Skip to content

Commit

Permalink
add lisi score calculation and annotations
Browse files Browse the repository at this point in the history
  • Loading branch information
ranzhang authored and ranzhang committed Dec 2, 2024
1 parent 4b5f792 commit 2d0f203
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ gene expression count matrix (rna_adata.X)

gene annotation (rna_adata.var)

cell annotation (rna_adata.obs): to enable cross-species imputation/alignment and batch correction, rna_adata.obs needs to contain "species" column (e.g. '0' 'human' 'mouse') and "batch" columns (e.g. '1' '0').
cell annotation (rna_adata.obs): to enable cross-species imputation/alignment and batch correction, rna_adata.obs needs to contain a "species" column (e.g. '0' 'human' 'mouse'). Optional columns includes: "batch" columns (e.g. '1' '0') that can represent batch, condition, or organs that the cells are collected from. Columns that represents cell type or tissue information, which can be used on the prediction and validation stage and is indicated using the --group argument.

Example input data: ../data/example.h5ad

Expand All @@ -48,14 +48,14 @@ Example input data: ../data/example.h5ad

### 1. Cross-species alignment:

```python ./run_pred.py --input_h5ad $input_h5ad --train train --predict embedding```
```python ./run_pred.py --input_h5ad $input_h5ad --train train --group celltype --predict embedding```
Where input_h5ad is the path of input h5ad file


### 2. Cross-species imputation:

For cross-species gene expression prediction, the target species and batch need to be specified so that the output gene expression profile is translated from all current data to the target batch and species:
`python ./run_pred.py --input_h5ad $input_h5ad --train train --predict expression --target_species 1 --target_batch 0`
`python ./run_pred.py --input_h5ad $input_h5ad --train train --predict expression --target_species 1 --target_batch 0 --group celltype`


## Hyperparameter tuning:
Expand Down

0 comments on commit 2d0f203

Please sign in to comment.