mirror of
https://github.com/K-Dense-AI/claude-scientific-skills.git
synced 2026-03-27 07:09:27 +08:00
Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation
- Introduced a comprehensive RNA velocity analysis pipeline using scVelo, including data loading, preprocessing, velocity estimation, and visualization. - Added a script for running RNA velocity analysis with customizable parameters and output options. - Created detailed documentation for IQ-TREE 2 phylogenetic inference, covering command syntax, model selection, bootstrapping methods, and output interpretation. - Included references for velocity models and their mathematical framework, along with a comparison of different models. - Enhanced the scVelo skill documentation with installation instructions, use cases, and best practices for RNA velocity analysis.
This commit is contained in:
huangkuanlin
191
scientific-skills/gtex-database/references/api_reference.md
Normal file
191
scientific-skills/gtex-database/references/api_reference.md
Normal file
@@ -0,0 +1,191 @@
|
||||
# GTEx API v2 Reference
|
||||
|
||||
## Base URL
|
||||
|
||||
```
|
||||
https://gtexportal.org/api/v2/
|
||||
```
|
||||
|
||||
All endpoints accept GET requests. Responses are JSON. No authentication required.
|
||||
|
||||
## Common Query Parameters
|
||||
|
||||
| Parameter | Description | Example |
|
||||
|-----------|-------------|---------|
|
||||
| `gencodeId` | GENCODE gene ID with version | `ENSG00000130203.10` |
|
||||
| `geneSymbol` | Gene symbol | `APOE` |
|
||||
| `variantId` | GTEx variant ID | `chr17_45413693_C_T_b38` |
|
||||
| `tissueSiteDetailId` | Tissue identifier | `Whole_Blood` |
|
||||
| `datasetId` | Dataset version | `gtex_v10` |
|
||||
| `itemsPerPage` | Results per page | `250` |
|
||||
| `page` | Page number (0-indexed) | `0` |
|
||||
|
||||
## Endpoint Reference
|
||||
|
||||
### Expression Endpoints
|
||||
|
||||
#### `GET /expression/medianGeneExpression`
|
||||
|
||||
Median TPM expression for a gene across tissues.
|
||||
|
||||
**Parameters:** `gencodeId`, `datasetId`, `itemsPerPage`
|
||||
|
||||
**Response fields:**
|
||||
```json
|
||||
{
|
||||
"data": [
|
||||
{
|
||||
"gencodeId": "ENSG00000130203.10",
|
||||
"geneSymbol": "APOE",
|
||||
"tissueSiteDetailId": "Liver",
|
||||
"tissueSiteDetail": "Liver",
|
||||
"median": 2847.9,
|
||||
"unit": "TPM",
|
||||
"datasetId": "gtex_v10"
|
||||
}
|
||||
]
|
||||
}
|
||||
```
|
||||
|
||||
#### `GET /expression/geneExpression`
|
||||
|
||||
Full expression distribution (box plot data) per tissue.
|
||||
|
||||
**Parameters:** `gencodeId`, `tissueSiteDetailId`, `datasetId`
|
||||
|
||||
**Response fields:**
|
||||
- `data[].tissueExpressionData.data`: array of TPM values per sample
|
||||
|
||||
### Association (QTL) Endpoints
|
||||
|
||||
#### `GET /association/singleTissueEqtl`
|
||||
|
||||
Significant single-tissue cis-eQTLs.
|
||||
|
||||
**Parameters:** `gencodeId` OR `variantId`, `tissueSiteDetailId` (optional), `datasetId`
|
||||
|
||||
**Response fields:**
|
||||
```json
|
||||
{
|
||||
"data": [
|
||||
{
|
||||
"gencodeId": "ENSG00000169174.14",
|
||||
"geneSymbol": "PCSK9",
|
||||
"variantId": "chr1_55516888_G_GA_b38",
|
||||
"snpId": "rs72646508",
|
||||
"tissueSiteDetailId": "Liver",
|
||||
"slope": -0.342,
|
||||
"slopeStandardError": 0.051,
|
||||
"pval": 3.2e-11,
|
||||
"qval": 2.1e-8,
|
||||
"maf": 0.089,
|
||||
"datasetId": "gtex_v10"
|
||||
}
|
||||
]
|
||||
}
|
||||
```
|
||||
|
||||
**Key fields:**
|
||||
- `slope`: effect of alt allele on expression (log2 scale after rank normalization)
|
||||
- `pval`: nominal p-value
|
||||
- `qval`: FDR-adjusted q-value
|
||||
- `maf`: minor allele frequency in the GTEx cohort
|
||||
|
||||
#### `GET /association/singleTissueSqtl`
|
||||
|
||||
Significant single-tissue sQTLs (splicing).
|
||||
|
||||
**Parameters:** Same as eQTL endpoint
|
||||
|
||||
#### `GET /association/egene`
|
||||
|
||||
All eGenes (genes with ≥1 significant eQTL) in a tissue.
|
||||
|
||||
**Parameters:** `tissueSiteDetailId`, `datasetId`
|
||||
|
||||
**Response fields:** gene ID, gene symbol, best eQTL variant, p-value, q-value
|
||||
|
||||
### Dataset/Metadata Endpoints
|
||||
|
||||
#### `GET /dataset/tissueSiteDetail`
|
||||
|
||||
List of all available tissues.
|
||||
|
||||
**Parameters:** `datasetId`, `itemsPerPage`
|
||||
|
||||
**Response fields:**
|
||||
- `tissueSiteDetailId`: API identifier (use this in queries)
|
||||
- `tissueSiteDetail`: Display name
|
||||
- `colorHex`: Color for visualization
|
||||
- `samplingSite`: Anatomical location
|
||||
|
||||
#### `GET /reference/gene`
|
||||
|
||||
Gene metadata from GENCODE.
|
||||
|
||||
**Parameters:** `geneSymbol` OR `gencodeId`, `referenceGenomeId` (GRCh38)
|
||||
|
||||
### Variant Endpoints
|
||||
|
||||
#### `GET /variant/variantPage`
|
||||
|
||||
Variant metadata and lookup.
|
||||
|
||||
**Parameters:** `snpId` (rsID) OR `variantId`
|
||||
|
||||
## Tissue IDs Reference (Common Tissues)
|
||||
|
||||
| ID | Display Name |
|
||||
|----|-------------|
|
||||
| `Whole_Blood` | Whole Blood |
|
||||
| `Brain_Cortex` | Brain - Cortex |
|
||||
| `Brain_Hippocampus` | Brain - Hippocampus |
|
||||
| `Brain_Frontal_Cortex_BA9` | Brain - Frontal Cortex (BA9) |
|
||||
| `Liver` | Liver |
|
||||
| `Kidney_Cortex` | Kidney - Cortex |
|
||||
| `Heart_Left_Ventricle` | Heart - Left Ventricle |
|
||||
| `Lung` | Lung |
|
||||
| `Muscle_Skeletal` | Muscle - Skeletal |
|
||||
| `Adipose_Subcutaneous` | Adipose - Subcutaneous |
|
||||
| `Colon_Transverse` | Colon - Transverse |
|
||||
| `Small_Intestine_Terminal_Ileum` | Small Intestine - Terminal Ileum |
|
||||
| `Skin_Sun_Exposed_Lower_leg` | Skin - Sun Exposed (Lower leg) |
|
||||
| `Thyroid` | Thyroid |
|
||||
| `Nerve_Tibial` | Nerve - Tibial |
|
||||
| `Artery_Coronary` | Artery - Coronary |
|
||||
| `Artery_Aorta` | Artery - Aorta |
|
||||
| `Pancreas` | Pancreas |
|
||||
| `Pituitary` | Pituitary |
|
||||
| `Spleen` | Spleen |
|
||||
| `Prostate` | Prostate |
|
||||
| `Ovary` | Ovary |
|
||||
| `Uterus` | Uterus |
|
||||
| `Testis` | Testis |
|
||||
|
||||
## Error Handling
|
||||
|
||||
```python
|
||||
import requests
|
||||
from requests.exceptions import HTTPError, Timeout
|
||||
|
||||
def safe_gtex_query(endpoint, params):
|
||||
url = f"https://gtexportal.org/api/v2/{endpoint}"
|
||||
try:
|
||||
response = requests.get(url, params=params, timeout=30)
|
||||
response.raise_for_status()
|
||||
return response.json()
|
||||
except HTTPError as e:
|
||||
print(f"HTTP error {e.response.status_code}: {e.response.text}")
|
||||
except Timeout:
|
||||
print("Request timed out")
|
||||
except Exception as e:
|
||||
print(f"Error: {e}")
|
||||
return None
|
||||
```
|
||||
|
||||
## Rate Limiting
|
||||
|
||||
GTEx API does not publish explicit rate limits but:
|
||||
- Add 0.5–1s delays between bulk queries
|
||||
- Use data downloads for genome-wide analyses instead of API
|
||||
- Cache results locally for repeated queries
|
||||
Reference in New Issue
Block a user