biotmle

DOI: 10.18129/B9.bioc.biotmle    

Moderated and Targeted Statistical Learning for Biomarker Discovery

Bioconductor version: Release (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 and enter:

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

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, Microarray, RNASeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.5 (R-3.4) (1.5 years)
License file LICENSE
Depends R (>= 3.4)
Imports dplyr, ggplot2, ggsci, superheat, doFuture, future, stats, methods, limma, BiocParallel, SummarizedExperiment, tmle
LinkingTo
Suggests testthat, knitr, rmarkdown, BiocStyle, SuperLearner, Matrix, DBI, biotmleData(>= 1.1.1)
SystemRequirements
Enhances
URL https://github.com/nhejazi/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_1.4.0.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 http://bioconductor.org/packages/biotmle/
Package Downloads Report Download Stats

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