Update README.md
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README.md
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@@ -115,7 +115,7 @@ OmniCellTOSG_Dataset/
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└── x_name_emb.csv
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```
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> **Notes
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> - Files in `expression_matrix/*.npy` are **sharded partitions** of single-cell expression matrices; merge shards (concatenate/stack) to reconstruct the full matrix for a given source/organ.
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> - `cell_metadata_with_mappings.csv` contains **standardized per-cell annotations** (e.g., tissue, disease, sex, cell type, ontology mappings).
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> - `edge_index.npy`, `s_bio.csv`, `s_name.csv`, and `s_desc.csv` provide the **graph topology** (COO `[2, E]`) and **entity metadata** (biological sequences, names, descriptions).
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@@ -194,7 +194,7 @@ x_name_emb, x_desc_emb, x_bio_emb = pre_embed_text(args, dataset, pretrain_model
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- `"combat_seq"`: apply ComBat-Seq
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- **output_dir** *(str, optional)* — Directory for loader outputs (extracted expression matrix, label,splits).
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> **Returns
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> - `extract_mode="inference"`:
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> - `dataset.data`: `pandas.DataFrame`
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> - `dataset.labels`: `pandas.DataFrame`
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└── x_name_emb.csv
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```
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+
> **Notes:**
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> - Files in `expression_matrix/*.npy` are **sharded partitions** of single-cell expression matrices; merge shards (concatenate/stack) to reconstruct the full matrix for a given source/organ.
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| 120 |
> - `cell_metadata_with_mappings.csv` contains **standardized per-cell annotations** (e.g., tissue, disease, sex, cell type, ontology mappings).
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| 121 |
> - `edge_index.npy`, `s_bio.csv`, `s_name.csv`, and `s_desc.csv` provide the **graph topology** (COO `[2, E]`) and **entity metadata** (biological sequences, names, descriptions).
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- `"combat_seq"`: apply ComBat-Seq
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- **output_dir** *(str, optional)* — Directory for loader outputs (extracted expression matrix, label,splits).
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| 196 |
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+
> **Returns:**
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> - `extract_mode="inference"`:
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> - `dataset.data`: `pandas.DataFrame`
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| 200 |
> - `dataset.labels`: `pandas.DataFrame`
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