SCENIC with R

Installation

BiocManager::install(c("AUCell", "RcisTarget"))
BiocManager::install(c("GENIE3")) # Optional. Can be replaced by GRNBoost

## Optional (but highly recommended):
# To score the network on cells (i.e. run AUCell):
BiocManager::install(c("zoo", "mixtools", "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"))
# To export/visualize in http://scope.aertslab.org
devtools::install_github("aertslab/SCopeLoomR", build_vignettes = TRUE)

# Install SCENIC
devtools::install_github("aertslab/SCENIC") 
packageVersion("SCENIC") # ‘1.3.1’

# Download Species-specific databases
## For human: https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc_v10_clust/gene_based/
dbFiles <- c("https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc_v10_clust/gene_based/hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather")

# mc9nr: Motif collection version 9: 24k motifs
## Save DB
for(featherURL in dbFiles)
{ download.file(featherURL, destfile=basename(featherURL)) # saved in current dir
}

👍 에러따위 나오지 않았다. 다음챕터로 바로 건너뛰기 버튼

🚨 ERROR: dependency ‘GSEABase’ is not available for package ‘AUCell’

BiocManager::install("GSEABase")

🚨 Error: package or namespace load failed for ‘XML’:

    Error: package or namespace load failed for ‘XML’:
    .onLoad failed in loadNamespace() for 'XML', details:
    call: dyn.load(file, DLLpath = DLLpath, ...)
    error: unable to load shared object '/sc/arion/projects/scMultiscale/chos14/source/R-4.3.1/lib64/R/library/XML/libs/XML.so':
    libxmlsec1.so.1: cannot open shared object file: No such file or directory

XMLsec 설치해줘야하는데, perl -> openssl -> xml 순으로 설치해야함.

• 👉 perl download page

    wget https://www.cpan.org/src/5.0/perl-5.38.0.tar.gz
     tar -xzf perl-5.38.0.tar.gz
     cd perl-5.38.0
     ./Configure -des -Dprefix=$HOME/localperl
     make && make install

• 👉 openssl homepage
• 👉 openssl git_release

    wget https://github.com/openssl/openssl/releases/download/openssl-3.1.2/openssl-3.1.2.tar.gz
    tar -xvzf openssl-3.1.2.tar.gz
    cd openssl-3.1.2 
    ./config --prefix=/source/openssl shared zlib #--openssldir=/source/openssl , source dir 따로 prefix는 완전 다른 dir에 해야함
    make & make install

• 👉 XMLsec homepage
• 👉 XMLsec git_release

    wget https://github.com/lsh123/xmlsec/releases/download/xmlsec_1_3_1/xmlsec1-1.3.1.tar.gz
    tar -xvzf xmlsec1-1.3.1.tar.gz
    cd xmlsec1-1.3.1
    ./configure --prefix=/source/xmlsec1-1.3.1
    make && make install

🚨 checking for default crypto library... configure: error: At least one crypto library should exist for xmlsec1

이거 해결못하고 `RcisTarget` 다시 설치 시도해봤는데 되네?

Run SCENIC

01. Make input

# load Seurat obj
GEX.Seurat <- readRDS("GEX.seurat.rds")

References