This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see biotmle.
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 (from within R,
enter citation("biotmle")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("biotmle")
For older versions of R, please refer to the appropriate Bioconductor release.
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 |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, Microarray, RNASeq, Sequencing, Software |
Version | 1.8.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (2.5 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 |
LinkingTo | |
Suggests | testthat, knitr, rmarkdown, BiocStyle, SuperLearner, Matrix, DBI, biotmleData(>= 1.1.1) |
SystemRequirements | |
Enhances | |
URL | https://code.nimahejazi.org/biotmle |
BugReports | https://github.com/nhejazi/biotmle/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
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 |
Package Short Url | https://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: