Unable to run cisTarget (pySCENIC)
0
0
Entering edit mode
9 weeks 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:

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: 
pySCENIC • 161 views
ADD COMMENT

Login before adding your answer.

Traffic: 2269 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6