https://github.com/lieberinstitute/speaqeasyworkshop2023

BioC2023 SPEAQeasy Workshop by Daianna Gonzalez-Padilla, Renee Garcia-Flores & Nicholas J. Eagles
https://github.com/lieberinstitute/speaqeasyworkshop2023

Last synced: about 1 year ago
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BioC2023 SPEAQeasy Workshop by Daianna Gonzalez-Padilla, Renee Garcia-Flores & Nicholas J. Eagles

• Host: GitHub
• URL: https://github.com/lieberinstitute/speaqeasyworkshop2023
• Owner: LieberInstitute
• Created: 2023-05-29T07:09:24.000Z (about 3 years ago)
• Default Branch: devel
• Last Pushed: 2023-07-28T05:33:47.000Z (about 3 years ago)
• Last Synced: 2025-01-28T16:45:49.909Z (over 1 year ago)
• Language: R
• Homepage: http://research.libd.org/SPEAQeasyWorkshop2023/
• Size: 94.2 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • Code of conduct: .github/CODE_OF_CONDUCT.md
  • Support: .github/SUPPORT.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%"

)

```

# SPEAQeasyWorkshop2023

[![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/SPEAQeasyWorkshop2023)](https://github.com/LieberInstitute/SPEAQeasyWorkshop2023/issues)

[![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/SPEAQeasyWorkshop2023)](https://github.com/LieberInstitute/SPEAQeasyWorkshop2023/pulls)

[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

[![R-CMD-check-bioc](https://github.com/LieberInstitute/SPEAQeasyWorkshop2023/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/SPEAQeasyWorkshop2023/actions/workflows/R-CMD-check-bioc.yaml)

The goal of `SPEAQeasyWorkshop2023` is to describe how outputs from the [SPEAQeasy](https://github.com/LieberInstitute/SPEAQeasy) pipeline enable differential-expression analyses powered by Bioconductor packages like [limma](https://bioconductor.org/packages/3.17/bioc/html/limma.html), [edgeR](https://bioconductor.org/packages/3.17/bioc/html/edgeR.html), and [clusterProfiler](https://bioconductor.org/packages/3.17/bioc/html/clusterProfiler.html).

## Installation instructions

Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `SPEAQeasyWorkshop2023` from [Bioconductor](http://bioconductor.org/) using the following code:

```{r 'install', eval = FALSE}

if (!requireNamespace("BiocManager", quietly = TRUE)) {

    install.packages("BiocManager")

}

BiocManager::install("SPEAQeasyWorkshop2023")

```

And the development version from [GitHub](https://github.com/LieberInstitute/SPEAQeasyWorkshop2023) with:

```{r 'install_dev', eval = FALSE}

BiocManager::install("LieberInstitute/SPEAQeasyWorkshop2023")

```

## Citation

Below is the citation output from using `citation('SPEAQeasyWorkshop2023')` in R. Please

run this yourself to check for any updates on how to cite __SPEAQeasyWorkshop2023__.

```{r 'citation', eval = requireNamespace('SPEAQeasyWorkshop2023')}

print(citation("SPEAQeasyWorkshop2023"), bibtex = TRUE)

```

Please note that the `SPEAQeasyWorkshop2023` 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 `SPEAQeasyWorkshop2023` 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://LieberInstitute.github.io/SPEAQeasyWorkshop2023) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.

* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.

* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.

For more details, check the `dev` directory.

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