Gianfilippo Coppola

download_cache.nf not found

3

### Description of the bug HI, I am trying to download cached annotations for VEP and SnpEff, but I get the following error Remote resource not found: https://api.github.com/repos/repos/sarek/contents/download_cache.nf Is this...

multi sample/batch data

1

Hi, what is the best way to run SE_fun in the case of multiple samples/batches ? do I run it on each sample, i.e. select genes with p.adj

Hi, I have a couple of questions about the pipeline. I am interested in CUT&RUN specifically, and do not have experience with it, yet is there a way to specify...

Hi, I am trying to run the pipeline on the bulk test data. I should mention that I could not install CUT-RUNTools-2.0 with Python 3.6. This is likely an issue...

epitopeprediction using mhcflurry vs running directly mhcflurry

2

Hi, I ran your pipeline using MHCflurry and MHCflurry directly, on the same data In the case of MHCflurry I used mhcflurry-predict and as input I had alleles from hlatyping...

Inferred Network: multiple edges between same source-target pair

2

Hi, following the DEA for CCC tutorial, I am having difficulty in properly saving the resulting network The call cn.methods.carnival.visualize_network(df_res) result in a graphviz.graphs.Digraph object I save it to a...

liana multi df_to_lr function using precomputed pseudobulk Differential Expression results

2

Hi, I did most of my analysis using Seurat and the cell type specific pseudobulk differential expression using Muscat. I can read and process the Seurat object exported as AnnData....