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A tool for building developmental tree from scRNA-seq

Project description


stagewiseNN is a computational tool for constructing developmental tree from Multi-staged single-cell RNA-seq data.

(see StagewiseNN Documentation for detailed guides)

It starts from building a single-cell graph by connecting each cell to its k-nearest neighbors in the parent stage, followed by voting-based tree-construction and adaptive cluster refinement.


It is easy to use:

import swnn

# ====== Inputs ======
# data_matrix = ..
# stage_labels = ..
# group_labels = ..
# stage_order = [f'stage_{i}' for i in range(5)]

builder = swnn.Builder(stage_order=stage_order)
# step 1:
# building (stage-wise) single-cell graph
distmat, connect = builder.build_graph(
        X=data_matrix, stage_lbs=stage_labels,
# step 2:
# build developmental tree from single-cell graph
builder.build_tree(group_labels, stage_labels,)



Install stagewiseNN by running (in the command line):

pip install swnn

or install from source code:

git clone
cd stagewiseNN
python install



If you are having issues, please let us know. We have a mailing list located at:


If you find StagewiseNN helps, Please cite:

Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al. Joint profiling of gene expression and chromatin accessibility of amphioxus development at single cell resolution, 18 May 2021, PREPRINT (Version 1) available at Research Square []

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