jgranja24
jgranja24
Hi @sylestiel, The Greenleaf Lab recommends using ArchR [https://github.com/GreenleafLab/ArchR](https://github.com/GreenleafLab/ArchR) to identify peaks and many of the chromVAR features are available there. We recommend fixed-width peaks which are not generated from...
Hi @dagarfield, Something is a bit screwed up with the featureDF (nCols should be equal to 5) ``` 2021-02-18 12:13:40 : earlyDev .addGeneScoreMat FeatureDF, Class = data.frame earlyDev .addGeneScoreMat FeatureDF:...
Sorry for the delay, can you retry with the new release branch. I have now added 2 methods for background peaks (1) being with chromVAR and (2) that is designed...
Closing this issue, feel free to reopen a new issue if this persists.
Hi, can you be a little more specific? I dont see that file being corrupt (i just downloaded it). Are you wanting the scRNA cells classified?
i used Seurat's default CLR normalization https://satijalab.org/seurat/v3.0/multimodal_vignette.html let me know if that helps
Sorry I am not familiar with Seurat V3, the error message seems to be focused on the fact that there are no rownames in the input counts object. Just add...
This was a bug my mistake I updated it to this `nTop
I used ggplot2 violin plots with some color touching. We are releasing a package called ArchR in the next few days with tons of plotting shortcuts that should be nice...
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139369 best jeff