Thapeachydude

Using partial genotype reference

2

Hi everyone, does the tool allow the use of partial genotype references? Say we have 10 patients multiplexed in a single sample, with reference information available for 6 of them....

Understanding the barcodes command

1

Hi, I'm trying to demultiplex a series of pools (9-11 donors) with known genotypes based on WES and WGS data. Some of the pools work really well, while others struggle...

How well does it scale?

32

Hi, I wanted to ask how well the tool scales with regards to the number of samples being multiplexed. We are planning an experiment with ≈ 20 samples, where we...

Tweaking the number of modules

2

Hello, I was wondering if there is a "good" / "correct" way for tweaking the number of discovered modules? I.e. I'm running a dataset of 300k cells, but I only...

Would this also be applicable to bulk data?

2

Hi, great package. I was wondering if this form of batch integration is also applicable to bulk RNA-Seq data. Sure the data is less sparse, but would that be an...

Expectations for UMAP of embeddings

2

Hi, interesting tool (and the use of the single-cell experiment class is much appreciated). We have single-cell RNA-Seq data from multiple samples at various conditions. This far, I've seen the...

Error during LDrefinement

1

Hi, I'm encountering an error during the final step of the SNV calling tutorial for scRNA-Seq data. Specifically, I get: ``` [2024-05-21 17:09:53,243] INFO Monopogen.py Run LD refinement ... Rscript...

Hi, I'm getting an error during `peudo_time()`: ``` File "/cluster/work/moor/.snakemake/conda/bf69db601187e32c2ff18c90452fc61d_/lib/python3.7/site-packages/celldancer/pseudo_time.py", line 419, in recur_cell_time_assignment_intracluster MAX_ALLOWED_TERM_CELLS=MAX_ALLOWED_TERM_CELLS) File "/cluster/work/moor/.snakemake/conda/bf69db601187e32c2ff18c90452fc61d_/lib/python3.7/site-packages/celldancer/pseudo_time.py", line 419, in recur_cell_time_assignment_intracluster MAX_ALLOWED_TERM_CELLS=MAX_ALLOWED_TERM_CELLS) File "/cluster/work/moor/.snakemake/conda/bf69db601187e32c2ff18c90452fc61d_/lib/python3.7/site-packages/celldancer/pseudo_time.py", line 419, in recur_cell_time_assignment_intracluster MAX_ALLOWED_TERM_CELLS=MAX_ALLOWED_TERM_CELLS) [Previous...

Dealing mit with multiple conditions and details on model parameters

1

Good morning, I'd like to try your tool, I don't have much experience with scVI and mainly work with the single-cell experiment class in Bioconductor, so it would be grea...