From d1ddd597fedc02faf22e1cbc6502c52468e65d97 Mon Sep 17 00:00:00 2001
From: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: Fri, 23 Feb 2024 10:46:06 +0100
Subject: [PATCH] Added package-level documentation

---
 DESCRIPTION                  |  4 ++--
 R/HybridExpress-package.R    |  6 ++++++
 man/HybridExpress-package.Rd | 31 +++++++++++++++++++++++++++++++
 3 files changed, 39 insertions(+), 2 deletions(-)
 create mode 100644 R/HybridExpress-package.R
 create mode 100644 man/HybridExpress-package.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index ce957f7..666afbf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -47,7 +47,7 @@ biocViews:
     DifferentialExpression
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Imports:
     ggplot2,
     patchwork,
@@ -68,5 +68,5 @@ Suggests:
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 Depends: 
-    R (>= 4.3)
+    R (>= 4.3.0)
 LazyData: true
diff --git a/R/HybridExpress-package.R b/R/HybridExpress-package.R
new file mode 100644
index 0000000..a65cf64
--- /dev/null
+++ b/R/HybridExpress-package.R
@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL
diff --git a/man/HybridExpress-package.Rd b/man/HybridExpress-package.Rd
new file mode 100644
index 0000000..1a57998
--- /dev/null
+++ b/man/HybridExpress-package.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/HybridExpress-package.R
+\docType{package}
+\name{HybridExpress-package}
+\alias{HybridExpress}
+\alias{HybridExpress-package}
+\title{HybridExpress: Comparative analysis of RNA-seq data for hybrids and their progenitors}
+\description{
+\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}
+
+HybridExpress can be used to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/almeidasilvaf/HybridExpress}
+  \item Report bugs at \url{https://support.bioconductor.org/tag/HybridExpress}
+}
+
+}
+\author{
+\strong{Maintainer}: Fabricio Almeida-Silva \email{fabricio_almeidasilva@hotmail.com} (\href{https://orcid.org/0000-0002-5314-2964}{ORCID})
+
+Authors:
+\itemize{
+  \item Lucas Prost-Boxoen (\href{https://orcid.org/0000-0003-2779-9097}{ORCID})
+  \item Yves Van de Peer \email{yves.vandepeer@psb.vib-ugent.be} (\href{https://orcid.org/0000-0003-4327-3730}{ORCID})
+}
+
+}
+\keyword{internal}