| Name | phosx JSON |
| Version |
0.6.0
JSON |
| download |
| home_page | None |
| Summary | None |
| upload_time | 2024-04-15 12:38:17 |
| maintainer | None |
| docs_url | None |
| author | Alessandro Lussana |
| requires_python | <4.0,>=3.10 |
| license | None |
| keywords |
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
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|
<p align="center">
<img width="190" src="https://i.imgur.com/OzGTvkt.png">
<br>
Kinase activity inference from phosphosproteomics data based on substrate sequence specificity
<br><br>
</p>
> Current version: `0.6.0`
> Research paper: [https://doi.org/10.1101/2024.03.22.586304](https://doi.org/10.1101/2024.03.22.586304)
# Overview
<p align="center">
<br>
<img width="900" src="https://i.imgur.com/6DdMDom.png">
<br>
</p>
PhosX infers differential kinase activities from phosphoproteomics data without requiring any prior knowledge database of kinase-phosphosite associations. PhosX assigns the detected phosphopeptides to potential upstream kinases based on experimentally determined substrate sequence specificities, and it tests the enrichment of a kinase's potential substrates in the extremes of a ranked list of phosphopeptides using a Kolmogorov-Smirnov-like statistic. A _p_ value for this statistic is extracted empirically by random permutations of the phosphosite ranks.
# Installation
## From [PyPI](https://pypi.org/project/phosx/)
```bash
pip install phosx
```
## From source (requires [Poetry](https://python-poetry.org))
```
poetry build
pip install dist/*.whl
```
# Usage
```bash
phosx [-h] [-p PSSM] [-q PSSM_QUANTILES] [-n N_PERMUTATIONS] [-k N_TOP_KINASES] [-m MIN_N_HITS] [-c N_PROC] [--plot-figures] [-d OUTPUT_DIR] [-o OUTPUT_PATH] [-v] seqrnk
```
```bash
positional arguments:
seqrnk Path to the seqrnk file.
options:
-h, --help show this help message and exit
-p PSSM, --pssm PSSM Path to the h5 file storing custom PSSMs; defaults to built-in PSSMs
-q PSSM_QUANTILES, --pssm-quantiles PSSM_QUANTILES
Path to the h5 file storing custom PSSM score quantile distributions under the key 'pssm_scores'; defaults to built-in PSSM scores quantiles
-n N_PERMUTATIONS, --n-permutations N_PERMUTATIONS
Number of random permutations; default: 1000
-k N_TOP_KINASES, --n-top-kinases N_TOP_KINASES
Number of top-scoring kinases potentially associatiated to a given phosphosite; default: 8
-m MIN_N_HITS, --min-n-hits MIN_N_HITS
Minimum number of phosphosites associated with a kinase for the kinase to be considered in the analysis; default: 4
-c N_PROC, --n-proc N_PROC
Number of cores used for multithreading; default: 1
--plot-figures Save figures in pdf format; see also --output_dir
-d OUTPUT_DIR, --output-dir OUTPUT_DIR
Output files directory; only relevant if used with --plot_figures; defaults to 'phosx_output/'
-o OUTPUT_PATH, --output-path OUTPUT_PATH
Main output table; if not specified it will be printed in STDOUT
-v, --version Print package version and exit
```
Minimal example to run PhosX with default parameters on an example dataset, using up to 8 cores, and redirecting the output table to `kinase_activities.tsv`:
```bash
phosx -c 8 tests/seqrnk/koksal2018_log2.fold.change.8min.seqrnk > kinase_activities.tsv
```
# Cite
BibTeX:
```bibtex
@article{Lussana2024,
title = {PhosX: data-driven kinase activity inference from phosphoproteomics experiments},
url = {http://dx.doi.org/10.1101/2024.03.22.586304},
DOI = {10.1101/2024.03.22.586304},
publisher = {Cold Spring Harbor Laboratory},
author = {Lussana, Alessandro and Petsalaki, Evangelia},
year = {2024},
month = mar
}
```
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"description": "<p align=\"center\">\n <img width=\"190\" src=\"https://i.imgur.com/OzGTvkt.png\">\n <br>\n Kinase activity inference from phosphosproteomics data based on substrate sequence specificity\n <br><br>\n</p>\n\n\n\n> Current version: `0.6.0`\n\n> Research paper: [https://doi.org/10.1101/2024.03.22.586304](https://doi.org/10.1101/2024.03.22.586304)\n\n# Overview\n\n<p align=\"center\">\n<br>\n <img width=\"900\" src=\"https://i.imgur.com/6DdMDom.png\">\n <br>\n</p>\n\nPhosX infers differential kinase activities from phosphoproteomics data without requiring any prior knowledge database of kinase-phosphosite associations. PhosX assigns the detected phosphopeptides to potential upstream kinases based on experimentally determined substrate sequence specificities, and it tests the enrichment of a kinase's potential substrates in the extremes of a ranked list of phosphopeptides using a Kolmogorov-Smirnov-like statistic. A _p_ value for this statistic is extracted empirically by random permutations of the phosphosite ranks.\n\n# Installation\n\n## From [PyPI](https://pypi.org/project/phosx/)\n\n```bash\npip install phosx\n```\n\n## From source (requires [Poetry](https://python-poetry.org))\n\n```\npoetry build\npip install dist/*.whl\n```\n\n# Usage\n\n```bash\nphosx [-h] [-p PSSM] [-q PSSM_QUANTILES] [-n N_PERMUTATIONS] [-k N_TOP_KINASES] [-m MIN_N_HITS] [-c N_PROC] [--plot-figures] [-d OUTPUT_DIR] [-o OUTPUT_PATH] [-v] seqrnk\n```\n```bash\npositional arguments:\n seqrnk Path to the seqrnk file.\n\noptions:\n -h, --help show this help message and exit\n -p PSSM, --pssm PSSM Path to the h5 file storing custom PSSMs; defaults to built-in PSSMs\n -q PSSM_QUANTILES, --pssm-quantiles PSSM_QUANTILES\n Path to the h5 file storing custom PSSM score quantile distributions under the key 'pssm_scores'; defaults to built-in PSSM scores quantiles\n -n N_PERMUTATIONS, --n-permutations N_PERMUTATIONS\n Number of random permutations; default: 1000\n -k N_TOP_KINASES, --n-top-kinases N_TOP_KINASES\n Number of top-scoring kinases potentially associatiated to a given phosphosite; default: 8\n -m MIN_N_HITS, --min-n-hits MIN_N_HITS\n Minimum number of phosphosites associated with a kinase for the kinase to be considered in the analysis; default: 4\n -c N_PROC, --n-proc N_PROC\n Number of cores used for multithreading; default: 1\n --plot-figures Save figures in pdf format; see also --output_dir\n -d OUTPUT_DIR, --output-dir OUTPUT_DIR\n Output files directory; only relevant if used with --plot_figures; defaults to 'phosx_output/'\n -o OUTPUT_PATH, --output-path OUTPUT_PATH\n Main output table; if not specified it will be printed in STDOUT\n -v, --version Print package version and exit\n```\n\nMinimal example to run PhosX with default parameters on an example dataset, using up to 8 cores, and redirecting the output table to `kinase_activities.tsv`:\n\n```bash\nphosx -c 8 tests/seqrnk/koksal2018_log2.fold.change.8min.seqrnk > kinase_activities.tsv\n```\n\n# Cite\n\nBibTeX:\n\n```bibtex\n@article{Lussana2024,\n title = {PhosX: data-driven kinase activity inference from phosphoproteomics experiments},\n url = {http://dx.doi.org/10.1101/2024.03.22.586304},\n DOI = {10.1101/2024.03.22.586304},\n publisher = {Cold Spring Harbor Laboratory},\n author = {Lussana, Alessandro and Petsalaki, Evangelia},\n year = {2024},\n month = mar \n}\n```\n",
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