4 files were added to this release more than 14 days after its initial publication. Inspect the release files before installing.
cuSingleR
基于python版本SingleR软件,使用cuda加速.
编译whl
系统环境需要安装 cuda-toolkit 11.4 / gcc<11
export PATH=/usr/local/cuda/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
python setup.py sdist bdist_wheel
编译后的whl存放在dist目录
运行
python test/test_basic.py data/GSE84133_GSM2230761_mouse1.h5ad data/GSE84133_GSM2230762_mouse2.h5ad data/result.tsv
参数解释:
- 第一个参数表示reference的数据,格式为h5ad
- 第二个参数表示query的数据,格式为h5ad
- 第三个参数为输出文件,按tab分割的三列数据,分别表示cell/firstLabel/finalLabel
详情见脚本 test/test_basic.py
注意: 由于h5ad格式可能存在不同字段,如果脚本报错需要修改正确的字段以保证程序能获取到数据
输入文件要求
-
ref/qry输入文件均需有/X/data /X/indices /X/indptr 存储矩阵数据; 有/var/_index 存储基因名
-
ref需有 /obs/ClusterName/codes /obs/ClusterName/categories 或/obs/celltype/codes /obs/celltype/categories 存储分类结果
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qry需有 /obs/_index 存储细胞名
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程序不会对h5ad数据做log2处理,如有此需要请客户自行对数据做预处理
-
如遇ref和qry的gene不完全一致,程序会自动取基因的交集参与计算,如果没有一个相同基因,则程序报错退出
1 maintainer
Metadata
1 maintainer
Release files for cusingler 1.1.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| cusingler-1.1.0.tar.gz | 6.1 kB | Without provenance | Details for cusingler-1.1.0.tar.gz |
Built distributions (wheels)
Total release size: 1.6 MB
Release files / cusingler-1.1.0.tar.gz
| Download URL | cusingler-1.1.0.tar.gz |
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| Tags | Source |
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| Download URL | cusingler-1.1.0-cp310-cp310-win_amd64.whl |
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| Size | 196.3 kB |
| Tags | CPython 3.10 Windows x86-64 |
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| Size | 344.5 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
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| Download URL | cusingler-1.1.0-cp39-cp39-win_amd64.whl |
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| Size | 196.0 kB |
| Tags | CPython 3.9 Windows x86-64 |
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| Download URL | cusingler-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 344.4 kB |
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| Download URL | cusingler-1.1.0-cp38-cp38-win_amd64.whl |
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| Size | 196.4 kB |
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