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aKNNO is a R package to build an optimized adaptive k-nearst neighbor graph for single-cell and spatial transcriptomics clustering.
devtools::install_github("liuqivandy/aKNNO")
aKNNO uses the PCA in a Seurat object to calculate distances and return a Seurat object with an optimized adaptive k-nearest neighbor graph (named as aKNN_O) stored in the respective slot
obj <- FindNeighbors_aKNNO(obj)- Analyze Mouse Instestinal Epithelium scRNAseq data
- Analyze 10x Visium data from mouse brain sagittal posterior
- Analyze Human Pancreas scRNAseq data
- Analyze Mouse Intestinal Organoid scRNAseq data
- Analyze Mouse Habenula scRNAseq data
Jia Li, Yu Shyr, Qi Liu. Clustering of Single-cell and Spatial Transcriptomics with an Optimized Adaptive K-nearest Neighbor Graph