https://github.com/ramiromagno/vermeulen

Biomarker data set by Vermeulen et al. (2009)
https://github.com/ramiromagno/vermeulen

qpcr qpcr-analysis r rstats-package

Last synced: 3 months ago
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Biomarker data set by Vermeulen et al. (2009)

• Host: GitHub
• URL: https://github.com/ramiromagno/vermeulen
• Owner: ramiromagno
• License: cc-by-4.0
• Created: 2022-10-31T14:28:10.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2024-04-22T20:57:02.000Z (9 months ago)
• Last Synced: 2024-09-30T02:43:24.642Z (3 months ago)
• Topics: qpcr, qpcr-analysis, r, rstats-package
• Language: R
• Homepage: https://rmagno.eu/vermeulen/
• Size: 76.4 MB
• Stars: 3
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • 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%"

)

```

# vermeulen

[![CRAN status](https://www.r-pkg.org/badges/version/vermeulen)](https://CRAN.R-project.org/package=vermeulen)

[![R-CMD-check](https://github.com/ramiromagno/vermeulen/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ramiromagno/vermeulen/actions/workflows/R-CMD-check.yaml)

`{vermeulen}` provides the Biomarker data set by [Vermeulen et al.

(2009)](https://doi.org/10.1016/S1470-2045(09)70154-8) in tidy format.

This data set is for a real-time quantitative PCR experiment that comprises:

-   The raw fluorescence data of 24,576 amplification curves.

-   64 targets: 59 genes of interest and 5 reference genes.

-   366 neuroblastoma cDNA samples and 18 dilution series samples.

## Installation

Install `{vermeulen}` from CRAN:

``` r

# Install from CRAN

install.packages("vermeulen")

```

You can instead install the development version of `{vermeulen}` from GitHub:

``` r

# install.packages("remotes")

remotes::install_github("ramiromagno/vermeulen")

```

## Usage

Because of CRAN size limits the data is not provided at installation time. The

data can be retrieved from this GitHub repository after installation with the

function `get_biomarker_dataset()`.

```{r message=FALSE, warning=FALSE}

library(vermeulen)

library(tibble)

library(dplyr)

# Takes a few seconds (downloading from GitHub...)

biomarker <- as_tibble(get_biomarker_dataset())

biomarker

```

Types of samples:

```{r}

count(

  distinct(biomarker, plate, well, sample_type, copies, dilution),

  sample_type,

  copies,

  dilution

)

```

## Code of Conduct

Please note that the `{vermeulen}` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

## References

1.  Vermeulen et al.. *Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study*. The Lancet Oncology 10, 663--671 (2009). doi: [10.1016/S1470-2045(09)70154-8](https://doi.org/10.1016/S1470-2045(09)70154-8).

2.  Ruijter et al.. *Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications*. Methods 59 32--46 (2013). doi: [10.1016/j.ymeth.2012.08.011](https://doi.org/10.1016/j.ymeth.2012.08.011).