Simone Procaccia

Installation error "Failed to install 'unknown package' from Github: ..."

1

I'm trying to install cisTopic in a conda environment launching R 4.2.0 and typing: ``` > devtools::install_github("aertslab/cisTopic") Error: Failed to install 'unknown package' from GitHub: Line starting 'NeedsCo ...' is...

scArches for PeakVI

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Hi all, is anyone thinking of an implementation for scArches of PeakVI? It might be useful for annotating scATAC-seq datasets: given also the rising amount of Multiome datasets around, annotating...

Running pycisTopic on very large datasets [PERFORMANCE]

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**What type of problem are you experiencing and which function is you problem related too** I am running cisTopic on a very large dataset (200k cells) and it takes apparently...

Many cells have zero non-trivial (>0.1) assignments

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Hello, I am running SEACells on a dataset of sc-ATAC-seq of 31000 cells and I am inferring 310 cells. When checking for quality of results, I am surprised at the...

I am having a huge amount of trouble getting SCENIC+ to work on my HPC due to dependencies clashes. And I can't seem to make the docker image work either....