Install

mamba create -n gsMap python>=3.10
mamba install -c conda-forge "numpy<2" pandas scipy scikit-learn matplotlib seaborn tqdm pyyaml python-kaleido zarr bitarray jinja2 plotly scanpy scikit-misc pyarrow
mamba install -c conda-forge -c bioconda "bitarray<3" pyranges sorted_nearest
git clone https://github.com/JianYang-Lab/gsMap
cd gsMap
pip install -e .

CA1椎体神经元

Wfs1

CsMKIIα

CA2椎体神经元

Amigo2

Pcp4

Rgs14

Avpr1b

CA3椎体神经元

Scgn

CaMKIIα

DG齿状回颗粒细胞

Prox1: 特异性转录因子

"Why, man, he doth bestride the narrow world
Like a Colossus, and we petty men
Walk under his huge legs and peep about
To find ourselves dishonourable graves."
— William Shakespeare, Julius Caesar, Act 1, Scene 2 (Cassius)

"For unto us a child is born, unto us a son is given:
and the government shall be upon his shoulder:
and his name shall be called Wonderful, Counsellor, The mighty God, The everlasting Father, The Prince of Peace."
— Isaiah 9:6 (King James Version)

①Install

需要手动将STalign.git上传到服务器上。

/cwStorage/home/chenzhh/package/python/STalign-main

Otaku

每次打开一个新的终端时

export RSTUDIO_WHICH_R="$(mamba run -n Otaku which R)"
/Applications/RStudio.app/Contents/MacOS/RStudio &

"For lust of knowing what should not be known,
We make the Golden Journey to Samarkand."
— James Elroy Flecker, The Golden Journey to Samarkand (1913)

①Install

没啥特别的，除了安装velocyto时需要numpy和Cython，所以不能像官网那样直接pip。

mamba create -n celloracle python=3.10
eval "$(mamba shell hook --shell bash)"
mamba activate celloracle
pip install numpy==1.26.4 cython==3.1.1
pip install celloracle
mamba install ipykernel
python -m ipykernel install --name=celloracle --display-name "Python celloracle"

链接指路:SCENIC+ Stein Aerts lab seminar.

讲解者：Seppe De Winter，文章的二作，来自巨无霸的Stein Aerts Lab - VIB - KULeuven组