30/03/2018 New releases:
- pySCENIC: lightning-fast python implementation of the SCENIC pipeline.
- Arboretum package including GRNBoost2 and scalable GENIE3: Easy to install Python library that supports distributed computing. It allows fast co-expression module inference (Step1) on large datasets, compatible with both, the R and python implementations of SCENIC.
- [Drosophila databases] for RcisTarget
Coming soon: Update of RcisTarget and (R) SCENIC pipeline.
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
To use SCENIC you will also need to install GENIE3 (or GRNBoost2), RcisTarget and AUCell. The current version of SCENIC (v0.1.6) requires AUCell 0.99.5 and RcisTarget 0.99.0.
Newer versions of these packages are available in the corresponding Github repositories and will soon be included in Bioconductor. We will update SCENIC to work with these updated versions once they are available in Bioconductor.
To install the versions compatible with this version of SCENIC, you can use:
# You might need to install some of these dependencies first:
c("R.utils", "utils", "graphics", "stats", "data.table", "mixtools", "GSEABase",
"SummarizedExperiment", "methods", "Biobase", "zoo", "DT", "NMF", "plotly",
"BiocStyle", "rmarkdown", "doMC", " doRNG", " zoo", "doParallel", "foreach","dynamicTreeCut")
# GENIE3 (or GRNBoost2):
install.packages("http://bioconductor.org/packages/release/bioc/src/contrib/GENIE3_1.0.0.tar.gz", repos=NULL)
# AUCell:
install.packages("http://scenic.aertslab.org/downloads/Rpackages/AUCell_0.99.5.tar.gz", repos=NULL)
# RcisTarget:
install.packages("http://scenic.aertslab.org/downloads/Rpackages/RcisTarget_0.99.0.tar.gz", repos=NULL)
RcisTarget databases (choose the appropiate organism):
# Human: install.packages("http://scenic.aertslab.org/downloads/databases/RcisTarget.hg19.motifDatabases.20k_0.1.1.tar.gz", repos=NULL)
# Mouse: install.packages("http://scenic.aertslab.org/downloads/databases/RcisTarget.mm9.motifDatabases.20k_0.1.1.tar.gz", repos=NULL)
# Fly: install.packages("http://scenic.aertslab.org/downloads/databases/RcisTarget.dm6.motifDatabases.20k_0.2.1____.tar.gz
", repos=NULL)
Finally, to install SCENIC:
(dep=FALSE is set to avoid that AUCell is updated to the latest version in Bioconductor. However, it requires that all other dependencies are already installed...)
# SCENIC:
devtools::install_github("aertslab/SCENIC", dep = FALSE)
The package includes tutorials describing the functionality and usage of SCENIC:
Advanced tutorials:
- Step 1 - Part 2: Co-expression modules
- Step 2: Regulons (DNA motif analysis with RcisTarget)
- Step 3 - Part 1: Network activity in each cell (AUCell)
- Step 3 - Part 2: Binary network activity
- Step 4: GRN-based cell states (Clustering)
(examples for follow-up coming soon)
For more information, please visit http://scenic.aertslab.org