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Hi!
I followed this tutorial [scvi-hugging-face](https://colab.research.google.com/github/scverse/scvi-tutorials/blob/1.0.4/hub/scvi_hub_intro_and_download.ipynb#scrollTo=89938623) to load pre-trai…
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sorry if my question is naive but its for better understanding
1-in a classical workflow, if i use Topometry, is the eigncomponents here considered the dimensionality reduction method?
2- for…
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Creating different files representing specific functional categories to store the functions will make them more accessible. I propose this be done by both analytical purpose aswell as the nature of th…
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May i ask 1 question:
if data is already pseudobulk object from scRNAseq data with logCPM value, how can i change it back to a seurat object with counts value? Can i still use above method to turn …
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Hi,
I've been running through the sc-tutorial using the most recent versions of Scanpy and AnnData (anndata 0.7.4 & scanpy 1.6.0 & anndata2ri 1.0.5). I ran into an issue when trying to run the Slings…
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vae = sca.models.SCVI(
adata_ref,
n_layers=2,
encode_covariates=True,
deeply_inject_covariates=False,
use_layer_norm="both",
use_batch_norm="none",
)
ValueError: Expe…
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I tried to install cuml using conda, but received an error. I am in a conda environment with cuda = 11.3 and glibc = 2.31. Any help diagnosing the problem would be appreciated. Is cuml compatible with…
rpeys updated
10 months ago
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Dear Authors:
Gene Trajectory is a great tool , but I've run into a couple of problems with it.
The code I used as follows:
run_dm(adata)
cell_graph_dist = get_graph_distance(adata, k=10)
gene_ex…
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Hi,
This is not an issue, I just wanted to give you my thanks. This work is awesome!
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Hello,
I tried to find an example of using external KNN graphs with UMAP. I wasn't able to find any so I created one and hope people find this snippet of code helpful. It's largely based on the int…