sylestiel

Results 17 comments of sylestiel

Choice of Peak files to use in chromVAR analysis

Can we still start the analysis by using Cell Ranger output files?

How to incorporate other motif databases aside from JASPAR in STREAM analysis of scATAC dataset

I want the program to be able to scan for motifs that are not present in the JASPAR database. I think the motif ipynb only scans 128. I want to...

How to incorporate other motif databases aside from JASPAR in STREAM analysis of scATAC dataset

Okay. Thanks! > On June 29, 2020 at 10:07 AM Huidong Chen wrote: > > > Thanks for clarifying the problem! The short answer is that in STREAM we are...

Monocle3 output directory not being created - Error in pdf(path, width = 6, height = 6, useDingbats = FALSE) :

@rcorces @jgranja24 Still waiting on some input to run the new trajectory html. Cannot get past the error encountered in the first step.

Pando Not Returning Expected GRNs and Limiting Target Genes to a Handful - Possibility of Problem with Mouse Genome?

@Sandman-1 Curious as to why the targets do not have gene names and have nomenclature like C6.... etc? I encountered the same problem.

Pando Not Returning Expected GRNs and Limiting Target Genes to a Handful - Possibility of Problem with Mouse Genome?

@joschif Can you help with a script that conforms to Homer or Jaspar or Cisbp motif datasets? chromVARmotifs::homer_pwms,chromVARmotifs::mouse_pwms_v2,chromVARmotifs::encode_pwms

Pando Not Returning Expected GRNs and Limiting Target Genes to a Handful - Possibility of Problem with Mouse Genome?

@joschif When running infer_grn() what can I enter for gene category because **the target is still not showing a gene name** when I run coef(muo_data).

Pando Not Returning Expected GRNs and Limiting Target Genes to a Handful - Possibility of Problem with Mouse Genome?

@joschif How can I share it? Can I upload rds file here?

Pando Not Returning Expected GRNs and Limiting Target Genes to a Handful - Possibility of Problem with Mouse Genome?

@joschif @Sandman-1 How can I remove the Rik genes?

Pando Not Returning Expected GRNs and Limiting Target Genes to a Handful - Possibility of Problem with Mouse Genome?

@Sandman-1 @changwenwang09 Have either of you gotten it to work yet? If so, I could use some help here. Thanks!