To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("biotmle")

In most cases, you don't need to download the package archive at all.

biotmle

 

Targeted Learning for Biomarker Discovery with Moderated Statistics

Bioconductor version: Release (3.5)

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 the moderated t-statistic with asymptotically linear statistical parameters estimated via targeted minimum loss-based estimation (TMLE).

Author: Nima Hejazi [aut, cre, cph]

Maintainer: Nima Hejazi <nhejazi at berkeley.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("biotmle")

Documentation

HTML R Script Identifying Biomarkers from an Exposure Variable
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DifferentialExpression, GeneExpression, Microarray, RNASeq, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License file LICENSE
Depends R (>= 3.4)
Imports tmle, limma, foreach, parallel, doParallel, ggplot2, wesanderson, magrittr, stats, dplyr, SummarizedExperiment, superheat, SuperLearner, biotmleData, Matrix
LinkingTo
Suggests testthat, rmarkdown, knitr
SystemRequirements
Enhances
URL https://github.com/nhejazi/biotmle
BugReports https://github.com/nhejazi/biotmle/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source biotmle_1.0.0.tar.gz
Windows Binary biotmle_1.0.0.zip
Mac OS X 10.11 (El Capitan) biotmle_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/biotmle/tree/release-3.5
Package Short Url http://bioconductor.org/packages/biotmle/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: