MalteDLuecken

scANVI classification uncertainty extraction method

2

It would be very useful to have some quantification of model uncertainty for the scANVI cell type classification output. In the simplest form this could be the softmax output from...

Adding DESC to data integration benchmarking

21

Hi @eleozzr, We were thinking about adding DESC to our benchmark of data integration tools (https://github.com/theislab/scib). We would be running our own pre-processing for the input to DESC for this,...

Support BiocSingular’s LowRankMatrix

6

Hi! I ran into a strange error when trying to write a quick script for Seurat -> Anndata conversion. I'm just loading data from a Seurat tutorial and then want...

Put non-count data in CDS objects

8

Hi, I'm afraid this is more of a question than a bug report. Thus, I am deviating from the template. I haven't been able to find out how to load...

Demuxlet filtering out vast majority of reads that 10X deems good

6

Hi! I've been trying to use demuxlet to demultiplex a mixture of cells from two donors as a test run. I have 10x data which was processed with CellRanger version...

Small multiple plots for clusters

10

- [ ] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in...

Order of plotting datapoints with categorical colouring should be amended

10

- [x] Additional function parameters / changed functionality / changed defaults? At the moment when we are plotting data points in e.g., `sc.pl.umap()` with `color='covariate'` we determine the plotting order...

Hi! Really cool tool and web portal! I was trying to understand how you have been building references for Azimuth. A lot of what you did makes sense to me,...

Improve documentation for violin plot to illustrate per-gene usage – violin(adata.T, 'gene_property')

13

Hey! I thought plotting `.var` columns in `sc.pl.violin()` worked previously (and the error message seems to suggest this as well). I am doing the following: ``` adata_counts.var['dropout_per_gene'] = (adata_counts.X >...

Issue with sanitize_anndata() in plotting functions with subsets of anndata objects are passed.

6

I get quite a strange scanpy error, which appears a bit stochastic... This is has happened for the first time in version 1.1. I am trying to get a scatter...