From 41e1acfefd9d8cfda1a1f275f23d89f50453e801 Mon Sep 17 00:00:00 2001
From: Chananchida Sang-aram VSCODE <sai.chananchida@gmail.com>
Date: Thu, 5 Sep 2024 14:24:03 +0200
Subject: [PATCH] bump to v2.2.0

---
 DESCRIPTION              |  4 ++--
 R/nichenetr-package.R    |  6 ++++++
 R/nichenetr.R            | 18 ------------------
 man/nichenetr-package.Rd | 28 ++++++++++++++++++++++++++++
 man/nichenetr.Rd         | 37 -------------------------------------
 5 files changed, 36 insertions(+), 57 deletions(-)
 create mode 100644 R/nichenetr-package.R
 delete mode 100644 R/nichenetr.R
 create mode 100644 man/nichenetr-package.Rd
 delete mode 100644 man/nichenetr.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index d1737d6..2026a3a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: nichenetr
 Type: Package
-Title: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes
-Version: 2.1.7
+Title: Modeling Intercellular Communication by Linking Ligands to Target Genes with NicheNet
+Version: 2.2.0
 Authors@R: c(person("Robin", "Browaeys",  role = c("aut")),
             person("Chananchida", "Sang-aram", role = c("aut", "cre"), email = "chananchida.sangaram@ugent.be"))
 Description: This package allows you the investigate intercellular communication from a computational perspective. More specifically, it allows to investigate how interacting cells influence each other's gene expression. Functionalities of this package (e.g. including predicting extracellular upstream regulators and their affected target genes) build upon a probabilistic model of ligand-target links that was inferred by data-integration.
diff --git a/R/nichenetr-package.R b/R/nichenetr-package.R
new file mode 100644
index 0000000..a65cf64
--- /dev/null
+++ b/R/nichenetr-package.R
@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL
diff --git a/R/nichenetr.R b/R/nichenetr.R
deleted file mode 100644
index 6b76a1d..0000000
--- a/R/nichenetr.R
+++ /dev/null
@@ -1,18 +0,0 @@
-## introduction to package, which functions to import,...
-#' nichenetr: Linking Extracellular Protein Signals to Target Genes by data-integration.
-#'
-#' This package allows you the investigate intercellular communication from a computational perspective. Functionalities of this package (e.g. including predicting extracellular upstream regulators) build upon a probabilistic model of ligand-target links that was inferred by data-integration.
-#'
-#' @section Construction of the probabilistic model:
-#' \code{\link{construct_weighted_networks}}, \code{\link{construct_ligand_target_matrix}}
-#'
-#' @section Evaluation functions:
-#' \code{\link{evaluate_target_prediction}}
-#'
-#' @docType package
-#' @name nichenetr
-#'
-#' @import dplyr
-#' @import tidyr
-#' @import tibble
-NULL
diff --git a/man/nichenetr-package.Rd b/man/nichenetr-package.Rd
new file mode 100644
index 0000000..bab2180
--- /dev/null
+++ b/man/nichenetr-package.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/nichenetr-package.R
+\docType{package}
+\name{nichenetr-package}
+\alias{nichenetr}
+\alias{nichenetr-package}
+\title{nichenetr: Modeling Intercellular Communication by Linking Ligands to Target Genes with NicheNet}
+\description{
+This package allows you the investigate intercellular communication from a computational perspective. More specifically, it allows to investigate how interacting cells influence each other's gene expression. Functionalities of this package (e.g. including predicting extracellular upstream regulators and their affected target genes) build upon a probabilistic model of ligand-target links that was inferred by data-integration.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/saeyslab/nichenetr}
+  \item Report bugs at \url{https://github.com/saeyslab/nichenetr/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Chananchida Sang-aram \email{chananchida.sangaram@ugent.be}
+
+Authors:
+\itemize{
+  \item Robin Browaeys
+}
+
+}
+\keyword{internal}
diff --git a/man/nichenetr.Rd b/man/nichenetr.Rd
deleted file mode 100644
index 9cffc80..0000000
--- a/man/nichenetr.Rd
+++ /dev/null
@@ -1,37 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/nichenetr.R
-\docType{package}
-\name{nichenetr}
-\alias{nichenetr-package}
-\alias{nichenetr}
-\title{nichenetr: Linking Extracellular Protein Signals to Target Genes by data-integration.}
-\description{
-This package allows you the investigate intercellular communication from a computational perspective. Functionalities of this package (e.g. including predicting extracellular upstream regulators) build upon a probabilistic model of ligand-target links that was inferred by data-integration.
-}
-\section{Construction of the probabilistic model}{
-
-\code{\link{construct_weighted_networks}}, \code{\link{construct_ligand_target_matrix}}
-}
-
-\section{Evaluation functions}{
-
-\code{\link{evaluate_target_prediction}}
-}
-
-\seealso{
-Useful links:
-\itemize{
-  \item \url{https://github.com/saeyslab/nichenetr}
-  \item Report bugs at \url{https://github.com/saeyslab/nichenetr/issues}
-}
-
-}
-\author{
-\strong{Maintainer}: Chananchida Sang-aram \email{chananchida.sangaram@ugent.be}
-
-Authors:
-\itemize{
-  \item Robin Browaeys
-}
-
-}