Artur Jaroszewicz

per-fragment methylation

2

Hello Devon! I was wondering if you had plans to implement a per-fragment methylation tool for MethylDackel. The problem with the per-read methylation is it doesn't take into account information...

Return overlap between PyRanges objects, keeping columns from both?

6

I am trying to implement a method to fetch and potentially summarize information from genomic intervals. For example, given a set of CpG sites with methylation (beta) values between 0...

[BUG] Overflow in `.deseq2()` and and `lfc_shrink()`

3

**To Reproduce** ``` dds = DeseqDataSet( counts=counts_df, metadata=metadata, design_factors=['condition', "RNA_Qubit_actual", 'treatment'], continuous_factors=["RNA_Qubit_actual"], refit_cooks=True, n_cpus=12, ) dds.deseq2() ``` Output: ```Fitting size factors... ... done in 0.09 seconds. /home/jupyter/env/mambaforge/envs/rome/lib/python3.11/site-packages/pydeseq2/utils.py:553: RuntimeWarning: overflow encountered...