Paola Benaglio

VCF files to use

1

Hello! I want to compare the genotype of 10 different samples obtained from either snp arrays and ATAC seq to check for sample swaps. For each of the 10 samples...

snap-add-gmat error

6

Hello! I am trying to run your pipeline following your examples to create snap files but had a few errors: 1) When running the **index-genome** and the **align-paired-end** commands, I...

Peak Calling with macs2

5

Hello, thanks again for the nice tool! I have been using your function for pseudobulk and macs2 peak calling and while it seems to work fine, after inspection of peak...

Inconsistent genes scores in scATAC analysis

7

Hello, thanks a lot for the useful tool! I am analysing a PBMC scATAC dataset with BPCells and Signac and I have calculated gene estimates with their respective functions: gene_score_archr...

Iterative overlap for peak merging

1

Hello, sorry to post this in the issue section, I just would like to point the attention to my question on the normalization of peak scores across celltypes in the...

Rbind error during permutations

1

Hello! Thanks for the tool! I am encountering an error that seems to be recurrent but should have been fixed according to the forums. I am using dmrseq_1.26.0 , installed...