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-0.1.4-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1ad27ac24cdbb48bf6547dc59178edbd9435d7dffe6fa9b2b52ab3a389cd5a7a |
|
MD5 | f0070a3700dcae48b6f30f89819523fe |
|
BLAKE2b-256 | 7f15c1179cc1f65020d2a9d0e8f1ea8271656da549554558a5d20e7614e25b9a |