https://github.com/pensoft/omicsdatapaper

A golem to import genomic metadata into an omics data paper manuscript according to Pensoft's template
https://github.com/pensoft/omicsdatapaper

golem omics-data-papers shiny

Last synced: about 2 months ago
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A golem to import genomic metadata into an omics data paper manuscript according to Pensoft's template

• Host: GitHub
• URL: https://github.com/pensoft/omicsdatapaper
• Owner: pensoft
• License: other
• Created: 2020-11-16T10:20:39.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2021-01-18T08:55:52.000Z (almost 4 years ago)
• Last Synced: 2024-10-11T22:22:01.200Z (2 months ago)
• Topics: golem, omics-data-papers, shiny
• Language: R
• Homepage:
• Size: 812 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • License: LICENSE.md
  • Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# omicsdatapaper

[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)

This golem is an installable version of the Omics data paper R shiny app: https://mdmtrv.shinyapps.io/Omics_data_paper/

The Omics Data Paper Generator app, packaged within this golem, emulates the functionality of the automatic workflow for streamlined import of ENA metadata into manuscript integrated inside Pensoft's ARPHA Writing Tool. You can read more about it in this [abstract](https://biss.pensoft.net/article/59041/) and [blogpost](https://blog.pensoft.net/2020/06/16/streamlined-import-of-omics-metadata-from-the-european-nucleotide-archive-ena-into-an-omics-data-paper-manuscript/).

## Requirements

You need R and R Studio to run this app. We've tested it with the following versions of R and RStudio:

- R 3.0.1+

- RStudio Desktop 1.3.1093

## Installation

You can install the latest version of omicsdatapaper from [github](https://github.com/) with:

``` r

devtools::install_github("mdmtrv/omicsdatapaper")

```

## Use

The omicsdatapaper golem has only one function: to run the Omics Data Paper Generator app locally on your machine. This is how to do it:

```{r example}

library(omicsdatapaper)

run_app()

```

That's all!

The package handles all dependencies and imports the required [jats-skeleton.xml](https://github.com/pensoft/omics-data-paper-shinyapp/blob/master/jats-skeleton.xml).