xjtu-omics / gCAnno

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

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Author	Gao Shenghan
E-mail	[e-mail]

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