https://github.com/theislab/singlecell_proteomics
https://github.com/theislab/singlecell_proteomics
Last synced: 10 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/theislab/singlecell_proteomics
- Owner: theislab
- Created: 2020-12-22T15:00:39.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2024-03-21T09:51:37.000Z (over 2 years ago)
- Last Synced: 2025-03-16T11:51:30.398Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 2.62 MB
- Stars: 5
- Watchers: 4
- Forks: 3
- Open Issues: 6
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Single-cell proteomics analysis in python
This repository contains analyses done for [Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation](https://doi.org/10.15252/msb.202110798), A Brunner, ..., M Mann, Molecular Systems Biology (2022). For replication you will need to download the files in DIANN1.8_SingleCells_CellCycle.7z from https://www.ebi.ac.uk/pride/archive/projects/PXD024043.
The analyses were performed in python and heavily use [scanpy](https://scanpy.readthedocs.io/en/stable/) and [anndata](https://anndata.readthedocs.io/en/latest/) functionality. Both python packages were originally created for single cell transcriptomics analyses, but can to a large part also directly be applied to protein data and thus help kick off this exciting new field! Especially scanpy enables easy data visualizations like PCA plots or UMAPs and provides some ready to use analysis methods like assigning cell cycle stage scores to single cells given some cell cycle markers.