fastqc-viz/README.Rmd at main · barreiro-r/fastqc-viz · GitHub

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---
output: github_document
---

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


# fastqcviz <a href='https://github.com/barreiro-r/fastqc-viz/'><img src='man/figures/logo.png' align="right" height="138" width="120"/></a>

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The `fastqcviz` package was developed to give [FastQC](https://github.com/s-andrews/FastQC) reports the aesthetic and functional love it deserves, transforming its insights into a more visually appealing experience without changing the core analysis. A modest re-desing update for the classic FastQC report.

classic report: [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc.html) | ✨ `fastqcviz` report : [fastqcviz](https://html-preview.github.io/?url=https://github.com/barreiro-r/fastqc-viz/blob/main/man/figures/example.html)


![Screenshots of original FastQC and fastqcviz reports.](man/figures/before-after.png)


## Installation

You can install the development version of fastqcviz from [GitHub](https://github.com/) with:

```{r}
#| label: install
#| eval : FALSE

# install.packages("remotes")
remotes::install_github("barreiro-r/fastqc-viz")
```

## Example

Using fastqcviz is as easy as:

```{r}
#| label: example
#| eval : FALSE
library(fastqcviz)

create_fastqcviz_report(
  fastqc_path = "path/to/sample_fastqc/fastqc_data.txt",
  output_dir = "fastqcviz_report",
  embed_resources = TRUE)
```