stagewiseNN - Building developmental tree from scRNA-seq

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

Install from source code:

git clone
cd stagewiseNN
python install

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)
# step1:
# building (stage-wise) single-cell graph
distmat, connect = builder.build_graph(
        X=data_matrix, stage_lbs=stage_labels,
# step2:
# build developmental tree from single-cell graph
builder.build_tree(group_labels, stage_labels,)


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Indices and tables