bedapub / bedapub/besca

Additional parameters `min_fract_pos` and `min_cells_per_group` in perform_dge()

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enhancement
Dominant language
Python
Stars
50
Forks
17
Avg merge
1d 4h
Merged PRs (30d)
3

Description

We are repeatedly asked to filter out lowly expressed genes **before** performing DGE analysis.

Currently, I only have a workaround by filtering the provided DGE results, but the correct way would be to filter them before applying the DGE test. Would it be possible to add such a parameter (e.g `min_fract_pos`) to the functions `perform_dge()` and `get_de()` , so that a gene should be positive > min_fract_pos in at least one group.
This parameter is routinely used in seurat FindMarkers(), see: https://www.rdocumentation.org/packages/Seurat/versions/2.3.0/topics/FindMarkers

PS: I would also include a `min_cells_per_group` in `get_de()`, as it's already the case for `perform_dge()`

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Research direction

Locate the definitions of perform_dge() and get_de(), then inspect how perform_dge() already handles min_cells_per_group. Compare the requested min_fract_pos behavior with the linked Seurat FindMarkers() reference. Done means both functions support the requested pre-test filtering parameters with the stated group-based semantics.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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