RNAAnnotateTranscriptionFactor - return all tfs?

liulab-dfci / MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline

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RNAAnnotateTranscriptionFactor - return all tfs? #124

Closed f6v closed 3 years ago

f6v commented 3 years ago

RNAAnnotateTranscriptionFactor has a top.tf argument. However, is there a way to return the whole list?

Thanks!

crazyhottommy commented 3 years ago

Hi, can you try a large top.tf number? @baigal628 is it possible to return the whole list?

baigal628 commented 3 years ago

Hi,

After running LISA2 with RNAAnnotateTranscriptionFactor(), you will get a list of predicted TFs for each cluster under {project}.lisa/ folder. The file name should be {cluster_id}.txt.lisa.tsv. Or you can also find a file called {project}_lisa.txt in your working directory which summarized all the common predicted TFs for each cluster.