-
Hi there! I'm excited to use this tool. I noticed in the fit function for fine tuning for imputation, ensembl_auto_conversion is set to False. I was wondering if there was a reason for not allowing au…
-
Hi,
I perform batch correction using scVI. But I perform celltypist prediction before batch correction. Is it better to perform celltypist after batch correction or it doesn't matter?
Good day.
-
when I selected ids, I can `Download Selected IDs`, would it possiable I can change the category name of selected ids and update the `clusters` to a new cluster name. The anndata should be updated and…
-
Dear authors of cellphoneDB, first of all, thanks for this very very useful tool!
I am using it to evaluate ligand-receptor interactions among different annotated cell type a scRNAseq dataset.
I am …
-
Hi,
I have few queries regarding scanpy.
1. As scanpy is using Louvain Leiden algorithms for clustering which optimize modularity 'Q', so how we can access and print modularity funciton?
2. R…
-
I would support JAX as another backend.
Would probably be worth opening another issue for tracking JAX as a backend. For IO, I was thinking that could be done with #659
_Originally posted by @iv…
-
Hi @yjgeno @jamesjcai @guanxunli
Thanks for developing GenKI. I was excited to use it to knockout a gene from Malaria Cell Atlas and see if it gives better results in terms of biology than `scTeni…
-
**Bug in H5 data assertion for h5ad files**
I tried to use `has_h5_attribute` and `has_h5_keys` to assert scanpy outputs ([here](https://github.com/galaxyproject/tools-iuc/pull/6162#discussion_r173…
-
Hi,
I downloaded the tar file and tried to run trapnell.ipynb.
The model in the notebook was not there: 'pretrained_models/sweep_sciplex3_old_reproduced_logsigm_model_seed=30_epoch=340.pt'
I pi…
-
Hello ! When I use this code: SEVtras.sEV_recognizer(input_path='./', sample_file='./skin1/sample_file.txt', out_path='./skin1/
outputs', species='Homo')
to anylsis my 10x-scRNAseq raw file, after…