{"id":23089246,"url":"https://github.com/nhejazi/biotmle","last_synced_at":"2025-08-16T08:31:44.341Z","repository":{"id":54761983,"uuid":"65854775","full_name":"nhejazi/biotmle","owner":"nhejazi","description":":package: :microscope: R/biotmle: Targeted Learning with Moderated Statistics for Biomarker Discovery","archived":false,"fork":false,"pushed_at":"2021-10-14T17:57:14.000Z","size":125679,"stargazers_count":4,"open_issues_count":2,"forks_count":2,"subscribers_count":6,"default_branch":"master","last_synced_at":"2023-04-13T17:56:11.230Z","etag":null,"topics":["bioconductor","bioconductor-package","bioconductor-packages","bioinformatics","biomarker-discovery","biostatistics","causal-inference","computational-biology","machine-learning","r","statistics","targeted-learning"],"latest_commit_sha":null,"homepage":"https://code.nimahejazi.org/biotmle/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nhejazi.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-08-16T21:26:06.000Z","updated_at":"2021-10-14T17:57:16.000Z","dependencies_parsed_at":"2022-08-14T02:01:02.990Z","dependency_job_id":null,"html_url":"https://github.com/nhejazi/biotmle","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nhejazi%2Fbiotmle","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nhejazi%2Fbiotmle/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nhejazi%2Fbiotmle/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nhejazi%2Fbiotmle/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nhejazi","download_url":"https://codeload.github.com/nhejazi/biotmle/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":230022906,"owners_count":18161074,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","bioconductor-package","bioconductor-packages","bioinformatics","biomarker-discovery","biostatistics","causal-inference","computational-biology","machine-learning","r","statistics","targeted-learning"],"created_at":"2024-12-16T20:31:11.004Z","updated_at":"2024-12-16T20:31:11.662Z","avatar_url":"https://github.com/nhejazi.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput:\n  rmarkdown::github_document\nbibliography: \"inst/REFERENCES.bib\"\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"README-\"\n)\n```\n\n# R/`biotmle`\n\n[![R-CMD-check](https://github.com/nhejazi/biotmle/workflows/R-CMD-check/badge.svg)](https://github.com/nhejazi/biotmle/actions)\n[![Coverage Status](https://img.shields.io/codecov/c/github/nhejazi/biotmle/master.svg)](https://codecov.io/github/nhejazi/biotmle?branch=master)\n[![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)\n[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/biotmle.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/biotmle)\n[![Bioc Time](http://bioconductor.org/shields/years-in-bioc/biotmle.svg)](https://bioconductor.org/packages/release/bioc/html/biotmle.html)\n[![Bioc Downloads](http://bioconductor.org/shields/downloads/biotmle.svg)](https://bioconductor.org/packages/release/bioc/html/biotmle.html)\n[![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)\n[![DOI](https://zenodo.org/badge/65854775.svg)](https://zenodo.org/badge/latestdoi/65854775)\n[![JOSS Status](http://joss.theoj.org/papers/02be843d9bab1b598187bfbb08ce3949/status.svg)](http://joss.theoj.org/papers/02be843d9bab1b598187bfbb08ce3949)\n\n\u003e Targeted Learning with Moderated Statistics for Biomarker Discovery\n\n__Authors:__ [Nima Hejazi](https://nimahejazi.org), [Mark van der\nLaan](https://vanderlaan-lab.org/about), and [Alan\nHubbard](https://hubbard.berkeley.edu)\n\n---\n\n## What's `biotmle`?\n\nThe `biotmle` R package facilitates biomarker discovery through a generalization\nof the moderated t-statistic [@smyth2004linear] that extends the procedure to\nlocally efficient estimators of asymptotically linear target parameters\n[@tsiatis2007semiparametric]. The set of methods implemented modify targeted\nmaximum likelihood (TML) estimators of statistical (or causal) target parameters\n(e.g., average treatment effect) to apply variance moderation to the standard\nvariance estimator based on the efficient influence function (EIF) of the target\nparameter [@vdl2011targeted; @vdl2018targeted]. By performing a moderated\nhypothesis test that pools the individual probe-specific EIF-based variance\nestimates, a robust variance estimator is constructed, which stabilizes the\nstandard error estimates and improves the performance of such estimators both in\nsmaller samples and in settings where the EIF is poorly estimated. The resultant\nprocedure allows for the construction of conservative hypothesis tests that\nreduce the false discovery rate and/or the family-wise error rate\n[@hejazi2021generalization]. Improvements upon prior TML-based approaches to\nbiomarker discovery (e.g., @bembom2009biomarker) include both the moderated\nvariance estimator as well as the use of conservative reference distributions\nfor the corresponding moderated test statistics (e.g., logistic distribution),\ninspired by tail bounds based on concentration\ninequalities [@rosenblum2009confidence]; the latter prove critical for obtaining\nrobust inference when the finite-sample distribution of the estimator deviates\nfrom normality.\n\n---\n\n## Installation\n\nFor standard use, install from\n[Bioconductor](https://bioconductor.org/packages/biotmle) using\n[`BiocManager`](https://CRAN.R-project.org/package=BiocManager):\n\n```{r bioc-installation, eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly=TRUE)) {\n  install.packages(\"BiocManager\")\n}\nBiocManager::install(\"biotmle\")\n```\n\nTo contribute, install the bleeding-edge _development version_ from GitHub via\n[`remotes`](https://CRAN.R-project.org/package=remotes):\n\n```{r gh-master-installation, eval = FALSE}\nremotes::install_github(\"nhejazi/biotmle\")\n```\n\nCurrent and prior [Bioconductor](https://bioconductor.org) releases are\navailable under branches with numbers prefixed by \"RELEASE_\". For example, to\ninstall the version of this package available via Bioconductor 3.6, use\n\n```{r gh-develop-installation, eval = FALSE}\nremotes::install_github(\"nhejazi/biotmle\", ref = \"RELEASE_3_6\")\n```\n\n---\n\n## Example\n\nFor details on how to best use the `biotmle` R package, please consult the most\nrecent [package\nvignette](https://bioconductor.org/packages/release/bioc/vignettes/biotmle/inst/doc/exposureBiomarkers.html)\navailable through the [Bioconductor\nproject](https://bioconductor.org/packages/biotmle).\n\n---\n\n## Issues\n\nIf you encounter any bugs or have any specific feature requests, please [file an\nissue](https://github.com/nhejazi/biotmle/issues).\n\n---\n\n## Contributions\n\nContributions are very welcome. Interested contributors should consult our\n[contribution\nguidelines](https://github.com/nhejazi/biotmle/blob/master/CONTRIBUTING.md)\nprior to submitting a pull request.\n\n---\n\n## Citation\n\nAfter using the `biotmle` R package, please cite both of the following:\n\n        @article{hejazi2017biotmle,\n          author = {Hejazi, Nima S and Cai, Weixin and Hubbard, Alan E},\n          title = {biotmle: Targeted Learning for Biomarker Discovery},\n          journal = {The Journal of Open Source Software},\n          volume = {2},\n          number = {15},\n          month = {July},\n          year  = {2017},\n          publisher = {The Open Journal},\n          doi = {10.21105/joss.00295},\n          url = {https://doi.org/10.21105/joss.00295}\n        }\n\n        @article{hejazi2021generalization,\n          author = {Hejazi, Nima S and Boileau, Philippe and {van der Laan},\n            Mark J and Hubbard, Alan E},\n          title = {A generalization of moderated statistics to data adaptive\n            semiparametric estimation in high-dimensional biology},\n          journal={under review},\n          volume={},\n          number={},\n          pages={},\n          year = {2021+},\n          publisher={},\n          doi = {},\n          url = {https://arxiv.org/abs/1710.05451}\n        }\n\n        @manual{hejazi2019biotmlebioc,\n          author = {Hejazi, Nima S and {van der Laan}, Mark J and Hubbard, Alan\n            E},\n          title = {{biotmle}: {Targeted Learning} with moderated statistics for\n            biomarker discovery},\n          doi = {10.18129/B9.bioc.biotmle},\n          url = {https://bioconductor.org/packages/biotmle},\n          note = {R package version 1.10.0}\n        }\n\n---\n\n## Related\n\n* [R/`biotmleData`](https://github.com/nhejazi/biotmleData) - R package with\n    example experimental data for use with this analysis package.\n\n---\n\n## Funding\n\nThe development of this software was supported in part through grants from the\nNational Institutes of Health: [P42 ES004705-29](https://projectreporter.nih.gov/project_info_details.cfm?aid=9260357\u0026map=y) and [R01 ES021369-05](https://projectreporter.nih.gov/project_info_description.cfm?aid=9210551\u0026icde=37849782\u0026ddparam=\u0026ddvalue=\u0026ddsub=\u0026cr=1\u0026csb=default\u0026cs=ASC\u0026pball=).\n\n---\n\n## License\n\n\u0026copy; 2016-2021 [Nima S. Hejazi](https://nimahejazi.org)\n\nThe contents of this repository are distributed under the MIT license. See file\n`LICENSE` for details.\n\n---\n\n## References\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnhejazi%2Fbiotmle","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnhejazi%2Fbiotmle","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnhejazi%2Fbiotmle/lists"}