Koen Van den Berge

low memory detected: 3GB instead of 4GB

27

When I initialise the mining with one AMD Radeon RX550 4GB card, the miner successfully detects a card, saying: gpu #0: gfx804, 3072 mb available, 8 compute units However, it...

Many methylation probabilities close to 0.5 using all-context model

7

We are using `megalodon` for methylation calling and it's been working well for us. We have been exploring the results, and noticed that in the `per_read_modified_base_calls.db` file, the majority of...

Looping over cell types to use as reference: discrepancy?

11

Hi All, I am using `scCODA` for differential abundance analysis of a scRNA-seq dataset. If I perform a manual reference cell type selection using e.g. B-cells as reference, and another...

GPfates bifurcation statistics on known pseudotime and posterior probabilities

8

Suppose that I would like to assess whether gene expression differs between two lineages of a trajectory, when I know the true pseudotime and posterior probabilities for each cell in...

Adding pseudobulk-level covariates defined across cell types, to a DE/DS analysis

1

Suppose I am working with a large study with lots of heterogeneity, and I calculate factors of unwanted variation (UV) using `RUVSeq` using all pseudobulk samples (several cell types, 2...

add weights in pseudbulkDGE for edgeR analysis

4

Hi, In some cases, one might want to add weights to the dispersion estimation and fitting of the edgeR model when using the `pseudobulkDGE` function. In my case this would...