BayraktarLab/cell2location

Issues

• Inputting nuclei counts into cell2location

  #344 opened a year ago by ssobt
  16

• RegressionModel use_gpu parameters not working

  #392 opened 2 months ago by Angel030331
  2

• Cell2Location on large datasets

  #356 opened 9 months ago by LinearParadox
  12

• Singularity container/tutorial compatability

  #391 opened 2 months ago by pear4321
  1

• Compatibility with VisiumHD

  #358 opened 5 months ago by Rafael-Silva-Oliveira
  8

• Both data are on the same spatial transcriptome slice

  #389 opened 2 months ago by GLking123
  7

• How do I set up multi-GPU parallel training?

  #388 opened 3 months ago by noob000007
  2

• A question about batch effect

  #390 opened 2 months ago by LiuJiamao521
  2

• 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 opened 3 months ago by chuangzhao0601
  2

• ValueError: Expected parameter rate (Tensor of shape (1, 1)) of distribution Gamma(concentration: tensor([[10.]], device='cuda:0')

  #343 opened a year ago by RolantusdataExp
  8

• Compatibility issues with scvi-tools

  #385 opened 3 months ago by ori-kron-wis
  4

• A question aboyt

  #382 opened 3 months ago by beilouer
  0

• A question about N_cells_per_location

  #383 opened 3 months ago by beilouer
  1

• Reference data: normalized or not

  #386 opened 3 months ago by Dillon214
  1

• ELBO loss plot was empty

  #361 opened 8 months ago by Donbbit
  1

• Issue installing cell2location

  #348 opened 10 months ago by szimmerman92
  19

• Inconsistence between N_cells_per_location and the deconvolution result

  #381 opened 4 months ago by thestarocean
  0

• Using scATAC-seq dataset to deconvolute 10x Visium dataset

  #374 opened 6 months ago by Jadeapple
  2

• Insight-question: Missing cell types & reliability of conditional expression-profiles

  #380 opened 4 months ago by floriankreten
  0

• Estimated cell type counts: adjusted for abundance or not?

  #377 opened 4 months ago by BaharehAjami
  4

• Gene imputation

  #379 opened 4 months ago by wangjiawen2013
  1

• How to Visualization NMF coloc result?

  #378 opened 4 months ago by yifanfu01
  0

• Using per-celltype counts for downstream analysis

  #376 opened 5 months ago by Dillon214
  0

• "OutOfMemoryError: CUDA out of memory." in GPU mode

  #372 opened 6 months ago by asmlgkj
  7

• Performance issues on a large (120724) location dataset

  #375 opened 5 months ago by Dillon214
  4

• AttributeError: module 'cell2location' has no attribute 'run_c2l'

  #373 opened 6 months ago by Lee-jiahao
  0

• >>> cell2location.models.Cell2location.setup anndata( adata=adata vis, batch_key=st_batch_key Segmentation fault (core dumped)

  #371 opened 6 months ago by Yubeiqi
  0

• Variable N_cell_per_location Hyperparameter

  #370 opened 6 months ago by Kwasi-Scientist
  0

• an unexpected keyword argument 'summ_sc_data_args'

  #367 opened 7 months ago by renyuan1988
  2

• How can I use cell2location output for downstream analysis in R Studio

  #369 opened 7 months ago by 532at
  2

• got an unexpected keyword argument 'sample_name_col ' when analyzing multiple slides

  #364 opened 7 months ago by renyuan1988
  2

• How do I find where run_colocation stores its results in adata?

  #368 opened 7 months ago by singhbhavya
  0

• Regarding memory required for the first tutorial of cell2location

  #360 opened 8 months ago by sudeepthi5
  2

• Best practices for multiple slides space mappings!

  #362 opened 7 months ago by Zhongzheng99
  2

• Loading a saved model immediately starts retraining it

  #365 opened 7 months ago by grst
  2

• "OutOfMemoryError: CUDA out of memory." in CPU mode?

  #366 opened 7 months ago by Li-ZhiD
  1

• The stability plots exhibit disparities compared to those referenced in the previous tutorial notebook.

  #363 opened 7 months ago by Zhongzheng99
  2

• InvalidIndexError: Reindexing only valid with uniquely valued Index objects

  #359 opened 8 months ago by xiang11bei
  1

• AttributeError: module 'cell2location' has no attribute 'models'

  #357 opened 8 months ago by chandraS76
  0

• Inconsistent cell type propotion between deconvoluted Visium and paired 10X Chromium

  #352 opened 10 months ago by kuang-da
  4

• Max steps always = 1 during training, despite change in parameter

  #345 opened a year ago by No2Ross
  6

• Using a single cell RNA-seq dataset to deconvolute a bulk RNA-seq data

  #349 opened 9 months ago by lihaowhusos
  2

• Installing Conda environment for A100 GPUs issue

  #354 opened 10 months ago by Nasrine26
  1

• cell2location installation on a Windows machine with GPU usage

  #355 opened 10 months ago by hkeremcil
  0

• Is it possible to run cell2location in local computers?

  #353 opened 10 months ago by hkeremcil
  2

• Error in export_posterior

  #346 opened a year ago by orange-3711
  1

• Make a new cell2location pip release

  #350 opened 10 months ago by vitkl
  0

• import cell2location -> AttributeError: module 'jax.random' has no attribute 'KeyArray'

  #347 opened a year ago by kevinrue
  5

• mod.plot_QC() is printing both plots on the same space

  #341 opened a year ago by JThomasWatson
  1

• Question: cell proportion, cell abundance and spatial clustering

  #342 opened a year ago by dyinboisry4u
  1