scarches-docs-complete

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scArches 文档本地镜像全量

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[Knowledge Base]

When & Why to Use This Skill

This Claude skill provides a comprehensive local mirror of the official scArches documentation, designed to assist developers and researchers in single-cell data analysis. It offers instant access to API references, tutorials, and optimized code patterns, facilitating the implementation of deep learning models for genomic architecture surgery without needing to leave the development environment.

Use Cases

  • Case 1: Mapping query single-cell datasets to reference atlases using scArches architecture surgery and transfer learning.
  • Case 2: Quickly retrieving API specifications and parameter details for scarches, scanpy, and torch-based bioinformatics workflows.
  • Case 3: Debugging complex data preprocessing pipelines, such as sparsity removal and data handling for trVAE models.
  • Case 4: Learning and implementing best practices for single-cell transcriptomics analysis through structured official tutorials and example code snippets.
namescarches-docs-complete
descriptionscArches 文档本地镜像全量

Scarches-Docs-Complete Skill

Comprehensive assistance with scarches-docs-complete development, generated from official documentation.

When to Use This Skill

This skill should be triggered when:

  • Working with scarches-docs-complete
  • Asking about scarches-docs-complete features or APIs
  • Implementing scarches-docs-complete solutions
  • Debugging scarches-docs-complete code
  • Learning scarches-docs-complete best practices

Quick Reference

Common Patterns

Quick reference patterns will be added as you use the skill.

Example Code Patterns

Example 1 (python):

train_adata

Example 2 (python):

query_adata

Example 3 (python):

import os
os.chdir('../')
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
warnings.simplefilter(action='ignore', category=UserWarning)

Example 4 (python):

import scanpy as sc
import torch
import scarches as sca
from scarches.dataset.trvae.data_handling import remove_sparsity
import matplotlib.pyplot as plt
import numpy as np
import gdown

Reference Files

This skill includes comprehensive documentation in references/:

  • api.md - Api documentation
  • other.md - Other documentation
  • tutorials.md - Tutorials documentation

Use view to read specific reference files when detailed information is needed.

Working with This Skill

For Beginners

Start with the getting_started or tutorials reference files for foundational concepts.

For Specific Features

Use the appropriate category reference file (api, guides, etc.) for detailed information.

For Code Examples

The quick reference section above contains common patterns extracted from the official docs.

Resources

references/

Organized documentation extracted from official sources. These files contain:

  • Detailed explanations
  • Code examples with language annotations
  • Links to original documentation
  • Table of contents for quick navigation

scripts/

Add helper scripts here for common automation tasks.

assets/

Add templates, boilerplate, or example projects here.

Notes

  • This skill was automatically generated from official documentation
  • Reference files preserve the structure and examples from source docs
  • Code examples include language detection for better syntax highlighting
  • Quick reference patterns are extracted from common usage examples in the docs

Updating

To refresh this skill with updated documentation:

  1. Re-run the scraper with the same configuration
  2. The skill will be rebuilt with the latest information