snap-stanford SATURN issues

snap-stanford / SATURN

MIT License

108 stars 17 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

TypeError: Concatenation requires list-likes containing only strings (or missing values). Offending values found in column integer

#78 zhuojiuqingyun opened 2 days ago
0
STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.

#77 Quianter opened 2 days ago
0
TypeError: descriptor 'union' of 'set' object needs an argument when generate protein embedding

#76 zhuojiuqingyun closed 3 weeks ago
2
Processed frog.h5ad and zebrafish.h5ad

#75 BioAmelie closed 1 month ago
0
RuntimeError: random_ expects 'from' to be less than 'to', but got from=0 >= to=0

#74 Shengqian95 opened 1 month ago
5
question in the dataset

#73 huawen-poppy closed 3 weeks ago
1
questions about the GPU needed for training

#72 zhuojiuqingyun opened 1 month ago
0
Installation issue with torch, version

#71 eisascience closed 3 weeks ago
2
Trouble installing SATURN

#70 weilu1998 closed 2 months ago
0
One of the species is experiencing this issue; can not create XXX.pkl

#69 Joyce121 closed 3 weeks ago
2
ValueError: cannot convert float NaN to integer in loss_string += [f"Avg Loss {species}: {round(np.average(epoch_ave_losses[species]))}"]

#68 micheladallangelo closed 4 weeks ago
2
What computer configuration is required to use this code

#67 idontwanttosayaword closed 3 months ago
1
Program running killed without errors

#66 yilevine closed 2 months ago
2
Can I use spatial transcriptome data as input data?

#65 jekim2022 closed 3 months ago
1
Can I integrate two mouse datasets together?

#64 vishnums007 closed 3 months ago
1
trouble installing the package

#63 RanZhang08 closed 3 months ago
3
Vertebrate-level brain atlas, questions about evolutionary distanct integration

#62 DiracZhu1998 opened 5 months ago
5
question about the input sequences for esm

#61 huawen-poppy closed 3 months ago
1
Which seed is the best in your frog_zebrafish_embryogenesis analysis?

#60 vishnums007 closed 6 months ago
1
The meaning of weights in macrogene?

#59 xuzhougeng closed 6 months ago
1
Example of label transfer with saturn?

#58 dariotommasini closed 6 months ago
1
RuntimeError: indices should be either on cpu or on the same device as the indexed tensor (cpu)

#57 matejasoretic closed 6 months ago
1
Out of memory error when using ESM2 for protein embeddings

#56 dariotommasini closed 6 months ago
5
SyntaxError while running saturn_multiple_seeds.py

#55 vishnums007 closed 6 months ago
2
What are seeds? What is the optimal number of seeds to run?

#54 vishnums007 closed 6 months ago
4
How to preserve all the metadata information in the Anndata from two species to the Final AnnData after integration?

#53 vishnums007 closed 6 months ago
2
Looking for "publicly available protein embedding datasets we have provided."

#52 vishnums007 closed 7 months ago
3
Error when training saturn

#51 Xicici-Yan closed 7 months ago
2
Question: protein embedding, are we only using protein sequences?

#50 YaoLi3 closed 7 months ago
2
KeyError: 'species_gene_name'

#49 matejasoretic closed 7 months ago
2
train.SATURN ERROR. Is a GPU necessary?

#48 Tongbcc closed 7 months ago
1
issue with barcodes if species in the run.csv are provided in a non-alphabetic order

#47 matejasoretic closed 7 months ago
1
New Data Integration

#46 cadyyuheng closed 7 months ago
3
unexpected keyword argument 'miner_type'

#45 matejasoretic closed 7 months ago
0
ValueError: b'Extrapolation not allowed with blending'

#44 cadyyuheng closed 7 months ago
1
Should I must provide the score_adata ?

#43 bitcometz closed 8 months ago
1
Failed for running frog_zebrafish_embryogenesis

#42 bitcometz closed 8 months ago
1
Similar to KeyError: 'cell_type' #4

#41 matejasoretic closed 8 months ago
3
Within species integration

#40 cadyyuheng closed 8 months ago
1
Which ESM2 transformer should be used for proteome-wide embedding generation?

#39 matejasoretic closed 8 months ago
1
Please help with GSE113074_Corrected_combined.annotated_counts.h5ad

#38 bitcometz closed 8 months ago
1
Help with file "zebrafish_cell_types_mapping"

#37 bitcometz closed 8 months ago
2
Error at the biginning of the training step : centroid_weights.append(torch.tensor(species_genes_scores[sgn]))

#36 Hweeseon closed 8 months ago
3
Error with installation？

#35 bitcometz closed 8 months ago
3
Question about availability

#34 levinhein closed 8 months ago
1
Question about centroid creation

#33 otoky closed 8 months ago
1
creation of celltype_map csv

#32 otoky closed 9 months ago
5
train-saturn.py debugging

#31 otoky closed 9 months ago
2
Trouble creating protein embeddings

#30 otoky closed 9 months ago
1
Sapiens (~15gb) data not available

#29 dummyindex closed 9 months ago
1