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README.Rmd
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---
output: github_document
title: ChangChang manual
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# changchang
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/changchang)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/changchang)
[](http://bioconductor.org/packages/stats/bioc/changchang/)
[](https://support.bioconductor.org/tag/changchang)
[](https://bioconductor.org/packages/release/bioc/html/changchang.html#since)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/changchang/)
[](https://bioconductor.org/packages/release/bioc/html/changchang.html#since)
<!-- badges: end -->
The goal of `changchang` is to ...
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `changchang` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("changchang")
```
## Input data
### `tantan`
To load output of `tantan` the simplest at the moment is to convert its output
to BED format and use the `loadTantan()` function. Here is an exmaple on how
to produce the BED file.
```
tantan -w 10 -f4 example.fasta | tee example.tantan.txt | awk 'OFS="\t" {print $1, $2, $3, $6, $5, "."}' > example.tantan.bed
```
### Other tandem repeat finder softwares
Not supported yet. Patches welcome!
## Example
This is a basic example which shows you how to solve a common problem:
```{r example, eval = requireNamespace('changchang')}
library("changchang") |> suppressPackageStartupMessages()
loadTantan(system.file('extdata/example.bed.xz', package="changchang"))
telomeres(exampleTantan, narrow="ends")
```
## Citation
Below is the citation output from using `citation('changchang')` in R. Please
run this yourself to check for any updates on how to cite __changchang__.
```{r 'citation', eval = requireNamespace('changchang')}
print(citation('changchang'), bibtex = TRUE)
```
Please note that the `changchang` 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 `changchang` 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 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')`.