Package: nichenetr
Type: Package
Title: Modeling Intercellular Communication by Linking Ligands to
        Target Genes with NicheNet
Version: 2.2.2
Authors@R: c(
    person("Zaoqu", "Liu", email = "liuzaoqu@163.com", role = c("aut", "cre")),
    person("Robin", "Browaeys", role = "aut"),
    person("Wouter", "Saelens", role = "aut"),
    person("Yvan", "Saeys", role = "aut"))
Description: NicheNet is a computational framework for modeling
        intercellular communication by linking extracellular ligands to
        intracellular gene regulatory changes. It integrates prior
        knowledge of ligand-receptor interactions, signaling pathways,
        and transcription factor regulation to predict which ligands
        from sender cells affect gene expression in receiver cells.
        This enables mechanistic hypothesis generation about cell-cell
        communication events observed in transcriptomic data.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/Zaoqu-Liu/nichenetr,
        https://zaoqu-liu.github.io/nichenetr/
BugReports: https://github.com/Zaoqu-Liu/nichenetr/issues
RoxygenNote: 7.3.3
Depends: R (>= 3.0.0)
biocViews:
Imports: tidyverse, data.table, dplyr, ggplot2, magrittr, purrr, readr,
        tibble, tidyr, igraph, Matrix, fdrtool, ROCR, caTools, Hmisc,
        caret, randomForest, DiagrammeR, mlrMBO, parallelMap, emoa,
        DiceKriging, e1071, Seurat, cowplot, ggpubr, circlize,
        ComplexHeatmap, grDevices, ggnewscale, ggforce, shadowtext,
        Rcpp (>= 1.0.0)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, RColorBrewer, rmarkdown, testthat, doMC, limma, mco,
        parallel, covr, sf, qs, digest, data.table, future,
        future.apply
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libgdal-dev gdal-bin
        libgeos-dev libglpk-dev libglu1-mesa-dev libgmp3-dev make
        libgsl0-dev libharfbuzz-dev jags libicu-dev libjpeg-dev
        libpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev
        libmpfr-dev libopenmpi-dev libssl-dev perl libproj-dev python3
        libx11-dev zlib1g-dev
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-23 18:38:03 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/nichenetr
RemoteRef: master
RemoteSha: 54c2cb1cc336fe166ee565f6a52cd4ba9fea801c
NeedsCompilation: yes
Packaged: 2026-06-24 01:21:49 UTC; root
Author: Zaoqu Liu [aut, cre],
  Robin Browaeys [aut],
  Wouter Saelens [aut],
  Yvan Saeys [aut]
Maintainer: Zaoqu Liu <liuzaoqu@163.com>