Liz Ing-Simmons

TOBIAS ATACorrect fails on some datasets, without any error message

4

Hello, I'm running TOBIAS on aggregated data from different single-cell ATAC-seq clusters. The ATACorrect step fails on a subset of clusters without any error message, but works on others. It...

Option to adjust geom_point stroke for FeaturePlot, DimPlot, etc to allow for smaller points

2

I often find that when I'm plotting relatively small plots (e.g. 4x4 inches pdf) with many points, reducing the point size with the`pt.size` argument to `FeaturePlot`, `DimPlot`, etc, seems to...

**Describe the bug** I'm running CellOracle in parallel on a computing cluster (using sge), and stochastically some of my jobs are failing with an error `KeyError: 'params'` coming from gimmemotifs...

Can't read re-segmented Xenium data

4

Hello, I have re-run cell segmentation for my Xenium data using Xenium Ranger version 2.0.0.12 to benefit from its improved segmentation algorithm. I can't read the re-segmented data with `spatialdata_io.xenium()`,...

I found it confusing to get set up to be able to build and preview this lesson locally. The README links to the old lesson template documentation rather than the...

### Describe the bug **context** When I enabled MyST-NB on a project that was already using MyST parser, I got a rather cryptic error message. **expectation** I expected to be...