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gCAnno-A tool for cell type annotation of single-cell transcriptome sequencing

Cell type annotation is essential for single cell data analysis.gCAnno can annotate cell types accurately.

Dependencies

python 3.6.4

conda create -n environment python=3.6.4
conda install packge=version
packges version
numpy 1.16.4
pandas 0.20.3
scipy 1.2.0
scikit-learn 0.21.3
matplotlib 3.0.3
networkx 2.1
gensim 3.4.0

Usage

example (detail)

  • build model
python ./buildModelPipline.py -o ./ref/ -e ./testData/ref/expdata_normal.xls -c ./testData/ref/cluster.xls -fr 0.3
  • cell type annotation--Bayes
python ./defineCellTypePipline_bayes.py -o ./test_bayes/ -d ./ref/embedding/02.embeddingDis.xls -q ./testData/test/expdata_normal.xls -sg 65
  • cell type annotation--SVM
python ./defineCellTypePipline_svm.py -o ./test_svm/ -d ./ref/embedding/02.embeddingDis.xls -q ./testData/test/expdata_normal.xls -rd ./testData/ref/expdata_normal.xls -rt ./testData/ref/cluster.xls -sg 65

Others

testData

We provide users a small dataset to test gCAnno. User can run sh testref.sh to build model and run sh testAnnotation_bayes.sh or sh testAnnotation_svm.sh to test model.

Contact

Author Gao Shenghan
E-mail gaoxian15002970749@163.com