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hemberg-lab / scRNA.seq.course

Analysis of single cell RNA-seq data course
https://www.singlecellcourse.org
GNU General Public License v3.0
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Leidenalg not found error #187

Open SimonDMurray opened 2 years ago

SimonDMurray commented 2 years ago

When running the single cell RNA seq course last week. We found that the command: srat <- FindClusters(srat, verbose = F, algorithm = 4, resolution = 0.9)

produced the error: Error: Cannot find Leiden algorithm, please install through pip (e.g. pip install leidenalg).

even though the dockerfile contains: RUN pip install --upgrade --no-cache leidenalg

This error occurred when students tried to run the Seurat notebook through Rstudio.

SimonDMurray commented 2 years ago

This was in chapter 8: https://www.singlecellcourse.org/single-cell-rna-seq-analysis-using-seurat.html