吉祥事变 Auspicious Incident

"Here let us all for death prepare,
Or on the last great journey fare."
— Vālmīki, Rāmāyaṇa (Ayodhyā-kāṇḍa 2.47.7); English verse trans. Ralph T. H. Griffith, The Ramayana, Book II, Canto XLVII (“The Citizens’ Return”)
Sanskrit: इहैव निधनं यामो महाप्रस्थानमेव वा।

自壬辰冬时至今，我们处于黑暗时代。——

耶尼切里 Janissary

——单细胞技术整理

Janissary

---

/ˈdʒænɪˌseri/ · n. 亲信，近卫；（奥斯曼帝国）土耳其禁卫军士兵

基础代码	简介
Convert	格式转换，格式
SCENIC+	SCENIC+
gsMap	gsMap
STalign	STalign 配准
hdWGCNA

Novae

mamba create --name novae python=3.12 -y
mamba activate novae
pip install 'novae[multimodal,conch,llm]'
python -m ipykernel install --user --name novae --display-name "Py312 novae"

novae_gpu

CONDA_OVERRIDE_GLIBC=2.17 mamba create -n novae_gpu -c conda-forge python=3.12 pip ipykernel "numpy=2.2.*" h5py pyarrow -y
python -m pip install     torch==2.5.1     torchvision==0.20.1     --index-url https://download.pytorch.org/whl/cu121
mamba install "numpy==2.2.6"   "pandas==2.2.3"   "h5py==3.14.0"   "scipy"   "scikit-learn==1.7.1"   "igraph"   "anndata==0.11.4"   "scanpy==1.11.5" -c bioconda -c conda-forge
python -m pip install   --constraint <(printf '%s\n' \                              
    'numpy==2.2.6' \
    'pandas==2.2.3' \
    'h5py==3.14.0' \
    'scipy==1.15.3' \
    'scikit-learn==1.7.1' \
    'igraph==0.11.9' \
    'anndata==0.11.4' \
    'scanpy==1.11.5')   "novae[conch,llm]==1.1.1"
    
python -m ipykernel install --user --name novae-gpu --display-name "Py312 novae-gpu"

Allensdk

mamba create -n allensdk -c conda-forge python=3.10 scanpy=1.11.5 pip ipykernel jupyterlab -y
python -m pip install "git+https://github.com/AllenInstitute/AllenSDK.git@master"
python -m ipykernel install --user --name allensdk --display-name "Py310 allensdk"

python - <<'PY'
import numpy
import pandas
import scipy
import scanpy
import allensdk

print("numpy   :", numpy.__version__)
print("pandas  :", pandas.__version__)
print("scipy   :", scipy.__version__)
print("scanpy  :", scanpy.__version__)
print("allensdk:", allensdk.__version__)
PY

spAlignDE

这些代码

cd /cwStorage/home/chenzhh/Env/spAlignDE-main
unset PYTHONPATH
export PYTHONNOUSERSITE=1
# mamba env create -f environment.yml -y
# mamba create -n spAlignDE -c conda-forge python=3.10.14 pip=26.0.1 setuptools=80.9.0 wheel=0.46.3 -y
# python -m pip install torch==2.10.0+cu128 torchvision==0.25.0+cu128 --index-url https://download.pytorch.org/whl/cu128
mamba create -y -n spAlignDE -c conda-forge --override-channels python=3.10.14 pip setuptools wheel git numpy=1.26.4 scipy=1.10.1 pandas=2.2.3 anndata=0.10.8 "h5py=3.11.*=nompi*" matplotlib-base=3.9.2 shapely=2.0.6 scanpy=1.10.3 scikit-image=0.24.0 scikit-learn=1.5.2 seaborn=0.13.2 harmonypy=0.2.0 python-igraph=0.11.9 leidenalg=0.10.2 louvain=0.8.2 umap-learn=0.5.11 einops=0.8.1 pynrrd=1.0.0 pyyaml=6.0 ipykernel ipywidgets jupyterlab nbconvert nbformat plotly

mamba activate spAlignDE
python -m pip install --only-binary=:all: pillow==12.1.0 imagecodecs==2025.3.30 opencv-python-headless==4.10.0.84 tifffile==2025.5.10 webdataset==1.0.2
python -m pip install torch==2.6.0+cu118 torchvision==0.21.0+cu118 --index-url https://download.pytorch.org/whl/cu118
python -c "import torch,torchvision; print('torch=',torch.__version__); print('torchvision=',torchvision.__version__); print('CUDA runtime=',torch.version.cuda); print('CUDA available=',torch.cuda.is_available()); print('GPU=',torch.cuda.get_device_name(0) if torch.cuda.is_available() else 'NONE'); print('capability=',torch.cuda.get_device_capability(0) if torch.cuda.is_available() else 'NONE')"
python -c "import torch; x=torch.randn(4096,4096,device='cuda'); y=x@x; torch.cuda.synchronize(); print(y.shape,y.device,torch.cuda.get_device_name(0))"

python -m pip install --no-deps "pybanksy @ git+https://github.com/prabhakarlab/Banksy_py.git@43e2d692db6705c0195039764194473912e4cfc2"
python -m pip install --only-binary=:all: pyarrow==17.0.0
mamba install -y -c conda-forge --override-channels "greenlet<3.5" "sqlalchemy<2.1" "jupyter-cache=1.0.1"
python -m pip install streamlit==1.60.0 myst-nb==1.1.2 pytest==9.1.1 sphinx==7.4.7 sphinx-rtd-theme==2.0.0
python -m pip install --no-deps --no-build-isolation -e .

# ↑ mamba -f 安装到pip的时候会卡住，目前没有更好的解决方案
python -m pip install --no-deps python-igraph==0.11.9
mamba install -y -c conda-forge --override-channels scikit-learn=1.6.1
python -m ipykernel install --user --name spAlignDE --display-name "Python310 spAlignDE"

坦齐马特 Tanzimat

——遗传相关技术整理

Tanzimat

---

/ˈtanzɪmat/ · n. 改革；（奥斯曼帝国 1839–1876 年的）整顿、重组改革

- 隶属于[三二七汉边改革](/medicine/enthalpy.md)

代码分区块整理：

PLINK

遗传度

GCTA

👉🏻文档地址

MPH

👉🏻文档地址

注释

ANNOVAR

👉🏻文档地址

VEP

👉🏻文档地址

Fine-mapping

SuSiE

FINEMAP

GCTB

STAAR

👉🏻STAAR github

👉🏻cellSTAAR github

👉🏻MetaSTAARlite github

进化基因组学

👉🏻HARE

与scRNA-seq的联合分析

gsMap

👉🏻文档地址

freesurfer&fsl

👉🏻文档地址

花厅御诏（Gülhane Hatt-ı Şerif）

——WGS数据基础处理

hail

👉🏻教程

👉🏻hail-is/HAIL

👉🏻Nealelab/whole_genome_analysis_pipeline

改革敕令（Hatt-ı Hümayun）

——数据下载与整理

SingleBrain

gsmap数据