mang30/myskills/bioinformatics-sc

Name: bioinformatics-sc
Author: mang30

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Install

npx vskill@latest install mang30/myskills/bioinformatics-sc

SKILL.md

单细胞多组学数据处理规范

适用场景

处理 scRNA、scATAC、scHiC、scHiCAR 等单细胞多组学数据

数据加载规范

MTX 格式（10x Genomics）

python

import scanpy as sc
adata = sc.read_10x_mtx(
    path,
    var_names='gene_symbols',
    cache=True  # 必须开启缓存
)

pairsam / Hi-C 格式

python

# 禁止一次性读取，必须用流式
import gzip
with gzip.open('file.pairsam.txt.gz', 'rt') as f:
    for line in f:  # 逐行处理
        if line.startswith('#'):
            continue

质控标准（scRNA）

最小基因数：200
最大基因数：根据数据分布决定（通常 <6000）
线粒体基因比例：<20%
最小细胞数：3

必须固定随机种子

python

import numpy as np
import random
SEED = 42
np.random.seed(SEED)
random.seed(SEED)

内存安全

单个文件 >1GB 必须流式处理
使用 backed 模式读取大 h5ad
及时释放不用的变量

结果可复现性

所有中间结果保存为 h5ad 格式
记录软件版本到 results/env.txt
数据集划分方式与论文一致

Security

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Source

SKILL.md in the repositoryCheckingskills/bioinformatics-sc/SKILL.md

Popularity

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