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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biotmle")
In most cases, you don't need to download the package archive at all.
biotmle
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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("https://bioconductor.org/biocLite.R")
biocLite("biotmle")
Documentation
| HTML | R Script | Identifying Biomarkers from an Exposure Variable |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | DifferentialExpression, GeneExpression, Microarray, RNASeq, Sequencing, Software |
| Version | 1.0.4 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 years) |
| License | file LICENSE |
| Depends | R (>= 3.4) |
| Imports | tmle, limma, foreach, parallel, doParallel, ggplot2, wesanderson, magrittr, dplyr, stats, Matrix, methods, SummarizedExperiment, superheat, SuperLearner, biotmleData |
| 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.
| Source Package | biotmle_1.0.4.tar.gz |
| Windows Binary | biotmle_1.0.4.zip |
| Mac OS X 10.11 (El Capitan) | biotmle_1.0.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/biotmle |
| Package Short Url | http://bioconductor.org/packages/biotmle/ |
| Package Downloads Report | Download Stats |
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