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Starlitnightly
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omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
https://starlitnightly.github.io/omicverse/
GNU General Public License v3.0
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Hoping for Updates to Pandas and NumPy Versions in Future Releases, Along with Other Suggestions
#216
GhostInTheShellwjc
opened
2 days ago
0
ValueError: 'box_aspect' and 'fig_aspect' must be positive
#215
GhostInTheShellwjc
closed
2 days ago
1
UnicodeEncodeError using SCSA
#214
pandaqiuqiu
opened
1 week ago
1
I tried to use GPU to run the ov.pp.qc function, but I got a lot of NaNs. Is it because the set filter conditions did not work? Do I need to delete them manually later? Thank you very much for your answer.
#213
xzt199610
opened
1 week ago
1
I want to reproduce the examples in the code tutorial, but the following problem occurs. Is it due to version inconsistency?
#212
xzt199610
opened
2 weeks ago
3
Bugs that occur when running VIA
#211
Zstark11
opened
2 weeks ago
7
ov.utils.cluster:LinAlgError: 28-th leading minor of the array is not positive definite,ValueError: Fitting the mixture model failed because some components have ill-defined empirical covariance (for instance caused by singleton or collapsed samples). Try to decrease the number of components, or increase reg_covar.
#210
GhostInTheShellwjc
closed
2 weeks ago
0
ov.space.pySTAligner:AttributeError: 'ArrayView' object has no attribute 'todense'
#209
GhostInTheShellwjc
opened
2 weeks ago
2
Bug in ov.space.svg():TypingError:Failed in nopython mode pipeline (step: nopython frontend) Untyped global name 'tqdm': Cannot determine Numba type of <class 'type'>
#208
GhostInTheShellwjc
opened
2 weeks ago
6
Bug in ov.space.svg module :KeyError "None of [Index(['array_row', 'array_col'], dtype='object')] are in the [columns]"&&KeyError: 'spatial'
#207
GhostInTheShellwjc
closed
2 weeks ago
0
A small expectation for the pySIMBA module
#206
GhostInTheShellwjc
closed
2 weeks ago
0
NotImplementedError when using the function ov.pp.scale()
#205
GhostInTheShellwjc
opened
2 weeks ago
1
error in Function: ov.pl.embedding_celltype
#204
summer-4-DESIGH
opened
2 weeks ago
2
KeyError in ov.pp.preprocess
#203
GhostInTheShellwjc
closed
2 weeks ago
0
Varm 'replaced' needs to be of one of np.ndarray
#202
CarrieChen0530
opened
2 weeks ago
3
Add security check
#201
HendricksJudy
opened
3 weeks ago
1
pydeseq2 version conflicts with omicverse 1.6.8
#200
pandaqiuqiu
opened
3 weeks ago
1
Can Not get marker genes for a given cell type
#199
Dexterssssss
closed
3 weeks ago
2
Efficiency changes in pyWCGNA
#198
cypher004
opened
3 weeks ago
1
Unable to draw PCA
#197
Dexterssssss
closed
1 week ago
4
ImportError: cannot import name '_handle_mask_var' from 'scanpy.preprocessing._pca' in omicverse with rapids_singlecell
#196
pandaqiuqiu
closed
3 weeks ago
1
updated the tutorials of scMulan.
#195
DBinary
closed
4 weeks ago
0
A bug when running ov.pp.qc
#194
Zstark11
closed
4 weeks ago
2
AttributeError: can't set attribute 'categories'
#193
GhostInTheShellwjc
opened
1 month ago
1
Dependency error&Function Error
#192
GhostInTheShellwjc
closed
2 weeks ago
4
Installation issue
#191
RunyuXia
opened
1 month ago
1
Fix conflict between scanpy and omicverse
#190
HendricksJudy
closed
1 month ago
1
scipy version adaptation issues
#189
Zstark11
closed
3 weeks ago
2
Error reported when running gsea_obj.feedback function
#187
Zstark11
closed
3 weeks ago
1
Inquiry about Integrating Bulk RNA-seq Data with Single-Cell Data in OmicVerse
#186
md26meng
closed
1 month ago
0
fix the bug of pydeseq2
#185
DBinary
closed
1 month ago
0
gsea_obj.enrichment() error
#184
WeiQin2001
opened
1 month ago
2
ModuleNotFoundError: No module named 'transformers.generation'
#183
komais
closed
1 month ago
1
bulktb.gnn_generate() function error
#182
WeiQin2001
opened
1 month ago
0
it is perfect!
#181
Cong1975
opened
1 month ago
1
bulktb.gnn_load('./save_model/gnn.pth') error
#180
WeiQin2001
opened
1 month ago
0
ov.bulk2single.bulk2single_plot_cellprop（）error
#179
WeiQin2001
opened
1 month ago
2
ov.single.cellfategenie function error #175
#178
jung233
closed
1 month ago
1
Fix a bug in SCSA
#177
jung233
closed
1 month ago
0
ModuleNotFoundError: No module named 'pandas.core.indexes.numeric' when using SCSA
#176
jung233
opened
1 month ago
5
ov.single.cellfategenie function error
#175
WeiQin2001
opened
1 month ago
3
cnmf_obj.k_selection_plot() get ValueError: Number of labels is 2. Valid values are 2 to n_samples - 1 (inclusive)
#174
Roger-GOAT
closed
1 month ago
1
A bug in function ov.space.svg in OV 1.6.7
#173
Zstark11
closed
1 month ago
2
self.bulk_seq_group in _bulk2single.py is defined but not use
#172
hitwbt
opened
1 month ago
0
Dependency Error and AttributeError in Omicverse
#171
drkuang
closed
1 month ago
3
Update gseapy
#170
Rafael-Silva-Oliveira
closed
1 month ago
1
error in bulk deg part
#169
baconchan
opened
2 months ago
2
error in CellPhoneDB
#168
baconchan
opened
2 months ago
2
scvi version bug
#167
Famingzhao
opened
2 months ago
5
bulktb.vae_train function error
#166
WeiQin2001
opened
2 months ago
0
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