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.
2026-03-27 07:09:27 +08:00 · 2026-03-03 07:15:36 -05:00
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--- a/scientific-skills/jaspar-database/references/api_reference.md
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+# JASPAR API v1 Reference
+
+## Base URL
+
+```
+https://jaspar.elixir.no/api/v1/
+```
+
+No authentication required. Responses are JSON.
+
+## Core Endpoints
+
+### `GET /matrix/`
+
+Search and list TF binding profiles.
+
+**Parameters:**
+
+| Parameter | Type | Description | Example |
+|-----------|------|-------------|---------|
+| `name` | string | TF name (partial match) | `CTCF` |
+| `matrix_id` | string | Exact matrix ID | `MA0139.1` |
+| `collection` | string | Collection name | `CORE` |
+| `tax_group` | string | Taxonomic group | `vertebrates` |
+| `species` | string | Species name or tax ID | `9606`, `Homo sapiens` |
+| `tf_class` | string | TF structural class | `C2H2 zinc finger factors` |
+| `tf_family` | string | TF family | `BEN domain factors` |
+| `type` | string | Experimental method | `ChIP-seq`, `SELEX` |
+| `version` | string | `latest` or specific version | `latest` |
+| `page` | int | Page number | `1` |
+| `page_size` | int | Results per page (max 500) | `25` |
+
+**Response:**
+```json
+{
+  "count": 1210,
+  "next": "https://jaspar.elixir.no/api/v1/matrix/?page=2",
+  "previous": null,
+  "results": [
+    {
+      "matrix_id": "MA0139.1",
+      "name": "CTCF",
+      "collection": "CORE",
+      "tax_group": "vertebrates"
+    }
+  ]
+}
+```
+
+### `GET /matrix/{id}/`
+
+Fetch a specific matrix with full details.
+
+**Response:**
+```json
+{
+  "matrix_id": "MA0139.1",
+  "name": "CTCF",
+  "collection": "CORE",
+  "tax_group": "vertebrates",
+  "pfm": {
+    "A": [87, 167, 281, ...],
+    "C": [291, 145, 49, ...],
+    "G": [76, 414, 504, ...],
+    "T": [205, 114, 27, ...]
+  },
+  "consensus": "CCGCGNGGNGGCAG",
+  "length": 19,
+  "species": [{"tax_id": 9606, "name": "Homo sapiens"}],
+  "class": ["C2H2 zinc finger factors"],
+  "family": ["BEN domain factors"],
+  "type": "ChIP-seq",
+  "uniprot_ids": ["P49711"],
+  "pubmed_ids": ["19172222"],
+  "version": 1,
+  "latest": true
+}
+```
+
+### `GET /matrix/{id}/logo/`
+
+Returns SVG/PNG logo for the matrix.
+
+**Parameters:** `format` = `svg` (default) or `png`
+
+### `GET /taxon/`
+
+List available species/taxa.
+
+### `GET /tf_class/`
+
+List available TF structural classes.
+
+### `GET /tf_family/`
+
+List available TF families.
+
+### `GET /collection/`
+
+List available collections.
+
+## Matrix ID Format
+
+```
+MA{number}.{version}
+```
+
+- `MA` prefix = Manual curation
+- `PB` prefix = Published (automatic)
+- `UN` prefix = Unvalidated
+- Version increments when profile is updated
+
+## Common Matrix IDs
+
+| Matrix ID | TF | Species | Method |
+|-----------|-----|---------|--------|
+| `MA0139.1` | CTCF | Human | ChIP-seq |
+| `MA0098.3` | ETS1 | Human | SELEX |
+| `MA0107.1` | RELA (NF-kB p65) | Human | SELEX |
+| `MA0048.2` | NHLH1 | Human | SELEX |
+| `MA0079.4` | SP1 | Human | SELEX |
+| `MA0080.4` | SPI1 (PU.1) | Human | ChIP-seq |
+| `MA0025.2` | NFIL3 | Human | SELEX |
+| `MA0002.2` | RUNX1 | Human | SELEX |
+| `MA0004.1` | Arnt | Mouse | SELEX |
+| `MA0009.2` | TAL1::GATA1 | Human | SELEX |
+
+## TF Classes (partial list)
+
+- `C2H2 zinc finger factors`
+- `Basic leucine zipper factors (bZIP)`
+- `Basic helix-loop-helix factors (bHLH)`
+- `Homeodomain factors`
+- `Forkhead box (FOX) factors`
+- `ETS-domain factors`
+- `Nuclear hormone receptors`
+- `Tryptophan cluster factors`
+- `p53-like transcription factors`
+- `STAT factors`
+- `MADS box factors`
+- `T-box factors`
+
+## Python Example: Batch Download
+
+```python
+import requests, json, time
+
+def download_all_human_profiles(output_file="jaspar_human_profiles.json"):
+    """Download all human TF profiles from JASPAR CORE collection."""
+    url = "https://jaspar.elixir.no/api/v1/matrix/"
+    params = {
+        "collection": "CORE",
+        "species": "9606",
+        "version": "latest",
+        "page_size": 500,
+        "page": 1
+    }
+
+    profiles = []
+    while True:
+        response = requests.get(url, params=params)
+        data = response.json()
+        profiles.extend(data["results"])
+
+        if not data["next"]:
+            break
+        params["page"] += 1
+        time.sleep(0.5)
+
+    # Fetch full details for each profile
+    full_profiles = []
+    for p in profiles:
+        detail_url = f"https://jaspar.elixir.no/api/v1/matrix/{p['matrix_id']}/"
+        detail = requests.get(detail_url).json()
+        full_profiles.append(detail)
+        time.sleep(0.1)  # Be respectful
+
+    with open(output_file, "w") as f:
+        json.dump(full_profiles, f)
+
+    return full_profiles
+```