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Hello Alevin-Fry team, and thank you for you cool tool!
I have a question about Alevin-Fry, which I use in my daily work.
There is a discrepancy between the expression of some genes depending on…
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Louise, looks you can do this with these commands https://stackoverflow.com/a/9781995. It's very similar to https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories
…
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We'll continue now with `code/09_snRNA-seq_re-processed/02_normalization.R` (and potentially a companion shell script generated with `sgejobs::job_single()` that can use the `hold_jid` to wait for the…
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This comes after #4. I recommend starting a new script instead of expanding https://github.com/LieberInstitute/DLPFC_snRNAseq/blob/main/code/03_build_sce/droplets.R.
- [x] Read this section of OSCA…
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This comes after #3
- [x] Do simple normalization and find top 1000 HVGs sample-by sample like at https://github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/master/10x_all-FACS-n10_2021rev_st…
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In `anndata_builders.py`:
```
class SpatialRNASeqAnnDataZarrViewConfBuilder(RNASeqAnnDataZarrViewConfBuilder):
"""Wrapper class for creating a AnnData-backed view configuration
for "second…
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Dear scCODA team,
Thanks a lot for this package, its turning out very useful for my snRNAseq analysis!
I am finding the same error mentioned in this other issue #40 however I have the versions r…
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Hi, thank you so much for developing this amazing tool! I've been wondering about the single-nucleus RNAseq workflow for RNA velocity. I've tried generating h5ad files following the kb RNA velocity tu…
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Hi,
I randomly stumbled across this project and it seems pretty interesting! I just had some basic thoughts about how it looks like `alevin-fry` is currently being run. One note is that when pr…
rob-p updated
2 years ago
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I have an .h5ad file I can load into python and seems to work with no issues. I want to instead read it into R. Here is the code to reproduce my issue:
```r
url