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
Release files for monocle2-python 2.9.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| monocle2_python-2.9.0.tar.gz | 68.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| monocle2_python-2.9.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 152.7 kB
Release files / monocle2_python-2.9.0.tar.gz
| Download URL | monocle2_python-2.9.0.tar.gz |
|---|---|
| Size | 68.6 kB |
| Tags | Source |
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| Download URL | monocle2_python-2.9.0-py3-none-any.whl |
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| Size | 84.0 kB |
| Tags | Python 3 |
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