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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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Input of cisTarget databases #486

Open Shin8a opened 1 year ago

Shin8a commented 1 year ago

Hello!

I recently started using pySCENIC for my mouse snRNAseq data and have a question regarding the input requirements for the cisTarget databases used to prune indirect targets. Should I include both ranking and scores in the input, as shown below?

[mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather] [mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.scores.feather] [mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather] [mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.scores.feather]

Or is ranking alone sufficient?

[mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather] [mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather]

Since pySCENIC tutorial only use ranking but updated version of the database includes two types of dataset, I am a bit confused and would appreciate confirmation on whether my analysis is correct or not.

Thank you in advance! I'm eagerly awaiting my results!

ghuls commented 11 months ago

You only need *.genes_vs_motifs.rankings.feather.

Shin8a commented 11 months ago

Thank you for your reply! Very appreciated! I will try it later:)

ctlshcxy commented 1 month ago

You only need *.genes_vs_motifs.rankings.feather.

Hi, I'm also confused about this question, could you please explain when to use scores.feather file?