From https://github.com/AlexsLemonade/alsf-scpca/pull/151#pullrequestreview-825323348 we may want to rerun the benchmarking notebook, 13-spatial-transcriptomics-benchmarking.Rmd after generating a new cellranger index using ensembl 104 to see if any of the results change. In particular if any of the effects on particular genes are altered.
If we do revisit this, we may also want to add in Alevin-fry unfiltered rather than using the knee filtering method as well before we discount using Alevin-fry.
From https://github.com/AlexsLemonade/alsf-scpca/pull/151#pullrequestreview-825323348 we may want to rerun the benchmarking notebook,
13-spatial-transcriptomics-benchmarking.Rmdafter generating a new cellranger index using ensembl 104 to see if any of the results change. In particular if any of the effects on particular genes are altered.If we do revisit this, we may also want to add in Alevin-fry unfiltered rather than using the knee filtering method as well before we discount using Alevin-fry.