bowang-lab scGPT issues

bowang-lab / scGPT

https://scgpt.readthedocs.io/en/latest/

MIT License

1.05k stars 206 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Data preprocessing for perturbation

#271 BoAtNY closed 3 days ago
2
Inconsistent Data Preprocessing in Tutorial_ZeroShot_Integration.ipynb

#270 nc1m opened 1 week ago
1
scgpt

#269 bioinf-gif closed 3 weeks ago
1
Issues with tokenization in embedding generation script

#268 xqiu625 closed 3 days ago
1
scb

#267 wenhao2024 closed 3 days ago
1
`tutorials/Tutorial_Perturbation.ipynb` - `pert_pad_id` is set to 0

#266 qianachen closed 3 weeks ago
1
Code for testing the model on the Adamson and Replogle datasets

#265 gefeiwang opened 1 month ago
1
what's the "loss_gen" during pre-training stage

#264 lishensuo opened 1 month ago
0
Census VERSION is not valid in cellxgene/data_config.py

#263 Fredrick-Kakembo opened 1 month ago
1
Cell Type Classification Datasets

#262 nc1m opened 1 month ago
1
Cell Type Annotation Tutorial - Added UMAP of Embeddings

#261 ManuelSokolov opened 1 month ago
0
Install issue with scvi dependency

#260 ERSchultz closed 3 weeks ago
1
Issue on Tutorial Annotation - UMAP is not from Learned Cell Embeddings

#259 ManuelSokolov opened 1 month ago
2
Update preprocess.py

#258 Liripo closed 1 month ago
1
Code to pretrain model from scratch on my own dataset

#257 igor-sadalski opened 1 month ago
1
Assistance Needed with Adding Cell-Type Column to h5ad File for scGPT Hub Submission

#256 msyed786 opened 2 months ago
1
Unable to resolve dependencies when fixing the lock file in developer mode

#255 igor-sadalski opened 2 months ago
2
`layer_data.A` in `preprocess.y`

#254 sklarz-bgu closed 3 weeks ago
3
TypeError: bwd(): incompatible function arguments.

#253 IchigoJiken opened 2 months ago
0
link to raw data origin of Immune Human dataset

#252 talbCgen opened 2 months ago
0
Why is X not standarized using the preprocess() funnction in Tutorial_Reference_Mapping.ipynb?

#251 Ale9806 opened 2 months ago
0
Why is X not standarized using the preprocess() funnction in the tutorial?

#250 Ale9806 closed 2 months ago
0
Request for FlashAttention v2 Support

#249 qianachen opened 2 months ago
0
about the masking procedure

#248 FUminlee opened 2 months ago
2
AttributeError: 'MultiheadAttention' object has no attribute 'Wqkv'

#247 yuhan1li opened 2 months ago
1
Try to reconstruct the exp

#246 YOU-k opened 2 months ago
1
An error when trying to predict perturbations in reploge dataset

#245 HelloWorldLTY opened 2 months ago
0
Poor quality of batch integration

#244 chrarnold opened 2 months ago
0
Bridging the gap: Creating a (corrected and/or imputed) gene expression matrix after the embedding

#243 chrarnold opened 2 months ago
0
About the pertaining part

#242 FUminlee opened 2 months ago
1
Help with the installation on colab

#241 bitcometz opened 3 months ago
2
question about gene2idx order

#240 hongruhu opened 3 months ago
0
33 million normal cells not match CELLxGENE census version 15 May 2023

#239 litxiaoyao opened 3 months ago
8
expression embeddings tutorial

#237 cherrysu0999 opened 3 months ago
0
Chemical perturbation exercise

#236 00dylan00 opened 3 months ago
0
Cell Type Annotation scGPT_Human model state dict not correct

#235 ManuelSokolov opened 3 months ago
2
fix a depreciated .A issue from newer versions of scipy

#234 davidliwei opened 3 months ago
0
CellxGene configure version issue in the current repo

#233 YubinXie closed 3 months ago
2
Installation Issues

#232 liusi2019 opened 3 months ago
1
Perturbation effects on atac/peak region

#231 Saranya-Balachandran opened 3 months ago
0
Iterative process of the generative pretraining

#230 olavdc opened 3 months ago
0
No 'compute_perturbation_metrics' from 'scgpt.utils'

#229 Heinyxiao opened 4 months ago
1
[help needed] complete loss of performance after fine-tuning for integration

#228 xoelmb opened 4 months ago
0
Multiple GPU support? (Fine-tuning)

#227 xoelmb opened 4 months ago
1
Pretraining dataset for pan-cancer scGPT model

#226 andrewsong90 opened 4 months ago
0
74% of the tokens in adata.var[feature_name] are not in vocab. Please check if using the correct vocab and token_col.

#225 Jasmine710-lab opened 4 months ago
1
Max sequence length differs in training and test sets

#224 tjeng opened 4 months ago
0
Generation steps during inference

#223 noob000007 opened 4 months ago
1
"Learning objective for pretraining" vs "Gene expression prediction."

#222 noob000007 opened 4 months ago
4
Question about CategoryValueEncoder and ContinuousValueEncoder for value encoder

#221 cristinaperez9 opened 4 months ago
2