biotmle

DOI: 10.18129/B9.bioc.biotmle    

Targeted Learning for Biomarker Discovery with Moderated Statistics

Bioconductor version: Release (3.6)

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 asymptotically linear statistical parameters estimated via targeted minimum loss-based estimation (TMLE).

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

Maintainer: Nima Hejazi <nhejazi at berkeley.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biotmle")

Documentation

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, Microarray, RNASeq, Sequencing, Software
Version	1.3.0
In Bioconductor since	BioC 3.5 (R-3.4) (1 year)
License	file LICENSE
Depends	R (>= 3.4)
Imports	dplyr, magrittr, ggplot2, superheat, wesanderson, doFuture, future, stats, Matrix, methods, DBI, limma, BiocParallel, SummarizedExperiment, biotmleData(>= 1.1.1), SuperLearner, tmle
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle
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.

Source Package	biotmle_1.3.0.tar.gz
Windows Binary	biotmle_1.3.0.zip
Mac OS X 10.11 (El Capitan)	biotmle_1.3.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biotmle
Package Short Url	http://bioconductor.org/packages/biotmle/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive