diff --git a/.Rbuildignore b/.Rbuildignore
index 5dba6b7..6d56640 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,2 +1,3 @@
 Makefile
 bookdown
+^data-raw$
diff --git a/DESCRIPTION b/DESCRIPTION
index 919228e..edc59d4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,8 +32,13 @@ Imports:
 Suggests:
     CellChat,
     ggsc,
+    RcisTarget,
+    SCENIC,
     Seurat
 License: Artistic-2.0
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Depends: 
+    R (>= 2.10)
+LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
index 8abda5c..182a5b2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -30,6 +30,7 @@ export(plot_list)
 export(rowData)
 export(runCellChat)
 export(runPCA)
+export(runSCENIC)
 export(subset_cell)
 export(subset_feature)
 importFrom(DropletUtils,read10xCounts)
@@ -86,6 +87,7 @@ importFrom(tinytable,group_tt)
 importFrom(tinytable,save_tt)
 importFrom(tinytable,style_tt)
 importFrom(tinytable,tt)
+importFrom(utils,data)
 importFrom(yulab.utils,get_fun_from_pkg)
 importFrom(yulab.utils,install_zip_gh)
 importFrom(yulab.utils,is.installed)
diff --git a/R/data_exports.R b/R/data_exports.R
new file mode 100644
index 0000000..fe9af53
--- /dev/null
+++ b/R/data_exports.R
@@ -0,0 +1,47 @@
+#' Documentation for the data
+
+#' Default databases by organism
+#' 
+#' @format Named character vector
+#' @source GEO number
+"defaultDbNames"
+
+#' Annotations of Motifs to Transcription Factors (TFs)
+#' 
+#' @rdname motifAnnotations
+#' @name motifAnnotations
+#' @aliases motifAnnotations_hgnc motifAnnotations_mgi motifAnnotations_dmel
+#' @title Annotations of Motifs to TFs
+#' @description 
+#' This dataset contains annotations linking motifs to transcription factors (TFs) 
+#' for different organisms (Human, Mouse, Fly) based on motif collection version 9.
+#' 
+#' \bold{Version 9}: 
+#' Annotations for motif collection version 9 ('mc9nr').
+#' \itemize{
+#'     \item{Human: motifAnnotations_hgnc_v9 (\emph{motifs-v9-nr.hgnc-m0.001-o0.0.tbl})}
+#'     \item{Mouse: motifAnnotations_mgi_v9 (\emph{motifs-v9-nr.mgi-m0.001-o0.0.tbl})}
+#'     \item{Fly: motifAnnotations_dmel_v9 (\emph{motifs-v9-nr.flybase-m0.001-o0.0.tbl})}
+#' }
+#' 
+#' These objects are designed for use with RcisTarget without modification, 
+#' but users can explore them to get more information about the motifs. 
+#' The original files are available from \code{https://resources.aertslab.org/cistarget/motif2tf/}.
+#' 
+#' \bold{Columns:}
+#' \itemize{
+#'  \item{\bold{motif}: }{Motif ID.}
+#'  \item{\bold{TF}: }{Transcription factor or inferred gene.}
+#'  \item{\bold{directAnnotation}, \bold{inferred_Orthology}, \bold{inferred_MotifSimil}: }{Boolean values indicating whether the motif is annotated to the TF 
+#'      directly ("directAnnotation") or inferred by orthology ("inferred_Orthology") or motif similarity ("inferred_MotifSimil").}
+#'  \item{\bold{Description}: }{Description of the annotation source.}
+#'  \item{\bold{annotationSource}: }{Source of the annotation as a factor. Levels: directAnnotation, 
+#'      inferredBy_Orthology, inferredBy_MotifSimilarity, inferredBy_MotifSimilarity_n_Orthology.}
+#' }
+#' 
+#' @docType data
+#' @seealso importAnnotations, RcisTarget
+#' @keywords datasets
+NULL
+
+
diff --git a/R/runSCENIC.R b/R/runSCENIC.R
new file mode 100644
index 0000000..73a1b8e
--- /dev/null
+++ b/R/runSCENIC.R
@@ -0,0 +1,85 @@
+#' wrapper function for running SCENIC on default parameter. 
+#' 
+#' https://htmlpreview.github.io/?https://github.com/aertslab/SCENIC/blob/master/inst/doc/SCENIC_Running.html
+#' 
+#' @param sce A singlecellExperiment object.
+#' @param species The species of the data, one of human, mouse or drosophila_melanogaster.
+#' @param nCores The number of cores to use for parallel processing.
+#' @param dbDir The directory path to the cisTarget databases files.
+#' @param assay_name the name of assay.
+#' 
+#' @return The class contains the options/settings for a run of SCENIC. 
+#' 
+#' @importFrom SummarizedExperiment assay assayNames
+#' @importFrom utils data
+#' @export 
+runSCENIC <- function(sce,species,nCores,dbDir,
+                      assay_name = "counts"){
+  # Create directories to store process data and output results
+  if (!dir.exists("int")) {
+    dir.create("int")
+  }
+  if (!dir.exists("output")) {
+    dir.create("output")
+  }
+
+  # Initialize settings
+  org <- switch(species, 
+                "human" = "hgnc", 
+                "mouse" = "mgi", 
+                "drosophila_melanogaster" = "dmel", 
+                stop("Unsupported species"))
+  data(defaultDbNames,envir = environment())
+  dbs <- SCENIC::defaultDbNames[[org]]
+  
+  if (org == "mgi") {
+    data(list = "motifAnnotations_mgi",envir = environment())
+  } else if (org == "hgnc") {
+    data(list = "motifAnnotations_hgnc",envir = environment())
+  } else if (org == "dmel") {
+    data(list = "motifAnnotations_dmel",envir = environment())
+  } else {
+    stop("Unsupported species. Please choose 'mgi', 'hgnc', or 'dmel'.")
+  }
+
+  scenicOptions <- SCENIC::initializeScenic(org = org, dbDir = dbDir, dbs = dbs, nCores = nCores)
+
+  # Process the cell annotation information of the sce object for plot later
+  if ("CellType" %in% colnames(SingleCellExperiment::colData(sce))) {
+    cellInfo <- as.data.frame(SingleCellExperiment::colData(sce))
+    saveRDS(cellInfo, file="int/cellInfo.Rds") 
+    scenicOptions@inputDatasetInfo$cellInfo <- "int/cellInfo.Rds"
+} else {
+  warning("Warning: 'cellInfo' not found, proceeding without cell annotations.")
+}
+
+  if ("CellTypeColor" %in% colnames(SingleCellExperiment::colData(sce))) {
+    colVars <- as.list(sce$CellTypeColor)
+    saveRDS(colVars, file="int/colVars.Rds")
+    scenicOptions@inputDatasetInfo$colVars <- "int/colVars.Rds"
+} else {
+  warning("Warning: 'colVars' not found, proceeding without color annotations.")
+}
+  
+  # Co-expression network 
+  exprMat <- SummarizedExperiment::assay(sce, assay_name)
+  genesKept <- SCENIC::geneFiltering(exprMat, scenicOptions = scenicOptions,
+                                     minCountsPerGene = 3 * 0.01 * ncol(exprMat),
+                                     minSamples = ncol(exprMat) * 0.01)
+  exprMat_filtered <- exprMat[genesKept, ]
+  SCENIC::runCorrelation(exprMat_filtered, scenicOptions)
+  
+  set.seed(123)
+  exprMat_filtered <- log2(exprMat_filtered+1) 
+  SCENIC::runGenie3(exprMat_filtered, scenicOptions)
+
+  # Build and score the GRN
+  exprMat_log <- log2(exprMat+1)
+  scenicOptions <- SCENIC::runSCENIC_1_coexNetwork2modules(scenicOptions)
+  scenicOptions <- SCENIC::runSCENIC_2_createRegulons(scenicOptions)
+  scenicOptions <- SCENIC::runSCENIC_3_scoreCells(scenicOptions, exprMat_log)
+  
+  saveRDS(scenicOptions,file="int/scenicOptions.Rds")
+  return(scenicOptions)
+}
+
diff --git a/data/defaultDbNames.rda b/data/defaultDbNames.rda
new file mode 100644
index 0000000..3cc9688
Binary files /dev/null and b/data/defaultDbNames.rda differ
diff --git a/data/motifAnnotations_dmel.rda b/data/motifAnnotations_dmel.rda
new file mode 100644
index 0000000..00b6805
Binary files /dev/null and b/data/motifAnnotations_dmel.rda differ
diff --git a/data/motifAnnotations_hgnc.rda b/data/motifAnnotations_hgnc.rda
new file mode 100644
index 0000000..269f843
Binary files /dev/null and b/data/motifAnnotations_hgnc.rda differ
diff --git a/data/motifAnnotations_mgi.rda b/data/motifAnnotations_mgi.rda
new file mode 100644
index 0000000..c5c7fb4
Binary files /dev/null and b/data/motifAnnotations_mgi.rda differ
diff --git a/inst/ext/defaultDbNames.RData b/inst/ext/defaultDbNames.RData
new file mode 100644
index 0000000..654738a
Binary files /dev/null and b/inst/ext/defaultDbNames.RData differ
diff --git a/inst/ext/motifAnnotations_dmel_v9.RData b/inst/ext/motifAnnotations_dmel_v9.RData
new file mode 100644
index 0000000..ce32705
Binary files /dev/null and b/inst/ext/motifAnnotations_dmel_v9.RData differ
diff --git a/inst/ext/motifAnnotations_hgnc_v9.RData b/inst/ext/motifAnnotations_hgnc_v9.RData
new file mode 100644
index 0000000..1973bd7
Binary files /dev/null and b/inst/ext/motifAnnotations_hgnc_v9.RData differ
diff --git a/inst/ext/motifAnnotations_mgi_v9.RData b/inst/ext/motifAnnotations_mgi_v9.RData
new file mode 100644
index 0000000..4c56d04
Binary files /dev/null and b/inst/ext/motifAnnotations_mgi_v9.RData differ
diff --git a/inst/prototype/read_SCENIC_dataset.R b/inst/prototype/read_SCENIC_dataset.R
new file mode 100644
index 0000000..e04f1d2
--- /dev/null
+++ b/inst/prototype/read_SCENIC_dataset.R
@@ -0,0 +1,17 @@
+## code to load the databases for runSCENIC
+
+# load the defaultDbNames.RData from SCENIC
+load("./inst/ext/defaultDbNames.RData")
+usethis::use_data(defaultDbNames, overwrite = TRUE)
+ 
+# load the motifAnootation of three species from RcisTarget
+load("./inst/ext/motifAnnotations_dmel_v9.RData")
+motifAnnotations_dmel <- motifAnnotations_dmel_v9
+load("./inst/ext/motifAnnotations_mgi_v9.RData")
+motifAnnotations_mgi <- motifAnnotations_mgi_v9
+load("./inst/ext/motifAnnotations_hgnc_v9.RData")
+motifAnnotations_hgnc <- motifAnnotations_hgnc_v9
+usethis::use_data(motifAnnotations_dmel, overwrite = TRUE)
+usethis::use_data(motifAnnotations_mgi, overwrite = TRUE)
+usethis::use_data(motifAnnotations_hgnc, overwrite = TRUE)
+
diff --git a/man/defaultDbNames.Rd b/man/defaultDbNames.Rd
new file mode 100644
index 0000000..f9f1728
--- /dev/null
+++ b/man/defaultDbNames.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_exports.R
+\docType{data}
+\name{defaultDbNames}
+\alias{defaultDbNames}
+\title{Documentation for the data
+Default databases by organism}
+\format{
+Named character vector
+}
+\source{
+GEO number
+}
+\usage{
+defaultDbNames
+}
+\description{
+Documentation for the data
+Default databases by organism
+}
+\keyword{datasets}
diff --git a/man/motifAnnotations.Rd b/man/motifAnnotations.Rd
new file mode 100644
index 0000000..204bcdc
--- /dev/null
+++ b/man/motifAnnotations.Rd
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_exports.R
+\docType{data}
+\name{motifAnnotations}
+\alias{motifAnnotations}
+\alias{motifAnnotations_hgnc}
+\alias{motifAnnotations_mgi}
+\alias{motifAnnotations_dmel}
+\title{Annotations of Motifs to TFs}
+\description{
+This dataset contains annotations linking motifs to transcription factors (TFs)
+for different organisms (Human, Mouse, Fly) based on motif collection version 9.
+
+\bold{Version 9}:
+Annotations for motif collection version 9 ('mc9nr').
+\itemize{
+\item{Human: motifAnnotations_hgnc_v9 (\emph{motifs-v9-nr.hgnc-m0.001-o0.0.tbl})}
+\item{Mouse: motifAnnotations_mgi_v9 (\emph{motifs-v9-nr.mgi-m0.001-o0.0.tbl})}
+\item{Fly: motifAnnotations_dmel_v9 (\emph{motifs-v9-nr.flybase-m0.001-o0.0.tbl})}
+}
+
+These objects are designed for use with RcisTarget without modification,
+but users can explore them to get more information about the motifs.
+The original files are available from \code{https://resources.aertslab.org/cistarget/motif2tf/}.
+
+\bold{Columns:}
+\itemize{
+\item{\bold{motif}: }{Motif ID.}
+\item{\bold{TF}: }{Transcription factor or inferred gene.}
+\item{\bold{directAnnotation}, \bold{inferred_Orthology}, \bold{inferred_MotifSimil}: }{Boolean values indicating whether the motif is annotated to the TF
+directly ("directAnnotation") or inferred by orthology ("inferred_Orthology") or motif similarity ("inferred_MotifSimil").}
+\item{\bold{Description}: }{Description of the annotation source.}
+\item{\bold{annotationSource}: }{Source of the annotation as a factor. Levels: directAnnotation,
+inferredBy_Orthology, inferredBy_MotifSimilarity, inferredBy_MotifSimilarity_n_Orthology.}
+}
+}
+\details{
+Annotations of Motifs to Transcription Factors (TFs)
+}
+\seealso{
+importAnnotations, RcisTarget
+}
+\keyword{datasets}
diff --git a/man/runSCENIC.Rd b/man/runSCENIC.Rd
new file mode 100644
index 0000000..6d30352
--- /dev/null
+++ b/man/runSCENIC.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runSCENIC.R
+\name{runSCENIC}
+\alias{runSCENIC}
+\title{wrapper function for running SCENIC on default parameter.}
+\usage{
+runSCENIC(sce, species, nCores, dbDir, assay_name = "counts")
+}
+\arguments{
+\item{sce}{A singlecellExperiment object.}
+
+\item{species}{The species of the data, one of human, mouse or drosophila_melanogaster.}
+
+\item{nCores}{The number of cores to use for parallel processing.}
+
+\item{dbDir}{The directory path to the cisTarget databases files.}
+
+\item{assay_name}{the name of assay.}
+}
+\value{
+The class contains the options/settings for a run of SCENIC.
+}
+\description{
+https://htmlpreview.github.io/?https://github.com/aertslab/SCENIC/blob/master/inst/doc/SCENIC_Running.html
+}