biotmle

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see biotmle.

Moderated and Targeted Statistical Learning for Biomarker Discovery


Bioconductor version: 3.7

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 parameters defined via causal inference (e.g., Average Treatment Effect) whose estimators admit asymptotically linear representations.

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

Maintainer: Nima Hejazi <nhejazi at berkeley.edu>

Citation (from within R, enter citation("biotmle")):

Installation

To install this package, start R (version "3.5") and enter:


if (!require("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")
Identifying Biomarkers from an Exposure Variable HTML R Script
Processing and Analyzing RNA-Seq Data HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GeneExpression, Microarray, RNASeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License file LICENSE
Depends R (>= 3.4)
Imports dplyr, ggplot2, ggsci, superheat, doFuture, future, stats, methods, limma, BiocParallel, SummarizedExperiment, tmle
System Requirements
URL https://github.com/nhejazi/biotmle
Bug Reports https://github.com/nhejazi/biotmle/issues
See More
Suggests testthat, knitr, rmarkdown, BiocStyle, SuperLearner, Matrix, DBI, biotmleData(>= 1.1.1)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package biotmle_1.4.0.tar.gz
Windows Binary biotmle_1.4.0.zip
Mac OS X 10.11 (El Capitan) biotmle_1.4.0.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
Old Source Packages for BioC 3.7 Source Archive