Package: CellOracleR
Type: Package
Title: In Silico Gene Perturbation Analysis with Single-Cell Data
Version: 0.1.0
Authors@R: c(
    person("Zaoqu", "Liu", email = "liuzaoqu@163.com", role = c("aut", "cre")),
    person("Kenji", "Kamimoto", role = "ctb",
           comment = "Original CellOracle Python package author"))
Description: An R implementation of the CellOracle framework for in
        silico gene perturbation analysis and gene regulatory network
        (GRN) inference from single-cell RNA-seq data. Predicts cell
        state transitions in response to transcription factor
        perturbations by combining GRN models with single-cell
        expression data. Key features include motif analysis for base
        GRN construction, cluster-specific GRN inference using
        regularized regression, perturbation simulation with signal
        propagation, and comprehensive visualization of predicted cell
        fate changes. Based on the methodology described in Kamimoto et
        al. (2023) <doi:10.15252/msb.202211547>.
URL: https://github.com/Zaoqu-Liu/CellOracleR
BugReports: https://github.com/Zaoqu-Liu/CellOracleR/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
License: Apache License (>= 2) | file LICENSE
RoxygenNote: 7.3.3
Depends: R (>= 4.0.0)
Imports: R6, Rcpp (>= 1.0.0), Matrix, methods, stats, utils, grDevices,
        Seurat (>= 4.0.0), SeuratObject, glmnet, igraph, ggplot2,
        scales, future, future.apply, progressr, data.table, FNN, rlang
Suggests: qs, testthat (>= 3.0.0), knitr, rmarkdown, BiocManager,
        TFBSTools, motifmatchr, BSgenome, GenomicRanges, Biostrings,
        GenomeInfoDb, IRanges, S4Vectors, SingleCellExperiment,
        SummarizedExperiment, clusterProfiler, org.Hs.eg.db,
        org.Mm.eg.db, JASPAR2020, viridis, patchwork, cowplot, ggraph,
        irlba, arrow, reshape2, e1071, rstanarm, networkD3, htmlwidgets
LinkingTo: Rcpp, RcppArmadillo
Config/testthat/edition: 3
VignetteBuilder: knitr
SystemRequirements: C++17
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-24 20:11:44 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/CellOracleR
RemoteRef: main
RemoteSha: e60a1b9d84a1b89c2e8f36efc8ea16065f673b57
NeedsCompilation: yes
Packaged: 2026-10-07 11:44:56 UTC; root
Author: Zaoqu Liu [aut, cre],
  Kenji Kamimoto [ctb] (Original CellOracle Python package author)
Maintainer: Zaoqu Liu <liuzaoqu@163.com>