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planttfhunter

An R package to identify plant transcription factors from protein sequence data and classify them in families

https://github.com/almeidasilvaf/planttfhunter

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.6%) to scientific vocabulary

Keywords

functional-genomics gene-families hidden-markov-models plant-genomics plants protein-domains rstats transcription-factors
Last synced: 11 months ago · JSON representation

Repository

An R package to identify plant transcription factors from protein sequence data and classify them in families

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
functional-genomics gene-families hidden-markov-models plant-genomics plants protein-domains rstats transcription-factors
Created over 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme Code of conduct

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# planttfhunter 


[![GitHub issues](https://img.shields.io/github/issues/almeidasilvaf/planttfhunter)](https://github.com/almeidasilvaf/planttfhunter/issues)
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![R-CMD-check-bioc](https://github.com/almeidasilvaf/planttfhunter/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/almeidasilvaf/planttfhunter/actions)
[![Codecov test
coverage](https://codecov.io/gh/almeidasilvaf/planttfhunter/branch/devel/graph/badge.svg)](https://codecov.io/gh/almeidasilvaf/planttfhunter?branch=devel)


The goal of __planttfhunter__ is to identify plant transcription factors from protein 
sequence data and classify them into families and subfamilies using the
classification scheme implemented 
in [PlantTFDB](https://doi.org/10.1093/nar/gkz1020).

## Installation instructions

Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). 
Then install __planttfhunter__ from [Bioconductor](http://bioconductor.org/) 
using the following code:

```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("planttfhunter")
```

And the development version from 
[GitHub](https://github.com/almeidasilvaf/planttfhunter) with:

```{r 'install_dev', eval = FALSE}
BiocManager::install("almeidasilvaf/planttfhunter")
```

## Citation

Below is the citation output from using `citation('planttfhunter')` in R. Please
run this yourself to check for any updates on how to cite __planttfhunter__.

```{r 'citation', eval = requireNamespace('planttfhunter')}
print(citation('planttfhunter'), bibtex = TRUE)
```

Please note that the __planttfhunter__ project was only made possible thanks to many 
other R and bioinformatics software authors, which are cited either in the 
vignettes and/or the paper(s) describing this package.

## Code of Conduct

Please note that the __planttfhunter__ project is released with 
a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). 
By contributing to this project, you agree to abide by its terms.

## Development tools

* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://almeidasilvaf.github.io/planttfhunter) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.

This package was developed using `r BiocStyle::Biocpkg('biocthis')`.

Owner

  • Name: Fabrício Almeida-Silva
  • Login: almeidasilvaf
  • Kind: user
  • Location: Technologiepark 71, Ghent, Belgium
  • Company: VIB-UGent Center for Plant Systems Biology

Bioinformatics. Network biology. Plant genomics and evolution. #rstats addict.

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 50
  • Total Committers: 1
  • Avg Commits per committer: 50.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 5
  • Committers: 1
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
almeidasilvaf f****a@h****m 50

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 3 days
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 3.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • PraveenOraon (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 4,953 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: planttfhunter

Identification and classification of plant transcription factors

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4,953 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 32.9%
Downloads: 98.6%
Maintainers (1)
fabricio_almeidasilva@hotmail.com
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.2.0 depends
  • Biostrings * imports
  • SummarizedExperiment * imports
  • methods * imports
  • utils * imports
  • BiocStyle * suggests
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • sessioninfo * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite