biotmle
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see biotmle.
Targeted Learning with Moderated Statistics for Biomarker Discovery
Bioconductor version: 3.9
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 causal parameters (e.g., Average Treatment Effect) whose estimators admit asymptotically linear representations (in terms of influence functions).
Author: Nima Hejazi [aut, cre, cph], Alan Hubbard [aut, ths], Mark van der Laan [ctb, ths], Weixin Cai [ctb]
Maintainer: Nima Hejazi <nhejazi at berkeley.edu>
citation("biotmle")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, Microarray, RNASeq, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | file LICENSE |
| Depends | R (>= 3.4) |
| Imports | stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma, tmle |
| System Requirements | |
| URL | https://code.nimahejazi.org/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_1.8.0.tar.gz |
| Windows Binary | biotmle_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | biotmle_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/biotmle |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/biotmle |
| Bioc Package Browser | https://code.bioconductor.org/browse/biotmle/ |
| Package Short Url | https://bioconductor.org/packages/biotmle/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |