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BayraktarLab
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cell2location
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
https://cell2location.readthedocs.io/en/latest/
Apache License 2.0
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ValueError: Expected parameter rate (Tensor of shape (1, 1)) of distribution Gamma(concentration: tensor([[10.]], device='cuda:0')
#343
RolantusdataExp
closed
10 months ago
8
Question: cell proportion, cell abundance and spatial clustering
#342
dyinboisry4u
closed
10 months ago
1
mod.plot_QC() is printing both plots on the same space
#341
JThomasWatson
opened
10 months ago
1
run_colocation NMF bug
#340
Famingzhao
closed
10 months ago
3
Test with scvi-tools 1.1.0 release candidate
#339
martinkim0
opened
11 months ago
1
Idependent executions with same params provide slightlhy different results - Problem with results reproducibility
#338
AlbertPlaPlanas
opened
12 months ago
2
High resolution model & distance function prior [draft]
#337
vitkl
opened
12 months ago
1
option to use torch.compile
#336
vitkl
closed
12 months ago
0
Conversion of NMF specific fator based scores to discrete groups
#335
archanabhardwaj
opened
1 year ago
2
[pre-commit.ci] pre-commit autoupdate
#333
pre-commit-ci[bot]
opened
1 year ago
0
Model loading fails on Apple Silicon Mac because of `device = 0` in `cpu` mode
#332
LucaMarconato
opened
1 year ago
4
around_target.py bug fix
#331
vitkl
closed
1 year ago
0
Quantifying signal abundance around target cell types (bug fixes)
#330
vitkl
closed
1 year ago
0
error in export posterior
#329
sokratiag
closed
1 year ago
1
"max_epochs=30000" in cell2location mod.train() make "-ELBO loss" up and down when passing 15000 epochs
#327
sciencepeak
closed
12 months ago
1
pip install question
#326
ianutin
closed
1 year ago
1
Feeding per-location number of cells instead of global N_cells_per_location hyper-parameter
#325
ssobt
opened
1 year ago
2
Is it feasible to use symbols?
#323
Biocxifu
opened
1 year ago
0
A temporary solution to (ValueError: The condensed distance matrix must contain only finite values.)
#322
watermelontreesjs
opened
1 year ago
3
plot spatial error with multiple slides
#321
jil100
closed
1 year ago
2
Expected parameter rate Value Error in tuning cell2location
#320
prakashraaz
opened
1 year ago
1
ValueError: You selected `Trainer(strategy='ddp_fork')` but process forking is not supported on this platform. We recommed `Trainer(strategy='ddp_spawn')` instead.
#319
realzehuali
closed
12 months ago
6
Using a bulk RNA-seq dataset to deconvolute a spatial (10x Visium) transcriptomics dataset
#318
cathalgking
opened
1 year ago
1
Request for Mouse Brain Dataset Due to Broken Download Link in Tutorial
#317
shiy-shiy
closed
1 year ago
1
Split data then run cell2location
#316
hahia
opened
1 year ago
4
abundance_around_target_cells illustration
#315
vitkl
closed
1 year ago
0
pin package version
#314
z5ouyang
opened
1 year ago
1
Error while computing log_prob at site 'data_target'
#313
Shiyc-Lab
opened
1 year ago
1
[pre-commit.ci] pre-commit autoupdate
#312
pre-commit-ci[bot]
closed
1 year ago
0
Re-scale of cell type abundances
#311
scg-dgist
opened
1 year ago
3
Upper-bound scvi-tools
#310
vitkl
closed
1 year ago
0
How to identify cell type of each cell (or spot)?
#309
wang-qf
opened
1 year ago
2
half precision for Mod.train
#308
chengarthur
opened
1 year ago
1
Can not save results with h5ad
#307
Zifeng-L
opened
1 year ago
1
ValueError: The condensed distance matrix must contain only finite values.
#306
hkeremcil
opened
1 year ago
4
Compatibility with scvi-tools 1.0.0+, lightning and pytorch 2.0 + signal gene and cell abundance quantification around candidate target cells
#305
vitkl
closed
1 year ago
1
Can't install cell2location in CentOS
#304
JiahuaQu
opened
1 year ago
1
Cant find ['spot_factors'] to run NMF analysis after I exported mod to adata_vis
#303
chengarthur
opened
1 year ago
2
AttributeError: 'Cell2location' object has no attribute 'samples'
#302
hkeremcil
closed
1 year ago
2
Error in the model when providing array to N_cells_per_location argument
#301
Tang-YH
opened
1 year ago
4
use of average cell types expression matrix directly from Seurat to cell2location
#300
archanabhardwaj
closed
1 year ago
2
Unmatched dataset. I have only visium data
#299
oghzzang
opened
1 year ago
0
Size of the single cell dataset
#298
Jaimomar99
opened
1 year ago
1
Update `read_all_and_qc` function to use `anndata.concat()`
#297
kuang-da
closed
1 year ago
1
cell type annotation
#296
wangjiawen2013
opened
1 year ago
8
ValueError in mod.train() running on HPC
#294
wangxin2873
opened
1 year ago
1
can't run export_posterior() on more than one model
#293
erbader
opened
1 year ago
4
Using MERFISH data as reference dataset.
#292
jeji0209
opened
1 year ago
1
What QC to show in a paper
#291
ThomasThaewel
opened
1 year ago
1
[pre-commit.ci] pre-commit autoupdate
#290
pre-commit-ci[bot]
closed
1 year ago
0
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