James Boot

Are some cDNAs omitted from the kallisto index?

12

Hi, During some comparisons of STAR and kallisto we saw that the number of genes/transcripts that STAR aligns to and outputs is much larger than kallisto. This obviously makes sense...

ValueError: columns cannot be a set

5

Hello, I'm getting the following error during UMI correction, when running CITE-seq-Count 1.4.5, Python 3.8. ``` Correcting umis Traceback (most recent call last): File "/data/home/hmy961/citeseq-counts-env/bin/CITE-seq-Count", line 8, in sys.exit(main()) File...

cosmx - ValueError: Affine matrix must be homogeneous.

7

Hi, I'm trying to read in some CosMx data - I have a dataset formatted into a folder with the CellLabels and CellComposite directories and then the relevant CSV files....

Compatibility with squidpy?

2

Hi, Thanks for creating such a great tool, love the pre-print. I'm thinking about applying this method to some CosMx data. I already have a pipeline for importing CosMx data...

## Description When loading CosMx data from FOVs are skipped because they "do not exist in CellComposite folder" or "do not exist in CellLabels folder", however the FOVs do exist...