Merge pull request #110 from tidyomics/copilot/create-package-help-man-page

Add package-level help documentation

Author: stemangiola

R/zzz.R

@@ -1,3 +1,56 @@
+#' tidySummarizedExperiment: Bringing SummarizedExperiment to the Tidyverse
+#'
+#' @description
+#' The tidySummarizedExperiment package provides a bridge between Bioconductor
+#' SummarizedExperiment objects and the tidyverse. It creates an invisible layer
+#' that enables viewing the Bioconductor SummarizedExperiment object as a tidyverse
+#' tibble, and provides SummarizedExperiment-compatible dplyr, tidyr, ggplot2 and
+#' plotly functions. This allows users to get the best of both Bioconductor and
+#' tidyverse worlds.
+#'
+#' @details
+#' The main functions and methods are:
+#'
+#' \itemize{
+#' \item \code{\link{tidy}} - Convert SummarizedExperiment to tidy format
+#' \item \code{\link{as_tibble}} - Convert to tibble representation
+#' \item \code{\link{filter}}, \code{\link{select}}, \code{\link{mutate}}, \code{\link{arrange}} - dplyr verbs
+#' \item \code{\link{pivot_longer}}, \code{\link{pivot_wider}}, \code{\link{nest}}, \code{\link{unnest}} - tidyr functions
+#' \item \code{\link{ggplot}} - ggplot2 visualization
+#' \item \code{\link{left_join}}, \code{\link{inner_join}}, \code{\link{right_join}}, \code{\link{full_join}} - dplyr joins
+#' }
+#'
+#' For detailed information on usage, see the package vignette, by typing
+#' \code{vignette("introduction", package = "tidySummarizedExperiment")}.
+#'
+#' All software-related questions should be posted to the Bioconductor Support Site:
+#'
+#' \url{https://support.bioconductor.org}
+#'
+#' The code can be viewed at the GitHub repository:
+#'
+#' \url{https://github.com/stemangiola/tidySummarizedExperiment}
+#'
+#' @references
+#' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics
+#' ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024).
+#' \doi{10.1038/s41592-024-02299-2}
+#'
+#' @seealso
+#' Useful links:
+#' \itemize{
+#'   \item \url{https://github.com/tidyomics/tidySummarizedExperiment}
+#'   \item Report bugs at \url{https://github.com/tidyomics/tidySummarizedExperiment/issues}
+#' }
+#'
+#' @author Stefano Mangiola
+#'
+#' @docType package
+#' @name tidySummarizedExperiment-package
+#' @aliases tidySummarizedExperiment
+#' @keywords internal
+"_PACKAGE"
+
 #' @importFrom utils packageDescription
 .onAttach <- function(libname, pkgname) {
     attached <- tidyverse_attach()
@@ -8,4 +61,4 @@
         "If you want to visualize the data in a tidy way, do library(tidyprint). ",
         "See https://github.com/tidyomics/tidyprint for more information."
     )
-}
+}