--- a +++ b/DESCRIPTION @@ -0,0 +1,72 @@ +Package: biotmle +Title: Targeted Learning with Moderated Statistics for Biomarker Discovery +Version: 1.17.1 +Authors@R: c( + person("Nima", "Hejazi", email = "nh@nimahejazi.org", + role = c("aut", "cre", "cph"), + comment = c(ORCID = "0000-0002-7127-2789")), + person("Alan", "Hubbard", email = "hubbard@berkeley.edu", + role = c("aut", "ths"), + comment = c(ORCID = "0000-0002-3769-0127")), + person("Mark", "van der Laan", email = "laan@stat.berkeley.edu", + role = c("aut", "ths"), + comment = c(ORCID = "0000-0003-1432-5511")), + person("Weixin", "Cai", email = "wcai@berkeley.edu", + role = "ctb", + comment = c(ORCID = "0000-0003-2680-3066")), + person("Philippe", "Boileau", email = "philippe_boileau@berkeley.edu", + role = "ctb", + comment = c(ORCID = "0000-0002-4850-2507")) + ) +Description: Tools for differential expression biomarker discovery based on + microarray and next-generation sequencing data that leverage efficient + semiparametric estimators of the average treatment effect for variable + importance analysis. Estimation and inference of the (marginal) average + treatment effects of potential biomarkers are computed by targeted minimum + loss-based estimation, with joint, stable inference constructed across all + biomarkers using a generalization of moderated statistics for use with the + estimated efficient influence function. The procedure accommodates the use + of ensemble machine learning for the estimation of nuisance functions. +Depends: R (>= 4.0) +License: MIT + file LICENSE +URL: https://code.nimahejazi.org/biotmle +BugReports: https://github.com/nhejazi/biotmle/issues +Encoding: UTF-8 +LazyData: false +Imports: + stats, + methods, + dplyr, + tibble, + ggplot2, + ggsci, + superheat, + assertthat, + drtmle (>= 1.0.4), + S4Vectors, + BiocGenerics, + BiocParallel, + SummarizedExperiment, + limma +Suggests: + testthat, + knitr, + rmarkdown, + BiocStyle, + arm, + earth, + ranger, + SuperLearner, + Matrix, + DBI, + biotmleData (>= 1.1.1) +VignetteBuilder: knitr +RoxygenNote: 7.1.2 +biocViews: + Regression, + GeneExpression, + DifferentialExpression, + Sequencing, + Microarray, + RNASeq, + ImmunoOncology