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ruijter

Technical data sets by Ruijter et al. (2013)

https://github.com/ramiromagno/ruijter

Science Score: 36.0%

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    Found 5 DOI reference(s) in README
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    Low similarity (13.5%) to scientific vocabulary

Keywords

qpcr r
Last synced: 10 months ago · JSON representation

Repository

Technical data sets by Ruijter et al. (2013)

Basic Info
  • Host: GitHub
  • Owner: ramiromagno
  • License: cc-by-4.0
  • Language: R
  • Default Branch: main
  • Homepage: http://rmagno.eu/ruijter/
  • Size: 25.5 MB
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
qpcr r
Created over 3 years ago · Last pushed about 2 years ago
Metadata Files
Readme Changelog License 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%"
)
```

# ruijter


[![CRAN status](https://www.r-pkg.org/badges/version/ruijter)](https://CRAN.R-project.org/package=ruijter)
[![R-CMD-check](https://github.com/ramiromagno/ruijter/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ramiromagno/ruijter/actions/workflows/R-CMD-check.yaml)


`{ruijter}` is an R data package that provides the real-time qPCR technical data
sets used in [Ruijter et al.
(2013)](https://doi.org/10.1016/j.ymeth.2012.08.011) in tidy format, namely:

- The 94-replicates-4-dilutions data set: `ds_94_4`
- The 380 replicates data set: `ds_380`
- The competimer data set: `ds_competimer`


## Installation

Install `{ruijter}` from CRAN:

``` r
# Install from CRAN
install.packages("ruijter")
```

You can install the development version of `{ruijter}` like so:

``` r
# install.packages("remotes")
remotes::install_github("ramiromagno/ruijter")
```

## Usage


### Four-point 10-fold dilution series `ds_94_4`

```{r dpi=300, fig.width=8, fig.height=4}
library(ruijter)
library(dplyr)
library(ggplot2)

head(ds_94_4)

dplyr::count(ds_94_4, well, replicate, sample_type, copies)

ds_94_4 %>%
  ggplot(mapping = aes(x = cycle, y = fluor, group = well, col = as.character(copies))) +
  geom_line(size = 0.1) +
  labs(y = "Raw fluorescence", colour="Copy number", title = "Four-point 10-fold dilution series") +
  guides(color = guide_legend(override.aes = list(size = 0.5)))
```

###  Replicates for assessment of precision `ds_380`

```{r dpi=300, fig.width=8, fig.height=4}
head(ds_380)

dplyr::count(ds_380, well, replicate, sample_type, copies)

ds_380 %>%
  ggplot(mapping = aes(x = cycle, y = fluor, group = well, col = as.factor(copies))) +
  geom_line(size = 0.1) +
  labs(y = "Raw fluorescence", colour="Copy number", title = "380 replicates data set") +
  guides(color = guide_legend(override.aes = list(size = 0.5)))
```

###  Competimer primers for PCR efficiency modulation `ds_competimer`

```{r dpi=300, fig.width=8, fig.height=8}
head(ds_competimer)

dplyr::count(ds_competimer, well, pct, conc, replicate, sample_type)

ds_competimer %>%
  ggplot(mapping = aes(x = cycle, y = fluor, group = interaction(pct, conc, replicate), col = interaction(pct, conc))) +
  geom_line(size = 0.2) +
  guides(color = "none") +
  labs(y = "Raw fluorescence", title = "Competimer data set") +
  facet_grid(rows = vars(pct), cols = vars(conc))
```

## Terms of use

If you use the data here provided please do not forget to cite the original
work by Ruijter et al. (2013), and this package.

## Code of Conduct
  
Please note that the `{ruijter}` 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

Jan M. Ruijter, Michael W. Pfaffl, Sheng Zhao, Andrej N. Spiess, Gregory Boggy,
Jochen Blom,Robert G. Rutledge, Davide Sisti, Antoon Lievens, Katleen De Preter,
Stefaan Derveaux, Jan Hellemans, Jo Vandesompele. *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).

Owner

  • Name: Ramiro Magno
  • Login: ramiromagno
  • Kind: user
  • Company: Pattern Institute

Data Scientist

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Last synced: almost 2 years ago

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Packages

  • Total packages: 1
  • Total downloads:
    • cran 562 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: ruijter

Technical Data Sets by Ruijter et al. (2013)

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 562 Last month
Rankings
Stargazers count: 28.5%
Forks count: 28.8%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 39.3%
Downloads: 73.9%
Maintainers (1)
rmagno@pattern.institute
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
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  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.5.0 composite
  • actions/checkout v4 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite