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BayraktarLab
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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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Docker image not working
#213
jamrute
opened
2 years ago
4
plot_spatial fails with visium cytassist data
#212
AlexanderAivazidis
closed
2 years ago
2
Reconstruct single cell gene expression matrix
#211
ggruenhagen3
opened
2 years ago
4
Amortised inference uses too much RAM during posterior sampling due to not hiding data samples
#210
vitkl
opened
2 years ago
0
RuntimeError: PyTorch is not linked with support for mps devices
#209
SunYong0821
closed
1 year ago
4
ImportError: cannot import name 'run_regression' from 'cell2location' despite setting the PYTHONNOUSERSITE param
#208
sunnyzwu
closed
1 year ago
1
Cell2location on Slide-seq data + over 100 cell types in my single-cell reference
#207
frankligy
closed
1 year ago
3
RuntimeError when using cell2location on MacOS (M1)
#206
sarahshuang
closed
3 months ago
11
Discrepancy in the average number of cells per spot between the input and prediction
#205
abayegan
closed
1 year ago
2
I don't have the raw count data, how can I do to deal with the mod.train() error
#204
FanZhang9
opened
2 years ago
6
Use new parse use gpu signature
#203
adamgayoso
closed
2 years ago
0
adding-usage-tips
#202
vitkl
closed
2 years ago
0
[Colab] Very slow installation of git repo because checking multiple versions of dependencies
#201
Keerthana910234
closed
2 years ago
1
Conflicting dependency error on Windows
#200
lampirl
opened
2 years ago
6
AttributeError: module 'cell2location' has no attribute 'run_cell2location'
#199
YaoZY157
closed
2 years ago
3
Cell abundance vs proportion? [within-section technical effects lead to misleading cell abundance estimates]
#198
livyring
opened
2 years ago
6
Cell type proportion per spot overrepresenting transcriptionally active cell types?
#197
mgrantpeters
opened
2 years ago
1
Extracting the spot barcodes of interested cell types after deconvolution
#196
Zhuang-Bio
closed
2 years ago
1
reloading data - RuntimeError: self.samples is missing, please run self.export_posterior() first
#195
livyring
opened
2 years ago
4
Fix history plotting bug
#194
yozhikoff
closed
2 years ago
0
spacejam (Nanostring WTA) cell2location model and tutorial
#193
AlexanderAivazidis
closed
2 years ago
0
AMD GPU support
#192
czackl
closed
1 year ago
1
Saving for QC and results plots.
#191
bednarsky
opened
2 years ago
14
Passing axis to mod.plot_history raises AttributeError
#190
bednarsky
closed
2 years ago
2
Improved posterior quantile computation
#186
vitkl
closed
1 year ago
1
cell2location.models.RegressionModel.load takes one hour with GPU and seems to be retraining
#185
bednarsky
closed
2 years ago
13
Setup amortized network for Cell2location
#184
canergen
closed
1 year ago
9
About the cell2location.plt.mapping_video.
#182
archanabhardwaj
opened
2 years ago
1
Improving downstream analysis NMF workflow
#181
vitkl
closed
2 years ago
0
How to show the min,med&max values on the multiple cell types plot
#180
rue1996
opened
2 years ago
3
Independent residual factor model
#179
vitkl
opened
2 years ago
0
Option to train the model with residual non-negative factors
#178
vitkl
opened
2 years ago
0
Reconstruction accuracy and QC plots
#177
wangjiawen2013
opened
2 years ago
3
Location-specific sampling of cell type signatures and background
#175
vitkl
opened
2 years ago
0
QC history plot error
#173
archanabhardwaj
closed
1 year ago
1
Question about numerically synthesizing mouse brain spatial dataset
#172
ZhanYangen
closed
1 year ago
2
The kernel appears to have died. It will restart automatically.
#171
lifan18
closed
2 years ago
2
Fail to import cell2location in HPC
#170
WT215
closed
2 years ago
3
Error in saving the signature output
#169
archanabhardwaj
closed
1 year ago
2
CUDA out of Memory while training the RegressionModel
#168
Rajarshi1001
closed
1 year ago
9
how to install cell2location on windows by anaconda3
#167
littleKaixin
closed
1 year ago
2
fix protobuf==3.20.1
#166
vitkl
closed
2 years ago
0
multi batches spatial datasets
#165
wangjiawen2013
closed
2 years ago
1
multi-samples integration
#164
wangjiawen2013
closed
1 year ago
4
Fail to import run_regression
#163
TaoShiyue
closed
2 years ago
2
Fail to import LocationModelWTA
#162
GoodSuun
closed
2 years ago
3
why w_s,f follow gamma distribution
#161
caiquanyou
closed
1 year ago
2
Conflicting dependency error on Windows machine
#160
rimelof
opened
2 years ago
7
Cell-type specific amortising NN & necessary changes to AutoGuide
#159
vitkl
opened
2 years ago
0
Removing old code (pymc-based) and updating the tutorial
#157
vitkl
closed
2 years ago
0
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