Ecosyste.ms: Issues
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GitHub / BayraktarLab/cell2location issues and pull requests
#385 - Compatibility issues with scvi-tools
Issue -
State: open - Opened by ori-kron-wis 6 days ago
Labels: bug
#384 - 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:
Issue -
State: open - Opened by chuangzhao0601 8 days ago
Labels: question
#383 - A question about N_cells_per_location
Issue -
State: open - Opened by beilouer 18 days ago
Labels: question
#382 - A question aboyt
Issue -
State: open - Opened by beilouer 18 days ago
Labels: question
#381 - Inconsistence between N_cells_per_location and the deconvolution result
Issue -
State: open - Opened by thestarocean 25 days ago
Labels: question
#380 - Insight-question: Missing cell types & reliability of conditional expression-profiles
Issue -
State: open - Opened by floriankreten about 1 month ago
Labels: question
#379 - Gene imputation
Issue -
State: open - Opened by wangjiawen2013 about 1 month ago
- 1 comment
Labels: question
#378 - How to Visualization NMF coloc result?
Issue -
State: open - Opened by yifanfu01 about 2 months ago
Labels: question
#377 - Estimated cell type counts: adjusted for abundance or not?
Issue -
State: open - Opened by BaharehAjami about 2 months ago
- 4 comments
Labels: question
#376 - Using per-celltype counts for downstream analysis
Issue -
State: open - Opened by Dillon214 2 months ago
Labels: question
#375 - Performance issues on a large (120724) location dataset
Issue -
State: open - Opened by Dillon214 3 months ago
- 4 comments
Labels: question
#374 - Using scATAC-seq dataset to deconvolute 10x Visium dataset
Issue -
State: open - Opened by Jadeapple 3 months ago
- 2 comments
Labels: question
#373 - AttributeError: module 'cell2location' has no attribute 'run_c2l'
Issue -
State: open - Opened by Lee-jiahao 3 months ago
Labels: bug
#372 - "OutOfMemoryError: CUDA out of memory." in GPU mode
Issue -
State: open - Opened by asmlgkj 3 months ago
- 7 comments
Labels: question
#371 - >>> cell2location.models.Cell2location.setup anndata( adata=adata vis, batch_key=st_batch_key Segmentation fault (core dumped)
Issue -
State: closed - Opened by Yubeiqi 3 months ago
Labels: bug
#370 - Variable N_cell_per_location Hyperparameter
Issue -
State: open - Opened by Kwasi-Scientist 4 months ago
Labels: question
#369 - How can I use cell2location output for downstream analysis in R Studio
Issue -
State: open - Opened by 532at 4 months ago
- 2 comments
Labels: question
#368 - How do I find where run_colocation stores its results in adata?
Issue -
State: open - Opened by singhbhavya 4 months ago
Labels: question
#367 - an unexpected keyword argument 'summ_sc_data_args'
Issue -
State: open - Opened by renyuan1988 4 months ago
- 2 comments
Labels: bug
#366 - "OutOfMemoryError: CUDA out of memory." in CPU mode?
Issue -
State: open - Opened by Li-ZhiD 4 months ago
- 1 comment
Labels: bug
#365 - Loading a saved model immediately starts retraining it
Issue -
State: closed - Opened by grst 4 months ago
- 2 comments
Labels: question
#364 - got an unexpected keyword argument 'sample_name_col ' when analyzing multiple slides
Issue -
State: closed - Opened by renyuan1988 4 months ago
- 2 comments
Labels: question
#363 - The stability plots exhibit disparities compared to those referenced in the previous tutorial notebook.
Issue -
State: closed - Opened by Zhongzheng99 5 months ago
- 2 comments
Labels: question
#362 - Best practices for multiple slides space mappings!
Issue -
State: closed - Opened by Zhongzheng99 5 months ago
- 2 comments
Labels: question
#361 - ELBO loss plot was empty
Issue -
State: open - Opened by Donbbit 5 months ago
- 1 comment
Labels: bug
#360 - Regarding memory required for the first tutorial of cell2location
Issue -
State: open - Opened by sudeepthi5 5 months ago
- 2 comments
Labels: question
#359 - InvalidIndexError: Reindexing only valid with uniquely valued Index objects
Issue -
State: open - Opened by xiang11bei 5 months ago
- 1 comment
Labels: question
#358 - Compatibility with VisiumHD
Issue -
State: closed - Opened by Rafael-Silva-Oliveira 6 months ago
- 7 comments
Labels: enhancement, discussion
#357 - AttributeError: module 'cell2location' has no attribute 'models'
Issue -
State: closed - Opened by chandraS76 6 months ago
Labels: question
#356 - Cell2Location on large datasets
Issue -
State: open - Opened by LinearParadox 7 months ago
- 7 comments
Labels: enhancement
#355 - cell2location installation on a Windows machine with GPU usage
Issue -
State: open - Opened by hkeremcil 7 months ago
Labels: question
#354 - Installing Conda environment for A100 GPUs issue
Issue -
State: open - Opened by Nasrine26 7 months ago
- 1 comment
Labels: question
#353 - Is it possible to run cell2location in local computers?
Issue -
State: closed - Opened by hkeremcil 7 months ago
- 2 comments
Labels: question
#352 - Inconsistent cell type propotion between deconvoluted Visium and paired 10X Chromium
Issue -
State: open - Opened by kuang-da 7 months ago
- 4 comments
Labels: question
#350 - Make a new cell2location pip release
Issue -
State: open - Opened by vitkl 7 months ago
Labels: bug
#349 - Using a single cell RNA-seq dataset to deconvolute a bulk RNA-seq data
Issue -
State: closed - Opened by lihaowhusos 8 months ago
- 2 comments
Labels: question
#348 - Issue installing cell2location
Issue -
State: open - Opened by szimmerman92 8 months ago
- 19 comments
Labels: bug
#347 - import cell2location -> AttributeError: module 'jax.random' has no attribute 'KeyArray'
Issue -
State: open - Opened by kevinrue 8 months ago
- 5 comments
Labels: bug
#346 - Error in export_posterior
Issue -
State: closed - Opened by orange-3711 8 months ago
- 1 comment
Labels: bug
#345 - Max steps always = 1 during training, despite change in parameter
Issue -
State: open - Opened by No2Ross 8 months ago
- 6 comments
Labels: bug
#344 - Inputting nuclei counts into cell2location
Issue -
State: open - Opened by ssobt 9 months ago
- 8 comments
Labels: bug
#343 - ValueError: Expected parameter rate (Tensor of shape (1, 1)) of distribution Gamma(concentration: tensor([[10.]], device='cuda:0')
Issue -
State: closed - Opened by RolantusdataExp 9 months ago
- 5 comments
Labels: question
#342 - Question: cell proportion, cell abundance and spatial clustering
Issue -
State: closed - Opened by dyinboisry4u 9 months ago
- 1 comment
Labels: question
#341 - mod.plot_QC() is printing both plots on the same space
Issue -
State: open - Opened by JThomasWatson 9 months ago
- 1 comment
Labels: question
#340 - run_colocation NMF bug
Issue -
State: closed - Opened by Famingzhao 9 months ago
- 3 comments
Labels: bug
#339 - Test with scvi-tools 1.1.0 release candidate
Issue -
State: open - Opened by martinkim0 10 months ago
- 1 comment
Labels: enhancement
#337 - High resolution model & distance function prior [draft]
Pull Request -
State: open - Opened by vitkl 10 months ago
#336 - option to use torch.compile
Pull Request -
State: closed - Opened by vitkl 10 months ago
#335 - Conversion of NMF specific fator based scores to discrete groups
Issue -
State: open - Opened by archanabhardwaj 10 months ago
Labels: question
#333 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: open - Opened by pre-commit-ci[bot] 11 months ago
#332 - Model loading fails on Apple Silicon Mac because of `device = 0` in `cpu` mode
Issue -
State: open - Opened by LucaMarconato 11 months ago
- 4 comments
Labels: bug
#331 - around_target.py bug fix
Pull Request -
State: closed - Opened by vitkl 11 months ago
#330 - Quantifying signal abundance around target cell types (bug fixes)
Pull Request -
State: closed - Opened by vitkl 11 months ago
#329 - error in export posterior
Issue -
State: closed - Opened by sokratiag 11 months ago
- 1 comment
Labels: question
#327 - "max_epochs=30000" in cell2location mod.train() make "-ELBO loss" up and down when passing 15000 epochs
Issue -
State: closed - Opened by sciencepeak 11 months ago
- 1 comment
Labels: question, FAQ
#326 - pip install question
Issue -
State: closed - Opened by ianutin 11 months ago
- 1 comment
Labels: question
#325 - Feeding per-location number of cells instead of global N_cells_per_location hyper-parameter
Issue -
State: open - Opened by ssobt 11 months ago
- 2 comments
Labels: question, FAQ
#323 - Is it feasible to use symbols?
Issue -
State: open - Opened by Biocxifu 12 months ago
Labels: question
#322 - A temporary solution to (ValueError: The condensed distance matrix must contain only finite values.)
Issue -
State: open - Opened by watermelontreesjs 12 months ago
- 1 comment
Labels: bug
#321 - plot spatial error with multiple slides
Issue -
State: closed - Opened by jil100 about 1 year ago
- 2 comments
Labels: bug
#320 - Expected parameter rate Value Error in tuning cell2location
Issue -
State: open - Opened by prakashraaz about 1 year ago
- 1 comment
Labels: question
#319 - ValueError: You selected `Trainer(strategy='ddp_fork')` but process forking is not supported on this platform. We recommed `Trainer(strategy='ddp_spawn')` instead.
Issue -
State: closed - Opened by realzehuali about 1 year ago
- 6 comments
Labels: bug
#318 - Using a bulk RNA-seq dataset to deconvolute a spatial (10x Visium) transcriptomics dataset
Issue -
State: open - Opened by cathalgking about 1 year ago
- 1 comment
Labels: question
#317 - Request for Mouse Brain Dataset Due to Broken Download Link in Tutorial
Issue -
State: closed - Opened by shiy-shiy about 1 year ago
- 1 comment
Labels: bug
#316 - Split data then run cell2location
Issue -
State: open - Opened by hahia about 1 year ago
- 4 comments
Labels: question
#315 - abundance_around_target_cells illustration
Pull Request -
State: closed - Opened by vitkl about 1 year ago
#314 - pin package version
Issue -
State: open - Opened by z5ouyang about 1 year ago
- 1 comment
Labels: enhancement
#313 - Error while computing log_prob at site 'data_target'
Issue -
State: open - Opened by Shiyc-Lab about 1 year ago
- 1 comment
Labels: bug
#312 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] about 1 year ago
#311 - Re-scale of cell type abundances
Issue -
State: open - Opened by scg-dgist about 1 year ago
- 3 comments
Labels: enhancement
#310 - Upper-bound scvi-tools
Pull Request -
State: closed - Opened by vitkl about 1 year ago
#309 - How to identify cell type of each cell (or spot)?
Issue -
State: open - Opened by wang-qf about 1 year ago
- 2 comments
Labels: question
#308 - half precision for Mod.train
Issue -
State: open - Opened by chengarthur about 1 year ago
- 1 comment
Labels: enhancement
#307 - Can not save results with h5ad
Issue -
State: open - Opened by Zifeng-L about 1 year ago
- 1 comment
Labels: bug
#306 - ValueError: The condensed distance matrix must contain only finite values.
Issue -
State: open - Opened by hkeremcil about 1 year ago
- 4 comments
Labels: bug
#305 - Compatibility with scvi-tools 1.0.0+, lightning and pytorch 2.0 + signal gene and cell abundance quantification around candidate target cells
Pull Request -
State: closed - Opened by vitkl about 1 year ago
- 1 comment
#304 - Can't install cell2location in CentOS
Issue -
State: open - Opened by JiahuaQu about 1 year ago
- 1 comment
Labels: bug
#303 - Cant find ['spot_factors'] to run NMF analysis after I exported mod to adata_vis
Issue -
State: open - Opened by chengarthur about 1 year ago
- 2 comments
Labels: question
#302 - AttributeError: 'Cell2location' object has no attribute 'samples'
Issue -
State: closed - Opened by hkeremcil about 1 year ago
- 2 comments
Labels: bug
#301 - Error in the model when providing array to N_cells_per_location argument
Issue -
State: open - Opened by Tang-YH about 1 year ago
- 4 comments
Labels: bug
#300 - use of average cell types expression matrix directly from Seurat to cell2location
Issue -
State: closed - Opened by archanabhardwaj about 1 year ago
- 2 comments
Labels: question
#299 - Unmatched dataset. I have only visium data
Issue -
State: open - Opened by oghzzang about 1 year ago
Labels: question
#298 - Size of the single cell dataset
Issue -
State: open - Opened by Jaimomar99 about 1 year ago
- 1 comment
Labels: question
#297 - Update `read_all_and_qc` function to use `anndata.concat()`
Pull Request -
State: closed - Opened by kuang-da about 1 year ago
- 1 comment
Labels: replaced/inactive
#296 - cell type annotation
Issue -
State: open - Opened by wangjiawen2013 about 1 year ago
- 8 comments
Labels: question
#294 - ValueError in mod.train() running on HPC
Issue -
State: open - Opened by wangxin2873 about 1 year ago
- 1 comment
Labels: question
#293 - can't run export_posterior() on more than one model
Issue -
State: open - Opened by erbader about 1 year ago
- 4 comments
Labels: bug
#292 - Using MERFISH data as reference dataset.
Issue -
State: open - Opened by jeji0209 about 1 year ago
- 1 comment
Labels: question
#291 - What QC to show in a paper
Issue -
State: open - Opened by ThomasThaewel about 1 year ago
Labels: question
#290 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] about 1 year ago
#289 - cannot import name 'run_regression' from 'cell2location'
Issue -
State: closed - Opened by limin321 about 1 year ago
- 1 comment
Labels: question, not_using_latest_cell2location
#288 - Can't open saved .h5ad after cell2location
Issue -
State: open - Opened by BenjaminDEMAILLE over 1 year ago
- 4 comments
Labels: bug
#287 - spatial data model training for bleeding corrected data
Issue -
State: open - Opened by parkjooyoung99 over 1 year ago
- 1 comment
Labels: enhancement
#285 - Idea of modifying model after assessing Reconstruction accuracy plot
Issue -
State: closed - Opened by parkjooyoung99 over 1 year ago
- 4 comments
Labels: question
#284 - Error in mod.train
Issue -
State: open - Opened by scauzhaos over 1 year ago
- 1 comment
Labels: question
#283 - Is it possible to conduct an enrichment analysis with predefined cluster, using cell abundance value?
Issue -
State: closed - Opened by jeji0209 over 1 year ago
- 2 comments
Labels: question
#282 - Estimated expression signature QC plot comes out splitted
Issue -
State: closed - Opened by jeji0209 over 1 year ago
- 2 comments
Labels: question
#281 - Documentation confusion: add_to_varm and add_to_obs argument of function mod.export_posterior()
Issue -
State: open - Opened by duyson1999 over 1 year ago
- 1 comment
Labels: bug
#280 - ModuleNotFoundError
Issue -
State: open - Opened by Linlinwangwang over 1 year ago
- 1 comment
Labels: bug
#279 - AttributeError
Issue -
State: open - Opened by Linlinwangwang over 1 year ago
Labels: bug