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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, 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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Dependencies and versions critical for successful running of pyscenic #407

Open bio-visualisation opened 2 years ago

bio-visualisation commented 2 years ago

Can anyone summarize what are the dependencies and versions critical for successful running of pyscenic. I have tried most of the methods described in the issues section by double checking the database and motif collection. I also tried using singularity container for pyscenic 0.10.0, but all produced an empty output after pyscenic ctx step.I am not getting any error but getting an empty file after running pyscenic ctx. Command: pyscenic ctx adj.tsv mm10refseq-r8010kb_up_and_down_tss.mc9nr.feather --annotations_fname motifs-v8-nr.mgi-m0.001-o0.0.tbl --expression_mtx_fname cortex_filtered.loom --mode "dask_multiprocessing" --output reg.csv --num_workers 20 --mask_dropouts

I am using

pyscenic 0.11.2, dask 2021.3.0, numba 0.53.1,

2022-07-12 13:01:52,693 - pyscenic.cli.pyscenic - INFO - Creating modules.

2022-07-12 13:01:52,717 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2022-07-12 13:02:10,528 - pyscenic.utils - INFO - Calculating Pearson correlations.

2022-07-12 13:02:10,537 - pyscenic.utils - WARNING - Note on correlation calculation: the default behaviour for calculating the correlations has changed after pySCENIC verion 0.9.16. Previously, the default was to calculate the correlation between a TF and target gene using only cells with non-zero expression values (mask_dropouts=True). The current default is now to use all cells to match the behavior of the R verision of SCENIC. The original settings can be retained by setting 'rho_mask_dropouts=True' in the modules_from_adjacencies function, or '--mask_dropouts' from the CLI. Dropout masking is currently set to [True].

2022-07-12 13:02:12,072 - pyscenic.utils - INFO - Creating modules.

2022-07-12 13:02:13,018 - pyscenic.cli.pyscenic - INFO - Loading databases.

2022-07-12 13:02:13,019 - pyscenic.cli.pyscenic - INFO - Calculating regulons. [########################################] | 100% Completed | 5.1s

2022-07-12 13:02:19,402 - pyscenic.cli.pyscenic - INFO - Writing results to file.

Please help me solving this issue.

340123J commented 2 years ago

you can try pyscenic 0.11.1.

ghuls commented 2 years ago

Do your gene names match any of the TFs listed in the motif annotation filename, else no genes will be selected. Also for mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather the matching motif annotation filename is https://resources.aertslab.org/cistarget/motif2tf/motifs-v9-nr.mgi-m0.001-o0.0.tbl