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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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"could not convert string to float: " error when running cisTarget #427

Open mchua4 opened 1 year ago

mchua4 commented 1 year ago

I ran the GrnBoost2 algorithm on my bulk transcriptomics data and now want to predict regulon using cisTarget. My code raised "could not convert string to float: " error.

ADJACENCIES_FNAME = "../input/gene-regulatory-network/inferred_network.tsv"

TF Target Importance
0 ZFY DDX3Y 271.644764
1 ZFY EIF1AY 249.632524
2 ZFY CYorf15A 249.479488
3 ZFY USP9Y 242.145026
4 ZFY KDM5D 215.670768

Run pySCENIC:

!pyscenic ctx {ADJACENCIES_FNAME} {DBS_PARAM} \
            --annotations_fname {MOTIF_ANNOTATIONS_FNAME} \
            --expression_mtx_fname {EXP_MTX_QC_FNAME} \
            --output {MOTIFS_FNAME} \
            --num_workers 26

Traceback:

2022-10-04 13:49:42,020 - pyscenic.cli.pyscenic - INFO - Creating modules.

2022-10-04 13:49:47,486 - pyscenic.cli.pyscenic - ERROR - could not convert string to float:
ghuls commented 1 year ago

What is the output of:

head ../input/gene-regulatory-network/inferred_network.tsv