Imports: mda, ncvreg, mboost, gbm, earth, elasticnet, rms, methods

Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data.
Imports: mda, mpath, mboost, gbm, earth, elasticnet, rms, methods,

Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data. See Wang and Wang (2010) <doi:10.2202/1544-6115.1550>.

Author: Zhu Wang <https://orcid.org/0000-0002-0773-0052> and others (see COPYRIGHTS)

Title: Interactive Shiny App for Bulk Sequencing Data
person("Ilias", "Moutsopoulos", , "im383@cam.ac.uk", c("aut", "cre")),
person("Eleanor", "Williams", , "ecw63@cam.ac.uk", role = c("aut", "ctb")),
person("Irina", "Mohorianu", , "iim22@cam.ac.uk", role = c("aut", "ctb"))
Description: Given an expression matrix from a bulk RNA-Seq experiment,
pre-processes it and creates a shiny app for interactive data
analysis and visualisation. The app contains quality checks,
differential expression analysis, volcano and cross plots,
enrichment analysis and gene regulatory network inference,
and can be customised to contain more panels by the user.
Imports: ggplot2, shinythemes, shiny, gprofiler2, edgeR, DESeq2, stats,
ggrepel, utils, RColorBrewer, ComplexHeatmap, circlize, grid,
shinyWidgets, shinyjqui, dplyr, magrittr, ggforce, rlang, glue,
preprocessCore, matrixStats, noisyr, tibble, ggnewscale,
ggrastr, GENIE3, visNetwork, DT, scales, shinyjs, tidyr
Suggests: rmarkdown, knitr, BiocManager, AnnotationDbi, org.Hs.eg.db,

Description: Given an expression matrix from a bulk sequencing experiment,
Imports: ggplot2, shiny, gprofiler2, edgeR, DESeq2, stats, ggrepel,
utils, RColorBrewer, ComplexHeatmap, circlize, grid,
ggrastr, GENIE3, visNetwork, DT, scales, shinyjs, tidyr,
Suggests: rmarkdown, knitr, shinythemes, BiocManager, AnnotationDbi,
org.Hs.eg.db, org.Mm.eg.db, readxl, testthat (>= 3.0.0)