gviz

This is a read-only mirror of the git repos at https://bioconductor.org

https://github.com/bioc/gviz

Science Score: 57.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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Found .zenodo.json file
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DOI references
Found 4 DOI reference(s) in README
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Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

This is a read-only mirror of the git repos at https://bioconductor.org

Basic Info

Host: GitHub
Owner: bioc
License: artistic-2.0
Language: R
Default Branch: devel
Size: 8.88 MB

Statistics

Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Created over 2 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog License Citation

Gviz - Plotting data and annotation information along genomic coordinates

Software status

| | Bioc (release) | Bioc (devel) | |:--------------------|----------------------------------------------------------------------------:|--------------------------------------------------------------------------------:| | OS | | | | Bioc Last Update | | | | Bioc Status | | | | GitHub Last Commit | | | | GitHub Actions | | | | Coverage | | |

Authors

Florian Hahne
Steffen Durinck
Robert Ivanek
Arne Mueller
Steve Lianoglou
Ge Tan
Lance Parsons
Shraddha Pai

Overview

Gviz UCSC like screenshot

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Installation

Release version

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Gviz", version = "release")

Developmental version

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Gviz", version = "devel")

Github

if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") remotes::install_github("ivanek/Gviz")

Usage

For detailed instructions check the package vignette (release or developmental version). Or check the GitHub.io page.

Citation

Hahne F, Ivanek R (2016). "Statistical Genomics: Methods and Protocols." In Mathé E, Davis S (eds.), chapter Visualizing Genomic Data Using Gviz and Bioconductor, 335–351. Springer New York, New York, NY. ISBN 978-1-4939-3578-9, doi: 10.1007/978-1-4939-3578-9_16.

Owner

Name: bioc
Login: bioc
Kind: organization

Repositories: 1
Profile: https://github.com/bioc

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.2.1
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "Gviz" in publications use:'
type: software
license: Artistic-2.0
title: 'Gviz: Plotting data and annotation information along genomic coordinates'
version: 1.39.5
doi: 10.1007/978-1-4939-3578-9_16
abstract: Genomic data analyses requires integrated visualization of known genomic
  information and new experimental data. Gviz uses the biomaRt and the rtracklayer
  packages to perform live annotation queries to Ensembl and UCSC and translates this
  to e.g. gene/transcript structures in viewports of the grid graphics package. This
  results in genomic information plotted together with your data.
authors:
- family-names: Hahne
  given-names: Florian
- family-names: Durinck
  given-names: Steffen
- family-names: Ivanek
  given-names: Robert
  email: robert.ivanek@unibas.ch
  orcid: https://orcid.org/0000-0002-8403-056X
- family-names: Mueller
  given-names: Arne
- family-names: Lianoglou
  given-names: Steve
- family-names: Tan
  given-names: Ge
- family-names: Parsons
  given-names: Lance
- family-names: Pai
  given-names: Shraddha
preferred-citation:
  type: book
  title: 'Statistical Genomics: Methods and Protocols'
  authors:
  - family-names: Hahne
    given-names: Florian
  - family-names: Ivanek
    given-names: Robert
    email: robert.ivanek@unibas.ch
    orcid: https://orcid.org/0000-0002-8403-056X
  editors:
  - family-names: Math\'e
    given-names: Ewy
  - family-names: Davis
    given-names: Sean
  section: Visualizing Genomic Data Using Gviz and Bioconductor
  year: '2016'
  publisher:
    name: Springer New York
    address: New York, NY
  isbn: 978-1-4939-3578-9
  doi: 10.1007/978-1-4939-3578-9_16
  url: http://dx.doi.org/10.1007/978-1-4939-3578-9_16
  start: '335'
  end: '351'
repository: https://bioconductor.org/
repository-code: https://github.com/ivanek/Gviz
url: https://github.com/ivanek/Gviz
contact:
- family-names: Ivanek
  given-names: Robert
  email: robert.ivanek@unibas.ch
  orcid: https://orcid.org/0000-0002-8403-056X

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