# R/`biotmle`
[](https://travis-ci.org/nhejazi/biotmle)
[](https://ci.appveyor.com/project/nhejazi/biotmle)
[](https://codecov.io/github/nhejazi/biotmle?branch=master)
[](http://www.repostatus.org/#wip)
[](http://opensource.org/licenses/MIT)
> Targeted Learning with moderated statistics for biomarker discovery
---
## Description
`biotmle` is an R package that facilitates biomarker discovery by generalizing
the moderated t-statistic of Smyth for use with asymptotically linear target
parameters. The set of methods implemented in this R package rely on the use of
Targeted Minimum Loss-Based Estimation (TMLE) to transform biological sequencing
data (e.g., microarray, RNA-seq) based on the influence curve representation of
a particular causal target parameter (e.g., Average Treatment Effect). The
transformed data are then used to test for differences between the statistical
estimate of the target parameter and a hypothesized value of said parameter
using the approach of moderated statistics implemented in the R package
[`limma`](https://bioconductor.org/packages/release/bioc/html/limma.html).
---
## Installation
- For standard use, install from [Bioconductor](https://bioconductor.org):
```
source("https://bioconductor.org/biocLite.R")
biocLite("biotmle")
```
- Install the most recent _stable release_ from GitHub:
```
devtools::install_github("nhejazi/biotmle")
```
- To contribute, install the _development version_:
```
devtools::install_github("nhejazi/biotmle", ref = "develop")
```
---
## Issues
If you encounter any bugs or have any specific feature requests, please [file an
issue](https://github.com/nhejazi/biotmle/issues).
---
## Citation
After using the `biotmle` R package, please cite it:
@article{hejazi2017biotmle,
doi = {},
url = {},
year = {2017},
month = {},
publisher = {The Open Journal},
volume = {},
number = {},
author = {Hejazi, Nima S and Cai, Weixin and Hubbard, Alan E},
title = {biotmle: Targeted Learning for Biomarker Discovery},
journal = {The Journal of Open Source Software}
}
---
## Related
* [R/`biotmleData`](https://github.com/nhejazi/biotmleData) - R package with
example experimental data for use with this analysis package.
---
## References
* [Nima S. Hejazi, Sara Kherad-Pajouh, Mark J. van der Laan, and Alan E.
Hubbard. "Generalized application of the moderated t-statistic to
asymptotically linear target parameters." __in preparation__, 2017.]()
* [Gordon K. Smyth. "Linear models and empirical Bayes methods for assessing
differential expression in microarray experiments." _Statistical
Applications in Genetics and Molecular Biology_, 3(1),
2004.](http://www.statsci.org/smyth/pubs/ebayes.pdf)
---
## License
© 2016-2017 [Nima S. Hejazi](http://nimahejazi.org) & [Alan E.
Hubbard](http://hubbard.berkeley.edu/)
The contents of this repository are distributed under the MIT license. See file
`LICENSE` for details.
