The goal of TelescopeTools
is to provide commonly used functions and
data for downstream analysis of TE expression data.
Get the latest stable R
release from
CRAN. Then install TelescopeTools
from
Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("TelescopeTools")
And the development version from GitHub with:
BiocManager::install("nixonlab/TelescopeTools")
This is a basic example which shows you how to solve a common problem:
library("TelescopeTools")
## basic example code
What is special about using README.Rmd
instead of just README.md
?
You can include R chunks like so:
summary(cars)
#> speed dist
#> Min. : 4.0 Min. : 2.00
#> 1st Qu.:12.0 1st Qu.: 26.00
#> Median :15.0 Median : 36.00
#> Mean :15.4 Mean : 42.98
#> 3rd Qu.:19.0 3rd Qu.: 56.00
#> Max. :25.0 Max. :120.00
You’ll still need to render README.Rmd
regularly, to keep README.md
up-to-date.
You can also embed plots, for example:
In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub!
Below is the citation output from using citation('TelescopeTools')
in
R. Please run this yourself to check for any updates on how to cite
TelescopeTools.
print(citation('TelescopeTools'), bibtex = TRUE)
#> To cite package 'TelescopeTools' in publications use:
#>
#> nixonlab (2023). _TelescopeTools_.
#> doi:10.18129/B9.bioc.TelescopeTools
#> <https://doi.org/10.18129/B9.bioc.TelescopeTools>,
#> https://github.com/nixonlab/TelescopeTools/TelescopeTools - R package
#> version 0.99.0,
#> <http://www.bioconductor.org/packages/TelescopeTools>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {TelescopeTools},
#> author = {{nixonlab}},
#> year = {2023},
#> url = {http://www.bioconductor.org/packages/TelescopeTools},
#> note = {https://github.com/nixonlab/TelescopeTools/TelescopeTools - R package version 0.99.0},
#> doi = {10.18129/B9.bioc.TelescopeTools},
#> }
#>
#> nixonlab (2023). "TelescopeTools." _bioRxiv_. doi:10.1101/TODO
#> <https://doi.org/10.1101/TODO>,
#> <https://www.biorxiv.org/content/10.1101/TODO>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {TelescopeTools},
#> author = {{nixonlab}},
#> year = {2023},
#> journal = {bioRxiv},
#> doi = {10.1101/TODO},
#> url = {https://www.biorxiv.org/content/10.1101/TODO},
#> }
Please note that the TelescopeTools
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.
Please note that the TelescopeTools
project is released with a
Contributor Code of
Conduct. By
contributing to this project, you agree to abide by its terms.
- Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
- Code coverage assessment is possible thanks to codecov and covr.
- The documentation website is automatically updated thanks to pkgdown.
- The code is styled automatically thanks to styler.
- The documentation is formatted thanks to devtools and roxygen2.
For more details, check the dev
directory.
This package was developed using biocthis.