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https://github.com/K-Dense-AI/claude-scientific-skills.git
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- 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.
183 lines
4.3 KiB
Markdown
183 lines
4.3 KiB
Markdown
# JASPAR API v1 Reference
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## Base URL
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```
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https://jaspar.elixir.no/api/v1/
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```
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No authentication required. Responses are JSON.
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## Core Endpoints
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### `GET /matrix/`
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Search and list TF binding profiles.
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**Parameters:**
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| Parameter | Type | Description | Example |
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|-----------|------|-------------|---------|
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| `name` | string | TF name (partial match) | `CTCF` |
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| `matrix_id` | string | Exact matrix ID | `MA0139.1` |
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| `collection` | string | Collection name | `CORE` |
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| `tax_group` | string | Taxonomic group | `vertebrates` |
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| `species` | string | Species name or tax ID | `9606`, `Homo sapiens` |
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| `tf_class` | string | TF structural class | `C2H2 zinc finger factors` |
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| `tf_family` | string | TF family | `BEN domain factors` |
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| `type` | string | Experimental method | `ChIP-seq`, `SELEX` |
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| `version` | string | `latest` or specific version | `latest` |
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| `page` | int | Page number | `1` |
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| `page_size` | int | Results per page (max 500) | `25` |
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**Response:**
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```json
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{
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"count": 1210,
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"next": "https://jaspar.elixir.no/api/v1/matrix/?page=2",
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"previous": null,
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"results": [
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{
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"matrix_id": "MA0139.1",
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"name": "CTCF",
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"collection": "CORE",
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"tax_group": "vertebrates"
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}
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]
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}
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```
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### `GET /matrix/{id}/`
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Fetch a specific matrix with full details.
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**Response:**
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```json
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{
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"matrix_id": "MA0139.1",
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"name": "CTCF",
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"collection": "CORE",
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"tax_group": "vertebrates",
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"pfm": {
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"A": [87, 167, 281, ...],
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"C": [291, 145, 49, ...],
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"G": [76, 414, 504, ...],
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"T": [205, 114, 27, ...]
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},
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"consensus": "CCGCGNGGNGGCAG",
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"length": 19,
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"species": [{"tax_id": 9606, "name": "Homo sapiens"}],
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"class": ["C2H2 zinc finger factors"],
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"family": ["BEN domain factors"],
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"type": "ChIP-seq",
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"uniprot_ids": ["P49711"],
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"pubmed_ids": ["19172222"],
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"version": 1,
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"latest": true
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}
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```
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### `GET /matrix/{id}/logo/`
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Returns SVG/PNG logo for the matrix.
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**Parameters:** `format` = `svg` (default) or `png`
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### `GET /taxon/`
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List available species/taxa.
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### `GET /tf_class/`
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List available TF structural classes.
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### `GET /tf_family/`
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List available TF families.
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### `GET /collection/`
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List available collections.
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## Matrix ID Format
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```
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MA{number}.{version}
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```
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- `MA` prefix = Manual curation
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- `PB` prefix = Published (automatic)
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- `UN` prefix = Unvalidated
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- Version increments when profile is updated
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## Common Matrix IDs
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| Matrix ID | TF | Species | Method |
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|-----------|-----|---------|--------|
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| `MA0139.1` | CTCF | Human | ChIP-seq |
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| `MA0098.3` | ETS1 | Human | SELEX |
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| `MA0107.1` | RELA (NF-kB p65) | Human | SELEX |
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| `MA0048.2` | NHLH1 | Human | SELEX |
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| `MA0079.4` | SP1 | Human | SELEX |
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| `MA0080.4` | SPI1 (PU.1) | Human | ChIP-seq |
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| `MA0025.2` | NFIL3 | Human | SELEX |
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| `MA0002.2` | RUNX1 | Human | SELEX |
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| `MA0004.1` | Arnt | Mouse | SELEX |
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| `MA0009.2` | TAL1::GATA1 | Human | SELEX |
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## TF Classes (partial list)
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- `C2H2 zinc finger factors`
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- `Basic leucine zipper factors (bZIP)`
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- `Basic helix-loop-helix factors (bHLH)`
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- `Homeodomain factors`
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- `Forkhead box (FOX) factors`
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- `ETS-domain factors`
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- `Nuclear hormone receptors`
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- `Tryptophan cluster factors`
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- `p53-like transcription factors`
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- `STAT factors`
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- `MADS box factors`
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- `T-box factors`
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## Python Example: Batch Download
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```python
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import requests, json, time
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def download_all_human_profiles(output_file="jaspar_human_profiles.json"):
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"""Download all human TF profiles from JASPAR CORE collection."""
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url = "https://jaspar.elixir.no/api/v1/matrix/"
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params = {
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"collection": "CORE",
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"species": "9606",
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"version": "latest",
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"page_size": 500,
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"page": 1
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}
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profiles = []
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while True:
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response = requests.get(url, params=params)
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data = response.json()
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profiles.extend(data["results"])
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if not data["next"]:
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break
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params["page"] += 1
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time.sleep(0.5)
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# Fetch full details for each profile
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full_profiles = []
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for p in profiles:
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detail_url = f"https://jaspar.elixir.no/api/v1/matrix/{p['matrix_id']}/"
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detail = requests.get(detail_url).json()
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full_profiles.append(detail)
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time.sleep(0.1) # Be respectful
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with open(output_file, "w") as f:
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json.dump(full_profiles, f)
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return full_profiles
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```
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