Bruno Giotti

icon company Ichan School of Medicine icon location New York icon location Compu-molecular biologist working on epigenetics using scATAC-seq in lung diseases. Also working on scRNA-seq and spatial

Results 5 issues of Bruno Giotti

runHomer

5 comment

Hi Fang, Thanks for this great package! I'm stuck at the runHomer function as i need to pass the argument '-preparsedDir' from the findMotifsGenome.pl function but it doesnt seem to...

jaspar2016

1 comment

Hello there, Thanks for providing this amazing tool for single-cell analysis..I am running the stream_atac function on command line but it says that it cannot install the R package JASPAR2016....

change number of top genes in ModuleNetworkPlot

1 comment

Hello! Great package again! I was wondering if it's possible to add an argument in the `ModuleNetworkPlot` function to specify the number of genes to show in the network plots....

enhancement

chrombpnet prep nonpeaks does not complete

2 comment

Dear devs, I'm stuck at trying to generate non-peak regions using function `chrombpnet prep nonpeaks` as the progress bar freezes at 22% with my current peakset. I tested this on...

Plugging peak calls from ArchR

Dear chrombpnet devs, Thanks for this package I'm very excited to trying it out! I'm working on scatac-seq and wondering whether I could input the peaks called from ArchR to...