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

#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

#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

#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

#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

#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

#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

#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

#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

#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