Could not initialize SCENIC

[synatkeamsk]

Dear Developers,

Thanks for developing SCENIC. I apologized in advance as this could be a bit repetitive, but I could not solve it after trying all my best and read all resources. I am using SCENIC and I first installed it using the following script.

## Required, SCENIC R is based on three R packages:
BiocManager::install(c("AUCell")
                     
# Manually installed 
install.packages("RcisTarget_0.99.0.tar.gz",repos = NULL,type="source")

#GENIE3 ! 
BiocManager::install(c("GENIE3")) # Can be replaced by GRNBoost (Linux & MacOS)

## Optional (but highly recommended):
# To score the network on cells (i.e. run AUCell):
BiocManager::install(c("zoo", "mixtools"))

#rbokeh package! 
remotes::install_github("bokeh/rbokeh")

# For various visualizations and perform t-SNEs:
BiocManager::install(c("DT", "NMF", "ComplexHeatmap", "R2HTML", "Rtsne"))

# To support paralell execution (not available in Windows):
BiocManager::install(c("doMC", "doRNG"))

## SCENIC
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
devtools::install_github("aertslab/SCENIC") 
packageVersion("SCENIC")
devtools::install_github("aertslab/SCopeLoomR", build_vignettes = TRUE)

Alll worked successfully, I would like to highlight that installing RcisTarget using the following code did not work, 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RcisTarget")

and I have to download ```RcisTarget_0.99.0.tar.gz``` and manually installed it using ``` install.packages("RcisTarget_0.99.0.tar.gz",repos = NULL,type="source")``` 

# Next I attempted to initialized SCENIC using the following code 

library(SCENIC)
library(RcisTarget)
org <- "hgnc" # specify the organism, mouse: mgi, human: hgnc, fly:dmel
dbDir <- "Y:/Recurrent__Arthritis__Single cell/Single_Cell_Arthritis"
dbDir<- path.expand(dbDir)
myDatasetTitle <- "Recurrent arthritis" # choose a name for your analysis
data(defaultDbNames)
dbs <- defaultDbNames[[org]]
scenicOptions <- initializeScenic(org=org, 
        dbDir = dbDir, 
        dbs = dbs, 
        datasetTitle= myDatasetTitle, 
        nCores = 12)

# Here is error I got, 

Motif databases selected:    hg19-500bp-upstream-7species.mc9nr.feather    hg19-tss-centered-10kb-7species.mc9nr.feather [1] "'importRankings' is not an exported object from 'namespace:RcisTarget'" [1] "'importRankings' is not an exported object from 'namespace:RcisTarget'" Warning: It was not possible to load the following databses; check whether they are downloaded correctly:  hg19-500bp-upstream-7species.mc9nr.feather hg19-tss-centered-10kb-7species.mc9nr.featherWarning: data set ‘motifAnnotations_hgnc’ not foundError in h(simpleError(msg, call)) :    error in evaluating the argument 'object' in selecting a method for function 'getRanking': 'importRankings' is not an exported object from 'namespace:RcisTarget'

# I run the following code to load MotifAnnotations, 
data(MotifAnnoations),  Warning: data set ‘MotifAnnoations’ not found. 

Note: I have downloaded the old datasets of hg19-500bp-upstream-7species.mc9nr.feather    hg19-tss-centered-10kb-7species.mc9nr.feather  and have set the correct directory. 

Also, I am wondering installing RcisTargets using the following code did not work and it was not just me experience it. Have your team investigated why it did not work because it is the installation instruction your team has provided. Installation using install.packages("RcisTarget_0.99.0.tar.gz",repos = NULL,type="source"), I got a very old version. 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RcisTarget")

Hope you can help look and provide some suggestions.

Best Regards,

synat

[ghuls]

Try to use pySCENIC instead of SCENIC (deprecated).

Container versions are available:
https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images