biotmle

DOI: 10.18129/B9.bioc.biotmle    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see biotmle.

Targeted Learning with Moderated Statistics for Biomarker Discovery

Bioconductor version: 3.9

This package facilitates the discovery of biomarkers from biological sequencing data (e.g., microarrays, RNA-seq) based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of moderated statistics with targeted minimum loss-based estimates (TMLE) of causal parameters (e.g., Average Treatment Effect) whose estimators admit asymptotically linear representations (in terms of influence functions).

Author: Nima Hejazi [aut, cre, cph], Alan Hubbard [aut, ths], Mark van der Laan [ctb, ths], Weixin Cai [ctb]

Maintainer: Nima Hejazi <nhejazi at berkeley.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("biotmle")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("biotmle")

 

HTML	R Script	Identifying Biomarkers from an Exposure Variable
HTML	R Script	Processing and Analyzing RNA-Seq Data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, Microarray, RNASeq, Sequencing, Software
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	file LICENSE
Depends	R (>= 3.4)
Imports	stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma, tmle
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle, SuperLearner, Matrix, DBI, biotmleData(>= 1.1.1)
SystemRequirements
Enhances
URL	https://code.nimahejazi.org/biotmle
BugReports	https://github.com/nhejazi/biotmle/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	biotmle_1.8.0.tar.gz
Windows Binary	biotmle_1.8.0.zip
Mac OS X 10.11 (El Capitan)	biotmle_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biotmle
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biotmle
Package Short Url	https://bioconductor.org/packages/biotmle/
Package Downloads Report	Download Stats