BayraktarLab/cell2location issues and pull requests

#278 - Which quantile to use for the cell type mapping?

Issue - State: open - Opened by ankitbioinfo over 1 year ago - 3 comments
Labels: question

#277 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#276 - export_posterior() got an unexpected keyword argument 'add_to_obsm'

Issue - State: open - Opened by kuang-da over 1 year ago - 3 comments
Labels: bug

#275 - Cell number

Issue - State: open - Opened by wangjiawen2013 over 1 year ago - 1 comment
Labels: question

#273 - Using gpu even when use_gpu=False in cell2location.models.RegressionModel.load()

Issue - State: open - Opened by bhhlee over 1 year ago - 2 comments
Labels: bug

#272 - Error in row clustering of run_colocation clustermap

Issue - State: closed - Opened by ssobt over 1 year ago - 3 comments

#270 - Difficulties mapping immune cells in brain tumors

Issue - State: open - Opened by lgaspardboulinc31 over 1 year ago
Labels: question

#269 - GPU error in mod.train

Issue - State: open - Opened by renyuan1988 over 1 year ago - 3 comments

#266 - celltype SC-ST mapping

Issue - State: closed - Opened by JingGuo1997 over 1 year ago - 1 comment
Labels: enhancement

#259 - Pip downloads

Pull Request - State: closed - Opened by vitkl over 1 year ago

#256 - bug in installing in colab Pygments 2.6.1 Requirement.parse('pygments<3.0.0,>=2.14.0'), {'rich'})

Issue - State: open - Opened by yuanmuqing2000 over 1 year ago - 1 comment
Labels: bug

#253 - NotImplementedError: The Cell2location model currently does not support minified data.

Issue - State: open - Opened by forrwill over 1 year ago - 12 comments
Labels: question

#252 - `MPSAccelerator` can not run on your system since the accelerator is not available. The following accelerator(s) is available and can be passed into `accelerator` argument of `Trainer`: ['cpu']

Issue - State: open - Opened by AdrianaLecourieux over 1 year ago - 7 comments
Labels: question

#250 - Choosing one N_cells_per_location for multiple samples

Issue - State: closed - Opened by ThomasThaewel over 1 year ago
Labels: question

#249 - Cell2location reads raw counts as normalized values

Issue - State: closed - Opened by deconvolute over 1 year ago - 1 comment
Labels: question, FAQ

#245 - Error running plot in spatial coordinates

Issue - State: closed - Opened by ChristinaSteyn over 1 year ago - 1 comment
Labels: question

#244 - Error running 'Estimate cell-type specific expression of every gene in the spatial data (needed for NCEM)'

Issue - State: closed - Opened by ChristinaSteyn over 1 year ago - 1 comment
Labels: question, FAQ

#242 - Would the cell type proportion of the reference scRNA-seq dataset affect the performance or results of the deconvolution?

Issue - State: closed - Opened by Lesdormis over 1 year ago - 1 comment
Labels: question

#241 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#240 - changed kernel name

Pull Request - State: closed - Opened by vitkl over 1 year ago

#239 - KeyError: 'post_sample_means'

Issue - State: open - Opened by BenjaminDEMAILLE over 1 year ago - 4 comments
Labels: bug

#238 - Fix for numeric stability issue

Pull Request - State: closed - Opened by vitkl over 1 year ago

#237 - PyroModule' object has no attribute 'per_cluster_mu_fg_unconstrained'

Issue - State: open - Opened by BenjaminDEMAILLE over 1 year ago - 3 comments
Labels: bug

#236 - Cell2Location Tutorial no longer works with release 0.1.2

Issue - State: closed - Opened by AlbertPlaPlanas over 1 year ago - 6 comments
Labels: bug

#235 - Update environment.yml

Pull Request - State: closed - Opened by yozhikoff over 1 year ago

#234 - Update README.md

Pull Request - State: closed - Opened by vitkl over 1 year ago

#231 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#230 - Memory efficient option for export posterior (using quantiles explicitly)

Pull Request - State: closed - Opened by vitkl over 1 year ago - 1 comment

#227 - matrix factorisation (NMF) heatmap

Issue - State: open - Opened by wangjiawen2013 almost 2 years ago - 1 comment
Labels: question

#226 - cell2location is not compatible with sklearn 1.2.0

Issue - State: closed - Opened by wangjiawen2013 almost 2 years ago - 3 comments
Labels: bug

#225 - error in mod.train

Issue - State: closed - Opened by wanghf0501 almost 2 years ago - 2 comments
Labels: question

#224 - imune cell abundance

Issue - State: closed - Opened by wangjiawen2013 almost 2 years ago
Labels: question

#221 - Incompatible Tensor broadcasts with MPS accelerator - Mac M2

Issue - State: open - Opened by NicolasSompairac almost 2 years ago - 5 comments
Labels: bug

#220 - Add link to FAQ on issues page & NMF compatibility change

Pull Request - State: closed - Opened by vitkl almost 2 years ago

#219 - Estimated reference expression signatures

Issue - State: open - Opened by wangjiawen2013 almost 2 years ago - 1 comment
Labels: question, FAQ

#218 - reference model retraining

Issue - State: closed - Opened by wangjiawen2013 almost 2 years ago - 2 comments
Labels: question

#217 - Cell2location object has no attribute samples

Issue - State: closed - Opened by julie-jch almost 2 years ago - 1 comment
Labels: question

#216 - what's scale_average_detection and detection_y_c?

Issue - State: open - Opened by jefferyUstc almost 2 years ago - 1 comment
Labels: bug

#215 - How to plot images without showing the grid

Issue - State: closed - Opened by brianpenghe almost 2 years ago - 2 comments
Labels: question

#214 - fixed code style formatting

Pull Request - State: closed - Opened by vitkl almost 2 years ago

#213 - Docker image not working

Issue - State: open - Opened by jamrute almost 2 years ago - 4 comments
Labels: bug

#212 - plot_spatial fails with visium cytassist data

Issue - State: closed - Opened by AlexanderAivazidis almost 2 years ago - 2 comments
Labels: bug, good first issue, question

#211 - Reconstruct single cell gene expression matrix

Issue - State: open - Opened by ggruenhagen3 almost 2 years ago - 4 comments
Labels: enhancement, question, FAQ

#210 - Amortised inference uses too much RAM during posterior sampling due to not hiding data samples

Issue - State: open - Opened by vitkl almost 2 years ago
Labels: bug

#209 - RuntimeError: PyTorch is not linked with support for mps devices

Issue - State: closed - Opened by SunYong0821 almost 2 years ago - 4 comments
Labels: bug

#208 - ImportError: cannot import name 'run_regression' from 'cell2location' despite setting the PYTHONNOUSERSITE param

Issue - State: closed - Opened by sunnyzwu almost 2 years ago - 1 comment
Labels: question, not_using_latest_cell2location

#207 - Cell2location on Slide-seq data + over 100 cell types in my single-cell reference

Issue - State: closed - Opened by frankligy almost 2 years ago - 3 comments
Labels: question, FAQ

#206 - RuntimeError when using cell2location on MacOS (M1)

Issue - State: closed - Opened by sarahshuang almost 2 years ago - 11 comments
Labels: bug

#205 - Discrepancy in the average number of cells per spot between the input and prediction

Issue - State: closed - Opened by abayegan almost 2 years ago - 2 comments
Labels: question, FAQ

#204 - I don't have the raw count data, how can I do to deal with the mod.train() error

Issue - State: open - Opened by FanZhang9 almost 2 years ago - 6 comments
Labels: question

#200 - Conflicting dependency error on Windows

Issue - State: open - Opened by lampirl about 2 years ago - 6 comments
Labels: bug

#196 - Extracting the spot barcodes of interested cell types after deconvolution

Issue - State: closed - Opened by Zhuang-Bio about 2 years ago - 1 comment
Labels: enhancement

#195 - reloading data - RuntimeError: self.samples is missing, please run self.export_posterior() first

Issue - State: open - Opened by livyring about 2 years ago - 4 comments
Labels: question, FAQ

#193 - spacejam (Nanostring WTA) cell2location model and tutorial

Pull Request - State: closed - Opened by AlexanderAivazidis about 2 years ago

#192 - AMD GPU support

Issue - State: closed - Opened by czackl about 2 years ago - 1 comment
Labels: enhancement

#191 - Saving for QC and results plots.

Issue - State: open - Opened by bednarsky about 2 years ago - 13 comments
Labels: enhancement, question

#186 - Improved posterior quantile computation

Pull Request - State: closed - Opened by vitkl about 2 years ago - 1 comment

#184 - Setup amortized network for Cell2location

Issue - State: closed - Opened by canergen about 2 years ago - 9 comments
Labels: enhancement, discussion, FAQ

#181 - Improving downstream analysis NMF workflow

Pull Request - State: closed - Opened by vitkl about 2 years ago

#180 - How to show the min,med&max values on the multiple cell types plot

Issue - State: open - Opened by rue1996 about 2 years ago - 3 comments
Labels: question

#177 - Reconstruction accuracy and QC plots

Issue - State: open - Opened by wangjiawen2013 about 2 years ago - 3 comments
Labels: question

#173 - QC history plot error

Issue - State: closed - Opened by archanabhardwaj over 2 years ago - 1 comment
Labels: question

#172 - Question about numerically synthesizing mouse brain spatial dataset

Issue - State: closed - Opened by ZhanYangen over 2 years ago - 2 comments
Labels: question

#169 - Error in saving the signature output

Issue - State: closed - Opened by archanabhardwaj over 2 years ago - 2 comments
Labels: question

#168 - CUDA out of Memory while training the RegressionModel

Issue - State: closed - Opened by Rajarshi1001 over 2 years ago - 9 comments
Labels: question

#167 - how to install cell2location on windows by anaconda3

Issue - State: closed - Opened by Ziyu-Mu over 2 years ago - 2 comments
Labels: question

#164 - multi-samples integration

Issue - State: closed - Opened by wangjiawen2013 over 2 years ago - 4 comments
Labels: question

#161 - why w_s,f follow gamma distribution

Issue - State: closed - Opened by caiquanyou over 2 years ago - 2 comments
Labels: question

#156 - Model training failed

Issue - State: closed - Opened by xiaoxiaozhihuishu over 2 years ago - 4 comments
Labels: bug

#152 - Performance reduction when training the Cell2location model with CPU in the latest version

Issue - State: closed - Opened by tomasgomes over 2 years ago - 9 comments
Labels: bug

#151 - Interpretation of the deconvolution results

Issue - State: closed - Opened by Zhuang-Bio over 2 years ago - 4 comments
Labels: question

#150 - Failed to import cell2location in tutorial when colab has an update

Issue - State: closed - Opened by yxiaobme over 2 years ago - 2 comments
Labels: bug

#149 - package incompatibility with scvi-tools beyond 0.15.0 when running RegressionModel (or tutorial syntax needs update)

Issue - State: closed - Opened by nancyliy over 2 years ago - 2 comments
Labels: bug

GitHub / BayraktarLab/cell2location issues and pull requests