Gviz

This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
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Academic publication links
✓
Committers with academic emails
5 of 24 committers (20.8%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioinformatics pathway-analysis mirror similarity-measurement similarity gene-sets gene functional-similarity bioconductor

Last synced: 6 months ago · JSON representation ·

Repository

This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.

Basic Info

Host: GitHub
Owner: ivanek
License: artistic-2.0
Language: R
Default Branch: devel
Homepage: https://bioconductor.org/packages/Gviz/
Size: 39.3 MB

Statistics

Stars: 86
Watchers: 2
Forks: 12
Open Issues: 30
Releases: 0

Created about 7 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: Robert Ivánek
Login: ivanek
Kind: user
Location: Basel, Switzerland
Company: University of Basel

Website: https://biomedizin.unibas.ch/en/core-facilities/bioinformatics/
Repositories: 2
Profile: https://github.com/ivanek

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

GitHub Events

Total

Issues event: 8
Watch event: 18
Issue comment event: 2
Push event: 3
Fork event: 2

Last Year

Issues event: 8
Watch event: 18
Issue comment event: 2
Push event: 3
Fork event: 2

Committers

Last synced: over 2 years ago

All Time

Total Commits: 457
Total Committers: 24
Avg Commits per committer: 19.042
Development Distribution Score (DDS): 0.503

Past Year

Commits: 18
Committers: 3
Avg Commits per committer: 6.0
Development Distribution Score (DDS): 0.222

Top Committers

Name	Email	Commits
Robert Ivánek	r**k@u**h	227
Florian Hahne	f**e@d**e	116
Robert Ivanek	r**k@f**h	24
Dan Tenenbaum	d**a@f**g	23
Herve Pages	h**s@f**g	17
Nitesh Turaga	n**a@g**m	14
Felix Ernst	f**t@o**m	6
Lance Parsons	l**s@p**u	3
Martin Morgan	m**n@f**g	3
Arne Mueller	a**r@n**m	2
vobencha	v**a@g**m	2
vobencha	v**n@r**g	2
Mike Smith	g**h@g**m	2
Hervé Pagès	h**s@f**g	2
J Wokaty	j****y	2
Thomas Wayne McCarthyls	1****t	2
Vince Carey	s**c@c**u	2
J Wokaty	j**y@s**u	2
Steve Lianoglou	s**u@g**m	1
Marc Carlson	m**n@f**g	1
Michael Lawrence	l**i@i**u	1
Hervé Pagès	h**b@g**m	1
aoles	a**s@g**m	1
Robert Ivánek	i****k	1

Committer Domains (Top 20 + Academic)

fhcrc.org: 4 iastate.edu: 1 sph.cuny.edu: 1 channing.harvard.edu: 1 fredhutch.org: 1 roswellpark.org: 1 novartis.com: 1 princeton.edu: 1 fmi.ch: 1 dkfz-heidelberg.de: 1 unibas.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 14
Total pull requests: 0
Average time to close issues: 7 months
Average time to close pull requests: N/A
Total issue authors: 13
Total pull request authors: 0
Average comments per issue: 0.79
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 9
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 9
Pull request authors: 0
Average comments per issue: 0.22
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jayoung (2)
alex-d13 (1)
JuliusDeynet (1)
yonatans2 (1)
GimenaA (1)
shaman-yellow (1)
jennyujin22 (1)
rejo27 (1)
SmirnygaTotoshka (1)
foriin (1)
emidalla (1)
GGSonoda (1)
SEvisual (1)
davidcoffey (1)

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- bioconductor 918,525 total

Total dependent packages: 57
Total dependent repositories: 0
Total versions: 6
Total maintainers: 1

bioconductor.org: Gviz

Plotting data and annotation information along genomic coordinates

Homepage: https://github.com/ivanek/Gviz
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.pdf
License: Artistic-2.0
Latest release: 1.52.0
published 10 months ago

Versions: 6
Dependent Packages: 57
Dependent Repositories: 0
Downloads: 918,525 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 1.5%

Average: 2.7%

Downloads: 2.9%

Stargazers count: 3.0%

Forks count: 6.3%

Maintainers (1)

robert.ivanek@unibas.ch

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

GenomicRanges >= 1.17.20 depends
IRanges >= 1.99.18 depends
R >= 4.2 depends
S4Vectors >= 0.9.25 depends
grid * depends
methods * depends
AnnotationDbi >= 1.27.5 imports
BSgenome >= 1.33.1 imports
Biobase >= 2.15.3 imports
BiocGenerics >= 0.11.3 imports
Biostrings >= 2.33.11 imports
GenomeInfoDb >= 1.1.3 imports
GenomicAlignments >= 1.1.16 imports
GenomicFeatures >= 1.17.22 imports
RColorBrewer * imports
Rsamtools >= 1.17.28 imports
XVector >= 0.5.7 imports
biomaRt >= 2.11.0 imports
biovizBase >= 1.13.8 imports
digest >= 0.6.8 imports
ensembldb >= 2.11.3 imports
grDevices * imports
graphics * imports
lattice * imports
latticeExtra >= 0.6 imports
matrixStats >= 0.8.14 imports
rtracklayer >= 1.25.13 imports
stats * imports
utils * imports
BSgenome.Hsapiens.UCSC.hg19 * suggests
BiocStyle * suggests
knitr * suggests
rmarkdown * suggests
testthat * suggests
xml2 * suggests

.github/workflows/check-bioc.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact master composite
r-lib/actions/setup-pandoc master composite
r-lib/actions/setup-r master composite

Gviz

Science Score: 67.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

Gviz - Plotting data and annotation information along genomic coordinates

Software status

Authors

Overview

Installation

Release version

Developmental version

Github

Usage

Citation

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

bioconductor.org: Gviz

Rankings

Maintainers (1)

Dependencies