("kevinrue/TVTB", ref="99966dda")

Graphical User Interface

Although nothing offers more flexibility than the command line interface, a Shiny web-application, the Shiny Variant Explorer (tSVE), offers a GUI to get familiar with the major functionalities of the package.

Tests

Unit tests and coverage implemented using the testthat package (CRAN).

Coverage excludes files:

  • AllClasses.R (Not executed at runtime)
  • tSVE.R (Requires interactive session)

License

Artistic License 2.0

Owner

  • Name: Kevin Rue-Albrecht
  • Login: kevinrue
  • Kind: user
  • Location: Oxford
  • Company: University of Oxford

Ingénieur diplômé; Computational Biologist; Software engineer; Bioconductor contributor

GitHub Events

Total
  • Delete event: 1
  • Push event: 3
  • Pull request event: 3
  • Create event: 2
Last Year
  • Delete event: 1
  • Push event: 3
  • Pull request event: 3
  • Create event: 2

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 394
  • Total Committers: 9
  • Avg Commits per committer: 43.778
  • Development Distribution Score (DDS): 0.168
Past Year
  • Commits: 5
  • Committers: 2
  • Avg Commits per committer: 2.5
  • Development Distribution Score (DDS): 0.4
Top Committers
Name Email Commits
Kevin Rue-Albrecht k****e@u****e 328
Kevin Rue-Albrecht k****7@g****m 24
Nitesh Turaga n****a@g****m 18
J Wokaty j****y 8
Hervé Pagès h****s@f****g 7
Herve Pages h****s@f****g 4
vobencha v****a@g****m 2
vobencha v****n@r****g 2
Martin Morgan m****n@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 2 roswellpark.org: 1 fredhutch.org: 1 ucdconnect.ie: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 2
  • Total pull requests: 14
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 4.5
  • Average comments per pull request: 0.36
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • stefanucci-luca (1)
  • hsiaoyi0504 (1)
Pull Request Authors
  • kevinrue (20)
  • elgohr (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 13,961 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: TVTB

TVTB: The VCF Tool Box

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 13,961 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 18.4%
Average: 19.8%
Stargazers count: 24.9%
Downloads: 55.7%
Maintainers (1)
kevinrue67@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.4 depends
  • methods * depends
  • stats * depends
  • utils * depends
  • AnnotationFilter * imports
  • BiocGenerics >= 0.25.1 imports
  • BiocParallel * imports
  • Biostrings * imports
  • GGally * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • Gviz * imports
  • IRanges >= 2.21.6 imports
  • Rsamtools * imports
  • S4Vectors >= 0.25.14 imports
  • SummarizedExperiment * imports
  • VariantAnnotation >= 1.19.9 imports
  • ensemblVEP * imports
  • ensembldb * imports
  • ggplot2 * imports
  • limma * imports
  • reshape2 * imports
  • BiocStyle >= 2.5.19 suggests
  • DT >= 0.1.67 suggests
  • EnsDb.Hsapiens.v75 >= 0.99.7 suggests
  • covr * suggests
  • knitr >= 1.12 suggests
  • pander * suggests
  • rmarkdown * suggests
  • rtracklayer * suggests
  • shiny >= 0.13.2.9005 suggests
  • testthat * suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
Dockerfile docker
  • bioconductor/bioconductor_docker devel build