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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 1 year ago

You only need *.genes_vs_motifs.rankings.feather.

Shin8a commented 1 year ago

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

ctlshcxy commented 6 months 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?