leeanapeters

Homer run error

2

Hi, thanks for a great package! I am having some issues when trying to perform runHomer for motif discovery across my clusters. Here is the code I ran motifs =...

AIRR format output

25

Hi, thank you for the fantastic package! I initially ran TRUST4 with an earlier version that I guess did not output in an airr format. I know you can convert...

Spatial Transcriptomics Question

1

Hi, thank you for the great package! We have used this pipeline with scRNAseq data with great success. I am wondering if it would be possible to apply TRUST4 to...

Hi, thank you for this great package! I realized when I first ran this pipeline I only used one lane, when my data are spread across 2 lanes. However, when...

pyscenic aucell command does not complete

1

Hi, thank you for the great tool! I have managed to run the inital steps of the workflow but am not able to run aucell as the job is killed...

Recommendations for handling large datasets

1

Hi, thank you for creating this great tool! I was wondering if you could offer some guidance on handling large datasets in the unsupervised workflow? In particular this seems to...

pMHC data processing

1

Hi, thank you for the great package! I have run this pipeline successfully without incorporating pMHC information but would like to add this in. I was wondering if you could...

Issue loading single cell data

1

Hi, thank you for the great tool! I am experiencing some issues loading paired single cell data. I have csvs for each of my samples that have a barcode column...

Job killed before alignment is finished

1

Hi there, thank you for the great and detailed package! I was wondering if you could help me resolve an error with the pipeline where the process is killed before...

umap coordinates for NewPeakSeurat

3

Hi there, thank you for creating this interesting package! I am attempting to create my peak level Seurat object. I initially received an error when using PeakSeuratFromTransfer that there were...