chromVAR

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chromvar from signac wrapper is stuck (not progressing)

2

Hello, I would really appreciate your help. I am running chromvar from a Seurat object on 29K cells and 192K peaks. R version 4.1.1 (2021-08-10) chromVAR version 1.16.0 Signac version...

Dena2021

Chromvar is a good package to evaluate the motif activity in scATAC-seq data, but I noticed some studies using chromvar have said that there should be a negative correlation between...

jase11

Hello, I am trying to install chromVAR, But I got the folllowing errors: 1: In i.p(...) : installation of package ‘DirichletMultinomial’ had non-zero exit status 2: In i.p(...) : installation...

BenxiaHu

Error in chol.default(cov(norm_mat)) :

1

I am using chromVAR but getting such error for some files **Error in chol.default(cov(norm_mat)) : the leading minor of order 1 is not positive definite** also, I tried to solve...

neeteshpandey

Comparing Deviation scores across samples

2

Hi, I am comparing deviation scores for each motif across samples. However I realized these might be biased as I see some samples have generally higher values. You mention these...

rohitrrj

Sorry to bother you. I have calculated the TF scores of two different samples (healthy donors and tumor sample) with different peak sets and would like to ask if the...

tianchen2019

Thanks for creating chromVAR, I have a question about whether the average accessibility or summed accessibility across cells were used in background peak selection? Maybe I missed something and please...

q226

Dear all, I am encountering this error when running: `seurat_all

annaestevecodina

getCounts error

2

Hi, I am running into an error when using the getCounts function: fragment_counts

jf292

Error in counts_check(object) : ncol(object) > 1

4

When running `"dev

c2b2pss