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Hi Kai,
I have an anndata.AnnData, I can generate the snapatac2.AnnData as followed
```
# ann is an anndata.AnnData
sa2ann = snapatac2.AnnData(filename = "tmp.h5ad", X = ann.X)
```
When I perf…
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Hi! Thank you for developing this nice tool. I was wondering, is there an option to get mutation-level information about strand bias? i.e. for each mutation in each sample, is it leading/lagging or tr…
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Hi,
I was thinking of adapting this pipeline to take care of multiple reference genomes. Something like each sample would be aligned to different reference fasta file. Any votes for such a feature?…
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Currently, database doesn't seem to pull papers based on author(s) e.g.
```bash
python query_data.py "Do you know of any papers authored by Edward Yang?"
```
```output
Response: Yes, based on …
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I have multiple h5ad files that were generated from different samples (followed the multi-sample tutorial to run this). In this process, I saved the h5ad files for each sample as well as a single h5ad…
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Hi,
I ran into errors when trying to write the anndataset
data=snap.AnnDataSet(
adatas=filtered_adatas,
filename=output.dataset
)
data.write(output.final_d…
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@lpantano @gurgese @ThomasDesvignes @mhalushka @mlhack @keilbeck @BastianFromm @ivlachos @TJU-CMC @sbb25 @phillipeloher
Hi all,
It will be a little long email, but please take 15 min to go over…
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I noticed that "dorado duplex" doesn't have a --modified-bases-models parameter like "dorado basecaller".
Does that mean we can't do methylation calling?
Or can it be done in a separate step?
ymcki updated
8 months ago
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Hi Burçak,
Can you please help me answer some questions about your great program...
What do these parameters do?
- epigenomics_dna_elements
- mutation_annotation_integration
- sample_based
-…
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Dear,
Now users can analyze and explore multi-modal data with Seurat, are there any equivalent methods in Scanpy ? Cellranger3 adds some new features and now supports multi-modal data too.
Using S…