monocle2-python
Python port of the R monocle2 single-cell trajectory toolkit.
Installation
pip install monocle2-python # from PyPI
For local development:
git clone https://github.com/Bio-Babel/Monocle2-python.git
cd Monocle2-python
pip install -e ".[dev]"
Quickstart
import monocle2py as m2
cds = m2.load_hsmm_fpkm()
m2.estimate_size_factors(cds)
m2.estimate_dispersions(cds)
m2.reduce_dimension(cds, reduction_method="DDRTree")
m2.order_cells(cds)
m2.plot_cell_trajectory(cds, color_by="State")
Tutorials
Four runnable notebooks that reproduce the R monocle2 tutorials live under tutorials/:
| Notebook | Dataset |
|---|---|
V2_1_HSMM.ipynb |
HSMM myoblast differentiation |
V2_2_lung_BEAM.ipynb |
Lung epithelium BEAM walkthrough |
V2_3_Olsson_corrected.ipynb |
Olsson myeloid progenitors (WT + KOs) |
V2_4_Paul.ipynb |
Paul hematopoiesis |
License
Artistic-2.0, matching the upstream R monocle2.
1 maintainer
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