pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

https://github.com/pyprophet/pyprophet

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 16 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
7 of 20 committers (35.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary

Keywords

data-independent-acquisition mass-spectrometry openswath proteomics python semi-supervised-learning swath-ms

Keywords from Contributors

3-clause-bsd analyses metabolomics ms-data openms

Last synced: 6 months ago · JSON representation

Repository

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

Basic Info

Host: GitHub
Owner: PyProphet
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: http://www.openswath.org
Size: 57.5 MB

Statistics

Stars: 29
Watchers: 3
Forks: 21
Open Issues: 12
Releases: 30

Topics

data-independent-acquisition mass-spectrometry openswath proteomics python semi-supervised-learning swath-ms

Created over 9 years ago · Last pushed 6 months ago

Metadata Files

Readme License

README.md

PyPI - Python Version

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

PyProphet is a Python re-implementation of the mProphet algorithm [1] optimized for SWATH-MS data acquired by data-independent acquisition (DIA). The algorithm was originally published in [2] and has since been extended to support new data types and analysis modes [3,4].

Please consult the OpenSWATH website for usage instructions and help.

Installation

We strongly advice to install PyProphet in a Python virtualenv. PyProphet is compatible with Python 3.

Install the development version of pyprophet from GitHub:

$ pip install git+https://github.com/PyProphet/pyprophet.git@master

Install the stable version of pyprophet from the Python Package Index (PyPI):

$ pip install pyprophet

Running pyprophet

pyprophet is not only a Python package, but also a command line tool:

$ pyprophet --help

or:

$ pyprophet score --in=tests/test_data.txt

Docker

PyProphet is also available from Docker (automated builds):

Pull the latest version of pyprophet from DockerHub or Github Container Registry (synced with releases):

```` # Dockerhub $ docker pull pyprophet/pyprophet:latest

# Github Container Registry
$ docker pull ghcr.io/pyprophet/pyprophet:latest

````

Documentation

API and CLI documentation is available on Read the Docs.

Running tests

The pyprophet tests are best executed using py.test and the pytest-regtest plugin:

$ pip install pytest $ pip install pytest-regtest $ py.test -n auto ./tests

References

Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods. 2011 May;8(5):430-5. doi: 10.1038/nmeth.1584. Epub 2011 Mar 20.
Teleman J, Röst HL, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F. DIANA--algorithmic improvements for analysis of data-independent acquisition MS data. Bioinformatics. 2015 Feb 15;31(4):555-62. doi: 10.1093/bioinformatics/btu686. Epub 2014 Oct 27.
Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nat Biotechnol 2017 Aug;35(8):781-788. doi: 10.1038/nbt.3908. Epub 2017 Jun 12.
Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat Methods. 2017 Sep;14(9):921-927. doi: 10.1038/nmeth.4398. Epub 2017 Aug 21.

Owner

Name: PyProphet
Login: PyProphet
Kind: organization

Repositories: 4
Profile: https://github.com/PyProphet

GitHub Events

Total

Create event: 11
Issues event: 5
Release event: 9
Watch event: 1
Delete event: 6
Issue comment event: 21
Push event: 34
Pull request review comment event: 34
Pull request review event: 41
Pull request event: 35

Last Year

Create event: 11
Issues event: 5
Release event: 9
Watch event: 1
Delete event: 6
Issue comment event: 21
Push event: 34
Pull request review comment event: 34
Pull request review event: 41
Pull request event: 35

Committers

Last synced: over 2 years ago

All Time

Total Commits: 507
Total Committers: 20
Avg Commits per committer: 25.35
Development Distribution Score (DDS): 0.604

Past Year

Commits: 44
Committers: 4
Avg Commits per committer: 11.0
Development Distribution Score (DDS): 0.25

Top Committers

Name	Email	Commits
George Rosenberger	g**8@c**u	201
Uwe Schmitt	u**t@i**h	93
Uwe Schmitt	u**t@m**e	74
singjc	j**g@g**m	57
George Rosenberger	g**r@u**h	15
Hannes Roest	r**t@i**h	13
oliveralka	r**9@g**t	12
George Rosenberger	r**r@i**h	11
Johan Teleman	j**n@i**e	7
Hannes Roest	h**t@s**u	6
guoci	z**i@g**m	4
Hannes Roest	h**t@u**a	4
fickludd	j**n@g**m	2
Uwe Schmitt	u**t@s**)	2
Hannes Roest	h**t@g**h	1
Rohan Shah	r**h@c**u	1
Daniel Hyduke	d**e@s**m	1
George Rosenberger	g**r@n**l	1
Joshua Charkow	4****w	1
Justin Sing	3****c	1

Committer Domains (Top 20 + Academic)

imsb.biol.ethz.ch: 2 stemcentrx.com: 1 cmri.org.au: 1 gmx.ch: 1 srv005.(none): 1 utoronto.ca: 1 stanford.edu: 1 immun.lth.se: 1 gmx.net: 1 unibas.ch: 1 mineway.de: 1 id.ethz.ch: 1 cumc.columbia.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 42
Total pull requests: 105
Average time to close issues: about 1 year
Average time to close pull requests: about 2 months
Total issue authors: 32
Total pull request authors: 7
Average comments per issue: 3.26
Average comments per pull request: 0.53
Merged pull requests: 87
Bot issues: 0
Bot pull requests: 5

Past Year

Issues: 4
Pull requests: 37
Average time to close issues: N/A
Average time to close pull requests: 16 days
Issue authors: 2
Pull request authors: 3
Average comments per issue: 1.0
Average comments per pull request: 0.32
Merged pull requests: 26
Bot issues: 0
Bot pull requests: 5

View more stats

Top Authors

Issue Authors

hroest (4)
jcharkow (3)
singjc (2)
fangfeiz (2)
bretttully (2)
oliveralka (2)
mantouRobot (2)
dpryan79 (1)
HFan11 (1)
Allen188 (1)
Hitlikegh (1)
tachengxmu (1)
Matthias313 (1)
summerghw (1)
shubham1637 (1)

Pull Request Authors

singjc (40)
grosenberger (39)
jcharkow (19)
dependabot[bot] (5)
oliveralka (5)
hroest (4)
rohan-shah (1)

Top Labels

Issue Labels

refactor (1)

Pull Request Labels

dependencies (5) python (5) refactor (1)

Packages

Total packages: 1
Total downloads:
- pypi 254 last-month
Total docker downloads: 35

Total dependent packages: 2
Total dependent repositories: 4
Total versions: 84
Total maintainers: 2

pypi.org: pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

Documentation: https://pyprophet.readthedocs.io/
License: BSD
Latest release: 3.0.1
published 7 months ago

Versions: 84
Dependent Packages: 2
Dependent Repositories: 4
Downloads: 254 Last month
Docker Downloads: 35

Rankings

Docker downloads count: 1.6%

Dependent packages count: 3.1%

Average: 7.3%

Dependent repos count: 7.5%

Forks count: 8.2%

Downloads: 11.1%

Stargazers count: 12.2%

Maintainers (2)

grosenberger uweschmitt

Last synced: 6 months ago

Dependencies

setup.py pypi

Click *
cython *
hyperopt *
matplotlib *
numexpr *
numpy *
pandas *
scikit-learn *
scipy *
statsmodels *
tabulate *
xgboost *

.github/workflows/dockerpublish.yml actions

actions/checkout v3 composite
docker/build-push-action ad44023a93711e3deb337508980b4b5e9bcdc5dc composite
docker/login-action f054a8b539a109f9f41c372932f1ae047eff08c9 composite
docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite

.github/workflows/pythonpublish.yml actions

actions/checkout v1 composite
actions/setup-python v1 composite

Dockerfile docker

python 3.9.1 build

.github/workflows/ci.yml actions

actions/checkout v4 composite
actions/setup-python v5 composite

.github/workflows/dependabot.yml actions

pyproject.toml pypi

Click *
cython *
duckdb *
duckdb-extension-sqlite-scanner *
duckdb-extensions *
hyperopt *
matplotlib *
numexpr >= 2.10.1
numpy >= 1.26.4
pandas >= 2.0
polars >= 1.28.1
pyarrow *
pypdf *
scikit-learn >= 1.5
scipy *
statsmodels >= 0.8.0
tabulate *
xgboost *

requirements.txt pypi

click ==8.1.7
cloudpickle ==3.1.0
contourpy ==1.3.0
cycler ==0.12.1
cython ==3.0.11
duckdb ==1.1.3
duckdb-extension-sqlite-scanner ==1.1.3
duckdb-extensions ==1.1.3
exceptiongroup ==1.2.2
fonttools ==4.55.0
future ==1.0.0
hyperopt ==0.2.7
importlib-resources ==6.5.2
iniconfig ==2.0.0
joblib ==1.4.2
kiwisolver ==1.4.7
matplotlib ==3.9.2
networkx ==3.2.1
numexpr ==2.10.1
numpy ==2.0.2
nvidia-nccl-cu12 ==2.23.4
packaging ==24.2
pandas ==2.2.3
patsy ==1.0.1
pillow ==11.0.0
pluggy ==1.5.0
polars ==1.28.1
py4j ==0.10.9.7
pyarrow ==18.0.0
pyparsing ==3.2.0
pypdf ==5.1.0
pytest ==8.3.3
pytest-regtest ==2.3.3
python-dateutil ==2.9.0.post0
pytz ==2024.2
scikit-learn ==1.5.2
scipy ==1.13.1
six ==1.16.0
statsmodels ==0.14.4
tabulate ==0.9.0
threadpoolctl ==3.5.0
tomli ==2.2.1
tqdm ==4.67.0
typing-extensions ==4.13.2
tzdata ==2024.2
xgboost ==2.1.2
zipp ==3.21.0