BayraktarLab cell2location issues

BayraktarLab / 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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issues

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Regarding the reliability of the single-cell sequencing reconstruction plot, how should the N_cells_per_location and detection_alpha parameters be set?

#394 guo8139 opened 6 days ago
0
No module named 'numpy.lib.array_utils'

#393 Roger-GOAT closed 1 week ago
0
RegressionModel use_gpu parameters not working

#392 Angel030331 opened 2 weeks ago
3
Singularity container/tutorial compatability

#391 pear4321 opened 4 weeks ago
1
A question about batch effect

#390 LiuJiamao521 closed 1 month ago
2
Both data are on the same spatial transcriptome slice

#389 GLking123 opened 1 month ago
7
How do I set up multi-GPU parallel training?

#388 noob000007 opened 1 month ago
2
Test fix

#387 vitkl closed 1 month ago
0
Reference data: normalized or not

#386 Dillon214 opened 1 month ago
1
Compatibility issues with scvi-tools

#385 ori-kron-wis opened 1 month ago
4
ValueError: Expected parameter loc (Parameter of shape (23, 1)) of distribution Normal(loc: torch.Size([23, 1]), scale: torch.Size([23, 1])) to satisfy the constraint Real(), but found invalid values:

#384 chuangzhao0601 opened 2 months ago
2
A question about N_cells_per_location

#383 beilouer opened 2 months ago
1
A question aboyt

#382 beilouer closed 1 month ago
0
Inconsistence between N_cells_per_location and the deconvolution result

#381 thestarocean opened 2 months ago
0
Insight-question: Missing cell types & reliability of conditional expression-profiles

#380 floriankreten opened 2 months ago
0
Gene imputation

#379 wangjiawen2013 opened 3 months ago
1
How to Visualization NMF coloc result?

#378 yifanfu01 opened 3 months ago
0
Estimated cell type counts: adjusted for abundance or not?

#377 BaharehAjami opened 3 months ago
4
Using per-celltype counts for downstream analysis

#376 Dillon214 opened 3 months ago
0
Performance issues on a large (120724) location dataset

#375 Dillon214 opened 4 months ago
4
Using scATAC-seq dataset to deconvolute 10x Visium dataset

#374 Jadeapple opened 4 months ago
2
AttributeError: module 'cell2location' has no attribute 'run_c2l'

#373 Lee-jiahao opened 5 months ago
0
"OutOfMemoryError: CUDA out of memory." in GPU mode

#372 asmlgkj opened 5 months ago
7
>>> cell2location.models.Cell2location.setup anndata( adata=adata vis, batch_key=st_batch_key Segmentation fault (core dumped)

#371 Yubeiqi closed 5 months ago
0
Variable N_cell_per_location Hyperparameter

#370 Kwasi-Scientist opened 5 months ago
0
How can I use cell2location output for downstream analysis in R Studio

#369 532at opened 5 months ago
2
How do I find where run_colocation stores its results in adata?

#368 singhbhavya opened 5 months ago
0
an unexpected keyword argument 'summ_sc_data_args'

#367 renyuan1988 opened 5 months ago
2
"OutOfMemoryError: CUDA out of memory." in CPU mode?

#366 Li-ZhiD opened 5 months ago
1
Loading a saved model immediately starts retraining it

#365 grst closed 5 months ago
2
got an unexpected keyword argument 'sample_name_col ' when analyzing multiple slides

#364 renyuan1988 closed 5 months ago
2
The stability plots exhibit disparities compared to those referenced in the previous tutorial notebook.

#363 Zhongzheng99 closed 6 months ago
2
Best practices for multiple slides space mappings!

#362 Zhongzheng99 closed 5 months ago
2
ELBO loss plot was empty

#361 Donbbit opened 6 months ago
1
Regarding memory required for the first tutorial of cell2location

#360 sudeepthi5 opened 6 months ago
2
InvalidIndexError: Reindexing only valid with uniquely valued Index objects

#359 xiang11bei opened 7 months ago
1
Compatibility with VisiumHD

#358 Rafael-Silva-Oliveira closed 4 months ago
8
AttributeError: module 'cell2location' has no attribute 'models'

#357 chandraS76 closed 7 months ago
0
Cell2Location on large datasets

#356 LinearParadox opened 8 months ago
13
cell2location installation on a Windows machine with GPU usage

#355 hkeremcil opened 8 months ago
0
Installing Conda environment for A100 GPUs issue

#354 Nasrine26 opened 8 months ago
1
Is it possible to run cell2location in local computers?

#353 hkeremcil closed 8 months ago
2
Inconsistent cell type propotion between deconvoluted Visium and paired 10X Chromium

#352 kuang-da opened 9 months ago
4
Make a new cell2location pip release

#350 vitkl opened 9 months ago
0
Using a single cell RNA-seq dataset to deconvolute a bulk RNA-seq data

#349 lihaowhusos closed 8 months ago
2
Issue installing cell2location

#348 szimmerman92 opened 9 months ago
19
import cell2location -> AttributeError: module 'jax.random' has no attribute 'KeyArray'

#347 kevinrue opened 9 months ago
5
Error in export_posterior

#346 orange-3711 closed 9 months ago
1
Max steps always = 1 during training, despite change in parameter

#345 No2Ross opened 10 months ago
6
Inputting nuclei counts into cell2location

#344 ssobt opened 10 months ago
17