SEACells

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Hi all, I encountered several instances where a metacell is created from a large number of single cells. Is there a way to cap the number of single cells that...

yxsee

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.64 to 4.66.3. Release notes Sourced from tqdm's releases. tqdm v4.66.3 stable cli: eval safety (fixes CVE-2024-34062, GHSA-g7vv-2v7x-gj9p) tqdm v4.66.2 stable pandas: add DataFrame.progress_map (#1549) notebook: fix...

dependabot[bot]

The data cannot be downloaded

1

use wget to download data return **ERROR 403: Forbidden** , please help to check.

cfzgg

Circular import and GPU version

1

Hi, Thank you for developing such an interesting and practical tool. 1. I encountered a 'Circular import' error while running in the cluster, the details of the error are as...

GLking123

Handling metacell creation for rare cell types (<< 75 cells)

1

Thanks for developing this incredibly inspiring tool! I am currently analyzing a large scRNA-seq dataset consisting of hundreds of samples, each with ~ 3000 cells. Following the methodology outlined in...

uqzqiao

Hi all, So when using addGroupCoverages(proj, maxFragmentLength=147) in ArchR , it says unused argument: maxFragmentLength. I also tried to maxFragsize in CreateArrowfFiles, but it didn't work. Any suggestions please? Many...

Aya-Balbaa

Custom Neighborhood Graph for Metacells

1

Hello, I was wondering if it's possible to use a custom neighborhood graph for metacell construction. Looking through the source code and the tutorials, it seems that the methods depend...

shahrozeabbas

Fail to install seacells via conda due to conflicts in environment.yaml

2

Hi! I tried to install SEACells via option 2, i.e. ``` conda env create -n seacells --file environment.yaml conda activate seacells ``` However, there seems to be conflicts in the...

ChangSuBiostats

Aggregation of expression data ends up in matrix filled with NaN's

6

Dear SEACell team, first of all thank you for such an interesting and versatile tool. I have been recently using it for creating metacells from a scRNA-seq dataset with cells...

zvittorio

No speed increase was observed when use_gpu=True

1

The time consumption by the model.fit step seems almost the same with or without using gpu. What's going on here?

OMIC-coding