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 https://github.com/XingyanLiu/stagewiseNN.git
cd stagewiseNN
python setup.py 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,)
Contribute¶
Issue Tracker: https://github.com/XingyanLiu/stagewiseNN/issues
Source Code: https://github.com/XingyanLiu/stagewiseNN