STOmics Stereopy issues

STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.

MIT License

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issues

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seurat object

#250 Carissimo opened 3 months ago
1
Install Failed

#249 eisascience closed 3 months ago
1
No module named 'stereo.image.segmentation.seg_utils'

#248 zy-fang closed 1 month ago
1
Assistance Required in Creating Reference Samples for SingleR

#247 JungTaeKim103 closed 3 months ago
2
RuntimeError: CUDA out of memory at cell_seg

#246 Zjianglin closed 2 months ago
2
Connectivity for spatial_neighbors on cell_bin data

#245 garrick-chang opened 4 months ago
0
why the code for import image into seurat object is disabled by default in the latest h5ad2rds.R?

#244 zhangyz1997 opened 4 months ago
0
Changes in expression patterns after High Resolution Matrix Export.

#243 JungTaeKim103 closed 4 months ago
3
Error reading in cell binned gef file

#242 LeonieKuechenhoff closed 4 months ago
1
Error in pickle save object

#241 mengchengyao closed 4 months ago
3
data.tl.phenograph use error

#240 ffZhang2003 closed 4 months ago
1
annh5ad2rds.R: Error: Missing required datasets 'levels' and 'values'

#239 MISAKA-DaYu closed 5 months ago
2
data.plt.cells_plotting

#238 heziqing closed 4 months ago
2
stereodata.tl.raw_checkpoint(): TypeError: 'NoneType' object is not callable

#237 THZ34 closed 5 months ago
0
stereo.core.StPipeline.find_marker_genes in multi-sample

#236 sparkumr opened 5 months ago
5
slideio==0.5.225 is not available in PyPI.

#235 magcurly closed 5 months ago
4
Run error of "batch_qc": OSError: [Errno 6] No such device or address

#234 Zjianglin opened 6 months ago
8
how E10 score is calculate?

#233 limin321 closed 5 months ago
1
ins.add_selected_area() Exception: The selected area's data cannot be empty!

#232 UnseenAnchor closed 5 months ago
2
two slice can not be use for time serise page analysis,It getting error with ms_data.plt.paga_time_series_plot funciton

#231 honghh2018 closed 5 months ago
3
the batch qc in ms_data.tl.batch_qc(scope=slice_generator[:],mode='integrate', cluster_res_key='leiden', report_path='./batch_qc', res_key='batch_qc') getting error

#230 honghh2018 closed 4 months ago
3
the h5ad read error for st.io.read_h5ad('data1.h5ad')

#229 honghh2018 closed 5 months ago
2
Can I read h5ad file, and convert it into different bin resolution?

#228 YuchiQiu closed 5 months ago
1
Update plot_cluster_traj.py

#227 Tianyi-Summer closed 6 months ago
0
Update plot_vec.py

#226 Tianyi-Summer closed 6 months ago
0
Related issues about GEF file

#225 ultraypy closed 5 months ago
1
Segmentation fault(core dumped) on tissue_extraction_to_bgef

#224 OswaldZhang opened 6 months ago
2
"High Resolution Matrix Export" is not selecting regions of interest

#223 bmill3r closed 6 months ago
4
Problem with installation, no biopython in requirements.txt

#222 gitstanoje closed 6 months ago
2
Convert the data from bin100 to bin50

#221 Yungong1 closed 7 months ago
5
Can not select any ROI using data.plt.interact_spatial_scatter()

#220 cynthier closed 6 months ago
3
ms_data.integrate TypeError: merge() got an unexpected keyword argument 'var_type'

#219 Nh-code closed 6 months ago
3
MSData _var_type can be set as a "union"?

#218 Nh-code closed 7 months ago
0
Black rectangle at the bottom of Spatial plot by using transformed seurat Rds object?

#217 Li-ZhiD closed 4 months ago
2
Cell Segmentation.ipynb: Error: module 'torch' has no attribute 'Tensor'

#216 vladimirkovacevic closed 7 months ago
1
KeyError: "Unable to synchronously open object (object 'cellBin' doesn't exist)"

#215 yang050036 closed 7 months ago
7
pep517 mode required

#214 vladimirkovacevic closed 7 months ago
2
No module named 'stereo.core.ms_pipeline'

#213 vladimirkovacevic closed 7 months ago
2
data.plt.ccc_circos_plot does not exist any more

#212 vladimirkovacevic closed 7 months ago
1
st.io.read_h5ad still used in Tutorials

#211 vladimirkovacevic closed 7 months ago
1
Input data not available for CCC tutorial

#210 vladimirkovacevic closed 7 months ago
1
Can't perform High Resolution Matrix Export!

#209 Li-ZhiD closed 6 months ago
4
ValueError: Length mismatch: Expected axis has 1 elements, new values have 261800 elements during data.tl.cell_cell_communication

#208 THZ34 closed 8 months ago
0
ST(version0.14.0b1) has problem with anndata, which causes func read_h5ad failed in anndata,scanpy and stereopy itself.

#207 14MBD4 closed 8 months ago
0
Discrepancy between adata.X and data.exp_matrix when reading loom files using scanpy

#206 WeipengMO closed 4 months ago
4
how to change a seurat file into stereopy

#205 Dan-121 opened 8 months ago
2
A rotation function would be quite intriguing?

#204 Li-ZhiD closed 8 months ago
2
How to download the demo data in the tutorials？

#203 suye0620 closed 8 months ago
2
ValueError: All arrays must be of the same length

#202 Biomamba closed 7 months ago
1
Unable to reproduce the results in the report through stereopy

#201 AfterDream closed 8 months ago
0

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