Science Score: 31.0%
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 -
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: labinfo-lncc-br
- License: artistic-2.0
- Language: R
- Default Branch: main
- Size: 1.36 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
metavirus
metavirus aims to combine the three major virus data repositories (VirusHost, ViralZone, ICTV, NCBI Taxonomy and NCBI Refseq) into a R package for facilitating the application of the viruses descriptions, variants sequences and taxonomy data into the statistical environment of R. It is also developing a public API to explore the data integration mechanisms with phylogenetic, metagenome or machine learning approach.
Dependencies
The metavirus package has the following dependencies:
bash
R version 4.0.0 or later
Biostring
Installation
Use the devtools package to install from GitHub.
R
library(devtools)
install_github("labinfo-lncc/metavirus", ref="main")
Overview
Fig 1. Summary of workflow tasks, main functions and its outputs.
Environment setup
Get virus data
Retrive sequences from NCBI RefSeq
Preprocessing
Applicability and practical examples
Citation
The metavirus package is currently in press. To properly cite it, use the citation function.
R
citation("metavirus")
```R
To cite package ‘metavirus’ in publications use:
ANDRADE, A. A. S. (2022). metavirus: an public api and integrative tool to get viruses data into R system. R package version 1.0.
A BibTeX entry for LaTeX users is
@Manual{,
title = {metavirus: an public api and integrative tool to get viruses data into R system},
author = {Amanda Araújo Serrão de Andrade, Otavio Jose Bernardes Brustolini, Eduardo Wagner, Ana Tereza Ribeiro Vasconcelos},
year = {2022},
note = {R package version 1.0},
}
ATTENTION: This citation information has been auto-generated from the package
DESCRIPTION file and may need manual editing, see ‘help("citation")’.
```
License
Artistic License 2.0
If you have any queries or find a bug, please submit an issue on GitHub or email atrv@lncc.br.
Owner
- Login: labinfo-lncc-br
- Kind: user
- Repositories: 1
- Profile: https://github.com/labinfo-lncc-br
Citation (CITATION)
# To cite package ‘metavirus’ in publications use:
# ANDRADE, A. A. S. (2022). metaVirus: an public api and integrative tool to get viruses data into R system. R package version 1.0.
# A BibTeX entry for LaTeX users is
# @Manual{,
# title = {metaVirus: an public api and integrative tool to get viruses data into R system},
# author = {Amanda Araújo Serrão de Andrade, Otavio Jose Bernardes Brustolini, Eduardo Wagner, Ana Tereza Ribeiro Vasconcelos},
# year = {2022},
# note = {R package version 1.0},
# }
# ATTENTION: This citation information has been auto-generated from the package
# DESCRIPTION file and may need manual editing, see ‘help("citation")’.
GitHub Events
Total
Last Year
Dependencies
- Biostrings * depends
- R >= 4.2.0 depends
- utils * depends
- BiocStyle * suggests
- MLeval * suggests
- caret * suggests
- covr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests