dvp-io
Read/write functions to and from spatialdata for Deep Visual Proteomics
Science Score: 57.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
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○Academic publication links
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○Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary
Repository
Read/write functions to and from spatialdata for Deep Visual Proteomics
Basic Info
- Host: GitHub
- Owner: MannLabs
- License: apache-2.0
- Language: Python
- Default Branch: main
- Homepage: https://dvp-io.readthedocs.io/en/latest/
- Size: 9.76 MB
Statistics
- Stars: 8
- Watchers: 5
- Forks: 3
- Open Issues: 2
- Releases: 7
Metadata Files
README.md
dvp-io
Read and write funtionalities from and to spatialdata for deep visual proteomics
Getting started
Please refer to the documentation, in particular, the API documentation, tutorials, and the FAQs.
Installation
You need to have Python 3.10 or newer installed on your system.
Users
Install the latest release of dvp-io from PyPI:
```bash
Optional: Create a suitable conda envionemnt
conda create -n dvpio python=3.11 -y && conda activate dvpio ```
bash
pip install dvp-io
C++ dependencies
Some critical dependencies of dvpio require C++ bindings, so a suitable C++ compiler must be installed.
For Unix Users (Linux, macOS)
Ensure cmake and libssh2 are installed by running:
```shell
Unix
conda install -n dvpio conda-forge::cmake conda-forge::libssh2 ```
Windows users
Windows users require the Microsoft Visual C++ (MSVC) compiler. Before creating the dvpio environment, follow these steps:
- Download and install Visual Studio.
- In the installer, select Desktop Development with C++ as a workload.
- Complete the installation and restart your system if necessary.
After installation, proceed with the dvp-io installation steps above.
Developers
Install the latest development version
In your shell, go to your favorite directory and clone the repository. Then, make an editable install
```shell
Optional create environment
conda install -n dvpio-dev python=3.11 && conda activate dvpio-dev
Clone
git clone https://github.com/lucas-diedrich/dvp-io.git
Go into the directory
cd dvp-io
Make editable, local installation, including development dependencies
pip install -e ".[dev,doc]" ```
Release notes
Refer to the Releases page for information on releases and the changelog.
References
SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes Niklas Arndt Schmacke, Sophia Clara Maedler, Georg Wallmann, Andreas Metousis, Marleen Berouti, Hartmann Harz, Heinrich Leonhardt, Matthias Mann, Veit Hornung bioRxiv 2023.06.01.542416; doi: https://doi.org/10.1101/2023.06.01.542416
Marconato, L. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods 1–5 (2024) doi:10.1038/s41592-024-02212-x.
Zeng, W.-F. et al. AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics. Nat Commun 13, 7238 (2022).
Owner
- Name: Mann Labs
- Login: MannLabs
- Kind: organization
- Repositories: 16
- Profile: https://github.com/MannLabs
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: dvp-io
message: >-
Read and write funtionalities from and to spatialdata for
deep visual proteomics
type: software
authors:
- given-names: Lucas
family-names: Diedrich
email: diedrich@biochem.mpg.de
affiliation: Max-Planck-Institute of Biochemistry
name-suffix: †
orcid: "https://orcid.org/0009-0007-4884-1422"
repository-code: "https://github.com/lucas-diedrich/dvp-io"
url: "https://dvp-io.readthedocs.io/en/latest/index.html"
abstract: >
Read/write functions to and from spatialdata for Deep
Visual Proteomics
keywords:
- spatial-omics
- proteomics
license: Apache-2.0
GitHub Events
Total
- Delete event: 1
- Issue comment event: 1
- Push event: 5
- Pull request review event: 2
- Pull request review comment event: 5
- Pull request event: 5
- Create event: 2
Last Year
- Delete event: 1
- Issue comment event: 1
- Push event: 5
- Pull request review event: 2
- Pull request review comment event: 5
- Pull request event: 5
- Create event: 2
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 0
- Total pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.33
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.33
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- lucas-diedrich (3)
Top Labels
Issue Labels
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Dependencies
- actions/checkout v4 composite
- actions/setup-python v5 composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- actions/checkout v4 composite
- actions/setup-python v5 composite
- pypa/gh-action-pypi-publish release/v1 composite
- actions/checkout v4 composite
- actions/setup-python v5 composite
- codecov/codecov-action v3 composite
- dawidd6/action-download-artifact v2 composite
- anndata *
- napari-spatialdata *
- openslide-bin *
- openslide-python *
- py-lmd *
- pylibczirw *
- spatialdata *
- spatialdata-plot *