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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Installation Error #451

Open parkjooyoung99 opened 3 months ago

parkjooyoung99 commented 3 months ago

<-- I am using R 4.3.3 and trying to install SCENIC following the instruction here. At the step installing SCENIC, if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("aertslab/SCENIC")

i am getting an error below Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3: cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES' Error: Failed to install 'SCENIC' from GitHub: error reading from connection

Is there a way to solve this issue? -->

ghuls commented 2 months ago

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