Python implementation of the Slingshot pseudotime algorithm
Project description
Slingshot in Python
This is a Python implementation of the Slingshot pseudotime algorithm (Street et al., 2018). The original implementation is written in R: https://github.com/kstreet13/slingshot.
A complete working example is located in slingshot.ipynb
, using a synthetically generated dataset.
Installation:
pip install pyslingshot
Deprecated version
Older versions if pyslingshot (before v0.1.0) requires manually installing numpy
, scipy
, sklearn
, and my fork
of pcurvepy
(https://github.com/mossjacob/pcurvepy).
Contributing
- Fork & download source
- Install requirements with
poetry install
[1] Street, K., Risso, D., Fletcher, R.B., Das, D., Ngai, J., Yosef, N., Purdom, E. and Dudoit, S., 2018. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC genomics, 19(1), pp.1-16.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for pyslingshot-0.1.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1918327b3226d11aa3f3d2e82a8b353350eabb1d1592721a3d842ec830528f98 |
|
MD5 | c389fe8fd5ef9b39cf2c3d53643c6bac |
|
BLAKE2b-256 | 421d323afc730c1f6771a2514943dbeacadc8c855588bf035935285af30840d8 |