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Hi, Qian,
I am using adata as input of the h5ad file converted from Seurat. Adding data from RNA as X, adding counts from RNA as raw, transferring meta.data to obs.
During model training, I enc…
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**Describe the bug***Describe the bug**
Program crashes when trying to merge SCOPE and filtered looms.
**To Reproduce**
Steps to reproduce the behavior:
1. Configure with these options:
nextflo…
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Is there a reason y'all can think of that I would be getting an 'all counts filtered' error when using human genes?
I started with a mouse Seurat object and converted into a h5ad object with human …
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## User stories
- I am a computational biologist with my own data in H5AD or Seurat and I'd like to know which Census cells are the most similar to each of my own cells. I need to know the level of c…
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I am trying to run Conga on my integrated Seurat object. I already downsampled and integrated 4 CITEseq data in a Seurat object. I have TCR csv file for each sample separatly. I tried to use your mege…
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I am running scanpy anndata through CellChat and my code works except for when it gets to computing the communication probability. This is the error I get. ad ad_object # access normalized data matr…
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Hi,
I am using the pancera dataset with all parameters defaulted, why am I unable to reproduce the results of the paper? The code used is all functions within `TFvelo_run_demo.py` and `TFvelo_anal…
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pinging interested parties @lmweber @drighelli @HelenaLC @ivirshup
Nice to meet you all! I believe with some we crossed paths in some zoom dungeons or email thread. I'd like to use this issue to k…
giovp updated
7 months ago
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Hi,
Thank you for creating Seurat-disk.
I am running in the following error:
obj
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One issue that we see in GCID and will be an emerging issue in projectR is the ability to search for a gene by several alias names. Currently genes are linked to a single Ensembl ID (or other IDs if …