biotmle

DOI: 10.18129/B9.bioc.biotmle    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see biotmle.

Targeted Learning with Moderated Statistics for Biomarker Discovery

Bioconductor version: 3.10

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 variables by implementing an inferential procedure that combines a generalization of moderated statistics with targeted minimum loss estimates of the average treatment effect whose estimator admits an asymptotically linear representations (in terms of an efficient influence function).

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

Maintainer: Nima Hejazi <nh at nimahejazi.org>

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	1.10.0
In Bioconductor since	BioC 3.5 (R-3.4) (3 years)
License	file LICENSE
Depends	R (>= 3.4)
Imports	stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, future, doFuture, tmle (>= 1.4.0.1), S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle, earth, glmnet, randomForest, 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_1.10.0.tar.gz
Windows Binary	biotmle_1.10.0.zip
Mac OS X 10.11 (El Capitan)	biotmle_1.10.0.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