glycresoft
An LC-MS/MS glycan and glycopeptide search engine
Science Score: 57.0%
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✓CITATION.cff file
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✓DOI references
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○Scientific vocabulary similarity
Low similarity (17.3%) to scientific vocabulary
Repository
An LC-MS/MS glycan and glycopeptide search engine
Basic Info
- Host: GitHub
- Owner: mobiusklein
- License: apache-2.0
- Language: Python
- Default Branch: master
- Homepage: https://mobiusklein.github.io/glycresoft/
- Size: 30.6 MB
Statistics
- Stars: 13
- Watchers: 4
- Forks: 7
- Open Issues: 1
- Releases: 3
Metadata Files
README.md
GlycReSoft
Software for analyzing glycomics and glycoproteomics LC-MS/MS data.
Usage
This package provides several command line tools, available under the name glycresoft.
$ glycresoft -h
Commands:
analyze Identify structures in preprocessed data
build-hypothesis Build search spaces for glycans and glycopeptides
config Set persistent configuration options
export Write Data Collections To Text Files
mzml Inspect and preprocess mzML files
tools Odds and ends to help inspect data and diagnose issues
Installing
This program requires Python 3.8 or newer, last tested with Python 3.10. The simplest way to perform the installation is to use a virtual environment to isolate its dependencies.
bash
pip install -v glycresoft
To install from source after cloning this repository. The dependencies are listed in requirements.txt. The build system requirements in pyproject.toml, which includes numpy and Cython. A C compiler compatible with your version of Python for your platform is also required.
bash
pip install -v .
or alternatively to install certain dependencies from source
bash
make install-dependencies
This will install this library and all of its dependencies into the current Python environment. The command line tool will be made available under the name glycresoft.
If you want to build the standalone executable that bundles all of its dependencies with its own version of Python, next run
bash
pip install PyInstaller
make build-pyinstaller
This will install PyInstaller, a Python program which can package another Python program and all of its dependencies into a native executable, and run it on an entry point wrapper for GlycReSoft. Afterwards, the standalone executable and its static files are located in ./pyinstaller/dist/glycresoft-cli/, where the executable is named glycresoft-cli, which will operate essentially the same as the glycresoft executable installed above, save that it will do some platform specific configuration and can be used from outside the virtual environment it was created in.
When installing pre-compiled wheels from the package index, installation should take less than 5 minutes on a regular computer. Installing packages from source things may take up to 15 minutes.
For glycopeptide fragmentation modeling, please see https://github.com/mobiusklein/glycopeptidefeaturelearning.
GUI
For a web-based graphical user interface, see https://github.com/mobiusklein/glycresoft_app. The wrapping desktop application: https://github.com/mobiusklein/glycresoft_desktop.
Usage
The general CLI information, see the Documentation, or the command-level
--help menu.
For Glycopeptides
For a brief tutorial on the original high collision energy glycopeptide search tool, see the Original Tutorial.
For a tutorial on the stepped collision energy glycopeptide search tool, see the SCE Tutorial.
Citing
If you used glycresoft in your research, please cite
Klein, J., Carvalho, L., & Zaia, J. (2024). Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity. Nature Communications, 15(1), 6168. https://doi.org/10.1038/s41467-024-50338-5
Owner
- Name: Joshua Klein
- Login: mobiusklein
- Kind: user
- Location: Boston
- Repositories: 87
- Profile: https://github.com/mobiusklein
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
# https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
cff-version: 1.2.0
title: GlycReSoft
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Joshua
name-particle: A
family-names: Klein
email: jaklein@bu.edu
affiliation: 'Program for Bioinformatics, Boston University'
orcid: 'https://orcid.org/0000-0003-1279-6838'
- given-names: Joseph
family-names: Zaia
email: jzaia@bu.edu
affiliation: >-
Department of Biochemistry, Boston University
School of Medicine
preferred-citation:
authors:
- given-names: Joshua
name-particle: A
family-names: Klein
email: jaklein@bu.edu
affiliation: 'Program for Bioinformatics, Boston University'
orcid: 'https://orcid.org/0000-0003-1279-6838'
- given-names: Luis
family-names: Carvalho
- given-names: Joseph
family-names: Zaia
email: jzaia@bu.edu
affiliation: >-
Department of Biochemistry, Boston University
School of Medicine
title: >-
Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity
type: article
doi: 10.1021/10.1038/s41467-024-50338-5
journal: Nature Communications
references:
- authors:
- given-names: Joshua
name-particle: A
family-names: Klein
email: jaklein@bu.edu
affiliation: 'Program for Bioinformatics, Boston University'
orcid: 'https://orcid.org/0000-0003-1279-6838'
- given-names: Luis
family-names: Carvalho
- given-names: Joseph
family-names: Zaia
email: jzaia@bu.edu
affiliation: >-
Department of Biochemistry, Boston University
School of Medicine
title: >-
Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity
type: article
doi: 10.1021/10.1038/s41467-024-50338-5
journal: Nature Communications
- authors:
- given-names: Joshua
name-particle: A
family-names: Klein
email: jaklein@bu.edu
affiliation: 'Program for Bioinformatics, Boston University'
orcid: 'https://orcid.org/0000-0003-1279-6838'
- given-names: Joseph
family-names: Zaia
email: jzaia@bu.edu
affiliation: >-
Department of Biochemistry, Boston University
School of Medicine
title: >-
Relative Retention Time Estimation Improves
N-Glycopeptide Identifications by LC-MS/MS
type: article
doi: 10.1021/acs.jproteome.0c00051
journal: Journal of Proteome Research
- authors:
- given-names: Joshua
name-particle: A
family-names: Klein
email: jaklein@bu.edu
affiliation: 'Program for Bioinformatics, Boston University'
orcid: 'https://orcid.org/0000-0003-1279-6838'
- given-names: Le
family-names: Meng
affiliation: >-
Department of Biochemistry, Boston University
School of Medicine
- given-names: Joseph
family-names: Zaia
email: jzaia@bu.edu
affiliation: >-
Department of Biochemistry, Boston University
School of Medicine
title: >-
Deep Sequencing of Complex Proteoglycans: A
Novel Strategy for High Coverage and
Site-specific Identification of
Glycosaminoglycan-linked Peptides
journal: Molecular Cellular Proteomics
doi: 10.1074/mcp.RA118.000766
type: article
- authors:
- given-names: Joshua
name-particle: A
family-names: Klein
email: jaklein@bu.edu
affiliation: 'Program for Bioinformatics, Boston University'
orcid: 'https://orcid.org/0000-0003-1279-6838'
- given-names: Luis
family-names: Carvalho
- given-names: Joseph
family-names: Zaia
email: jzaia@bu.edu
affiliation: >-
Department of Biochemistry, Boston University
School of Medicine
title: >-
Application of network smoothing to glycan
LC-MS profiling
journal: Bioinformatics
year: 2018
doi: 10.1093/bioinformatics/bty397
type: article
url: https://www.bumc.bu.edu/msr/glycresoft/
repository: https://github.com/mobiusklein/glycresoft
identifiers:
- type: doi
value: 10.1021/acs.jproteome.0c00051
description: >-
Relative Retention Time Estimation Improves
N-Glycopeptide Identifications by LC-MS/MS
- type: doi
value: 10.1074/mcp.RA118.000766
description: >-
Deep Sequencing of Complex Proteoglycans: A
Novel Strategy for High Coverage and
Site-specific Identification of
Glycosaminoglycan-linked Peptides
- type: doi
value: 10.1093/bioinformatics/bty397
description: >-
Application of network smoothing to glycan
LC-MS profiling
keywords:
- mass spectrometry
- glycomics
- glycoproteomics
license: Apache-2.0
GitHub Events
Total
- Issues event: 1
- Watch event: 5
- Issue comment event: 1
- Push event: 2
Last Year
- Issues event: 1
- Watch event: 5
- Issue comment event: 1
- Push event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Joshua Klein | m****n@g****m | 2,457 |
| Christian Heckendorf | h****c@g****m | 6 |
Packages
- Total packages: 1
-
Total downloads:
- pypi 60 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
- Total maintainers: 1
pypi.org: glycresoft
Glycan and Glycopeptide Mass Spectrometry Database Search Tool
- Documentation: https://mobiusklein.github.io/glycresoft
- License: Apache Software License
-
Latest release: 0.4.24
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- SPARQLWrapper *
- click *
- dill *
- jinja2 >=2.11.1
- lxml *
- matplotlib *
- numpy *
- pyteomics *
- python-idzip >=0.3.2
- pyzstd *
- rdflib *
- requests *
- scikit-learn *
- scipy *
- six *
- sqlalchemy <1.4.0
- SPARQLWrapper *
- brain-isotopic-distribution >=1.5.8
- click *
- dill *
- glycopeptidepy >=0.0.15
- glypy >=1.0.6
- jinja2 >=2.11.1
- lxml *
- matplotlib *
- ms_deisotope >=0.0.36
- ms_peak_picker >=0.1.35
- numpy *
- pyteomics *
- python-idzip >=0.3.2
- pyzstd *
- rdflib *
- requests *
- scikit-learn *
- scipy *
- six *
- sqlalchemy <1.4.0
- actions/checkout v2 composite
- docker/build-push-action v2 composite
- docker/login-action v1 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- mobiusklein/ms_deisotope latest build