--- a
+++ b/README.Rmd
@@ -0,0 +1,188 @@
+---
+output:
+  rmarkdown::github_document
+bibliography: "inst/REFERENCES.bib"
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "README-"
+)
+```
+
+# R/`biotmle`
+
+[![R-CMD-check](https://github.com/nhejazi/biotmle/workflows/R-CMD-check/badge.svg)](https://github.com/nhejazi/biotmle/actions)
+[![Coverage Status](https://img.shields.io/codecov/c/github/nhejazi/biotmle/master.svg)](https://codecov.io/github/nhejazi/biotmle?branch=master)
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/biotmle.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/biotmle)
+[![Bioc Time](http://bioconductor.org/shields/years-in-bioc/biotmle.svg)](https://bioconductor.org/packages/release/bioc/html/biotmle.html)
+[![Bioc Downloads](http://bioconductor.org/shields/downloads/biotmle.svg)](https://bioconductor.org/packages/release/bioc/html/biotmle.html)
+[![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)
+[![DOI](https://zenodo.org/badge/65854775.svg)](https://zenodo.org/badge/latestdoi/65854775)
+[![JOSS Status](http://joss.theoj.org/papers/02be843d9bab1b598187bfbb08ce3949/status.svg)](http://joss.theoj.org/papers/02be843d9bab1b598187bfbb08ce3949)
+
+> Targeted Learning with Moderated Statistics for Biomarker Discovery
+
+__Authors:__ [Nima Hejazi](https://nimahejazi.org), [Mark van der
+Laan](https://vanderlaan-lab.org/about), and [Alan
+Hubbard](https://hubbard.berkeley.edu)
+
+---
+
+## What's `biotmle`?
+
+The `biotmle` R package facilitates biomarker discovery through a generalization
+of the moderated t-statistic [@smyth2004linear] that extends the procedure to
+locally efficient estimators of asymptotically linear target parameters
+[@tsiatis2007semiparametric]. The set of methods implemented modify targeted
+maximum likelihood (TML) estimators of statistical (or causal) target parameters
+(e.g., average treatment effect) to apply variance moderation to the standard
+variance estimator based on the efficient influence function (EIF) of the target
+parameter [@vdl2011targeted; @vdl2018targeted]. By performing a moderated
+hypothesis test that pools the individual probe-specific EIF-based variance
+estimates, a robust variance estimator is constructed, which stabilizes the
+standard error estimates and improves the performance of such estimators both in
+smaller samples and in settings where the EIF is poorly estimated. The resultant
+procedure allows for the construction of conservative hypothesis tests that
+reduce the false discovery rate and/or the family-wise error rate
+[@hejazi2021generalization]. Improvements upon prior TML-based approaches to
+biomarker discovery (e.g., @bembom2009biomarker) include both the moderated
+variance estimator as well as the use of conservative reference distributions
+for the corresponding moderated test statistics (e.g., logistic distribution),
+inspired by tail bounds based on concentration
+inequalities [@rosenblum2009confidence]; the latter prove critical for obtaining
+robust inference when the finite-sample distribution of the estimator deviates
+from normality.
+
+---
+
+## Installation
+
+For standard use, install from
+[Bioconductor](https://bioconductor.org/packages/biotmle) using
+[`BiocManager`](https://CRAN.R-project.org/package=BiocManager):
+
+```{r bioc-installation, eval = FALSE}
+if (!requireNamespace("BiocManager", quietly=TRUE)) {
+  install.packages("BiocManager")
+}
+BiocManager::install("biotmle")
+```
+
+To contribute, install the bleeding-edge _development version_ from GitHub via
+[`remotes`](https://CRAN.R-project.org/package=remotes):
+
+```{r gh-master-installation, eval = FALSE}
+remotes::install_github("nhejazi/biotmle")
+```
+
+Current and prior [Bioconductor](https://bioconductor.org) releases are
+available under branches with numbers prefixed by "RELEASE_". For example, to
+install the version of this package available via Bioconductor 3.6, use
+
+```{r gh-develop-installation, eval = FALSE}
+remotes::install_github("nhejazi/biotmle", ref = "RELEASE_3_6")
+```
+
+---
+
+## Example
+
+For details on how to best use the `biotmle` R package, please consult the most
+recent [package
+vignette](https://bioconductor.org/packages/release/bioc/vignettes/biotmle/inst/doc/exposureBiomarkers.html)
+available through the [Bioconductor
+project](https://bioconductor.org/packages/biotmle).
+
+---
+
+## Issues
+
+If you encounter any bugs or have any specific feature requests, please [file an
+issue](https://github.com/nhejazi/biotmle/issues).
+
+---
+
+## Contributions
+
+Contributions are very welcome. Interested contributors should consult our
+[contribution
+guidelines](https://github.com/nhejazi/biotmle/blob/master/CONTRIBUTING.md)
+prior to submitting a pull request.
+
+---
+
+## Citation
+
+After using the `biotmle` R package, please cite both of the following:
+
+        @article{hejazi2017biotmle,
+          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},
+          volume = {2},
+          number = {15},
+          month = {July},
+          year  = {2017},
+          publisher = {The Open Journal},
+          doi = {10.21105/joss.00295},
+          url = {https://doi.org/10.21105/joss.00295}
+        }
+
+        @article{hejazi2021generalization,
+          author = {Hejazi, Nima S and Boileau, Philippe and {van der Laan},
+            Mark J and Hubbard, Alan E},
+          title = {A generalization of moderated statistics to data adaptive
+            semiparametric estimation in high-dimensional biology},
+          journal={under review},
+          volume={},
+          number={},
+          pages={},
+          year = {2021+},
+          publisher={},
+          doi = {},
+          url = {https://arxiv.org/abs/1710.05451}
+        }
+
+        @manual{hejazi2019biotmlebioc,
+          author = {Hejazi, Nima S and {van der Laan}, Mark J and Hubbard, Alan
+            E},
+          title = {{biotmle}: {Targeted Learning} with moderated statistics for
+            biomarker discovery},
+          doi = {10.18129/B9.bioc.biotmle},
+          url = {https://bioconductor.org/packages/biotmle},
+          note = {R package version 1.10.0}
+        }
+
+---
+
+## Related
+
+* [R/`biotmleData`](https://github.com/nhejazi/biotmleData) - R package with
+    example experimental data for use with this analysis package.
+
+---
+
+## Funding
+
+The development of this software was supported in part through grants from the
+National Institutes of Health: [P42 ES004705-29](https://projectreporter.nih.gov/project_info_details.cfm?aid=9260357&map=y) and [R01 ES021369-05](https://projectreporter.nih.gov/project_info_description.cfm?aid=9210551&icde=37849782&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=).
+
+---
+
+## License
+
+&copy; 2016-2021 [Nima S. Hejazi](https://nimahejazi.org)
+
+The contents of this repository are distributed under the MIT license. See file
+`LICENSE` for details.
+
+---
+
+## References
+