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 -} - -}