sylestiel

Choice of Peak files to use in chromVAR analysis

2

Hi, Would you recommend using the peaks.bed file in the general outs folder or that in the filtered_peak_bc_matrix sub-folder for chromVAR? Are their advantages to using aggregated peak file vs...

Hi Alicia, How can we retrieve sample specific variability from the Merged chromVar object? If that is not feasible can we compare Variability determined for each sample separately? Thanks

Hi, If i wish to plot a handful of motifs of interest in the Variability plot how may I do so. I would like to do so by just showing...

@AliciaSchep how can i account for differences in sequencing depth among samples in the merged analysis of chromVAR. Thanks!

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

4

Hi, How can I incorporate homer pwms motif list and mouse pwms v2 list into the STREAM_scATAC-seq-motif.ipynb? Thanks! SH

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

5

Attempting to run the new trajectory html https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Trajectory.html Ran into following error:

@ghuls How may I read in a Multiome dataset from 10X Genomics for CisTopic analysis? Thanks!

regions parameter in initate_grn()

4

Hi @joschif, The vignette reads that we can constrain the set of candidate regions by providing a GenomiicRanges object in the regions argument. Does Pando package come with phastConsElements20Mammals.UCSC.mm10 or...

Hi @zhisonghe, I was trying to use your Multiome vignette to analyze rhesus datasets using the Macaca_mulatta.Mmul_10.109.gtf file from the ensembl database. However, I'm having issues with the RegionsStats() and...