pixelgen-pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

https://github.com/pixelgentechnologies/pixelator

Science Score: 57.0%

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

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CITATION.cff file
Found 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 5 DOI reference(s) in README
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary

Keywords

molecular-pixelation pixelgen-technologies protein proteomics proximity-network single-cell single-cell-omics spatial

Keywords from Contributors

sequences mesh interpretability generic projection interactive optim genomics hacking network-simulation

Last synced: 6 months ago · JSON representation ·

Repository

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

Basic Info

Host: GitHub
Owner: PixelgenTechnologies
License: mit
Language: Python
Default Branch: dev
Homepage: https://pixelgen.com
Size: 77.7 MB

Statistics

Stars: 15
Watchers: 4
Forks: 2
Open Issues: 2
Releases: 26

Topics

molecular-pixelation pixelgen-technologies protein proteomics proximity-network single-cell single-cell-omics spatial

Created over 2 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Citation

Pixelator

Pixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) and Proximity Network (PNA) assays and analyze PXL data.

It provides the pixelator commandline tool to process FASTQ files and generate PXL files and reports and can be used as a python library for further downstream processing.

Documentation

More information about pixelator is available on the Pixelgen Technologies Software documentation site.

Installation

Pixelgen Technologies has developed and tested pixelator extensively in Ubuntu 20.04.6 LTS. However, pixelator should run on computers installed with any recent version of the major Linux distributions, even if installed in Windows WSL.

It should only take a few minutes to install pixelator on any modern computer using any of the following methods.

Installation with pip

Our software pixelator is available on PyPi as pixelgen-pixelator and can be installed with pip. It is recommended to install pixelator in a separate virtual environment.

shell pip install pixelgen-pixelator

Installation with conda / mamba

A conda package is available on the bioconda channel and can be installed with conda or mamba.

shell conda install -c bioconda pixelator

shell mamba install -c bioconda pixelator

Installation from source

You can also install pixelator from source by cloning the repository.

shell git clone https://github.com/pixelgentechnologies/pixelator.git cd pixelator pip install .

Using docker

The pixelator command-line tool can be run with docker images available on the GitHub container registry.

shell docker pull ghcr.io/pixelgentechnologies/pixelator:latest docker run ghcr.io/pixelgentechnologies/pixelator:latest pixelator --help

You can also use the containers provided by the biocontainers project on quay.io.

Usage

Our recommendation is to use pixelator via the specific Nextflow pipeline, nf-core/pixelator.

It should take only a few seconds to download the pipeline and approx. 20 min to run the default test dataset in a normal commodity computer.

However, with MPX data, we recommend running pixelator in specialized hardware with at least 32GB RAM.

Contributing

Contribution are welcome! Please check out the contributing guidelines for more information.

Contact

For feature requests or bug reports, please use the GitHub issues. For questions, comments, or suggestions you can use the GitHub discussions.

You can also email the development team at developers@pixelgen.com.

License

Pixelator is licensed under the MIT license.

Credits

Pixelator is developed and maintained by the developers at Pixelgen Technologies.

When using pixelator in your research, please cite the following publication:

Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. "Molecular pixelation: spatial proteomics of single cells by sequencing." Nature Methods, May 8, 2024. https://doi.org/10.1038/s41592-024-02268-9.

Main development happened thanks to:

Jose Fernandez Navarro (@jfnavarro)
Alvaro Martinez Barrio (@ambarrio)
Johan Dahlberg (@johandahlberg)
Florian De Temmerman (@fbdtemme)

A huge thank you to all code contributors!

Citation (CITATIONS.md)

# pixelator: Citations

## Pipeline tools

- [pixelator](https://doi.org/10.1101/2023.06.05.543770)

  > Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular pixelation: spatial proteomics of single cells by sequencing.” Nature Methods, May 8, 2024. https://doi.org/10.1038/s41592-024-02268-9.

- [cutadapt](http://dx.doi.org/10.14806/ej.17.1.200)

  > Martin, Marcel. “Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads.” EMBnet.Journal 17, no. 1 (May 2, 2011): 10–12. https://doi.org/10.14806/ej.17.1.200.

- [fastp](https://doi.org/10.1002/imt2.107)

  > Chen, Shifu. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” IMeta 2, no. 2 (2023): e107. https://doi.org/10.1002/imt2.107.

- [networkx](https://networkx.org/)

  > Aric A. Hagberg, Daniel A. Schult and Pieter J. Swart, “Exploring network structure, dynamics, and function using NetworkX”, in Proceedings of the 7th Python in Science Conference (SciPy2008), Gäel Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA), pp. 11–15, Aug 2008

- [graspologic](https://microsoft.github.io/graspologic/latest/index.html)

  > Chung, J., Pedigo, B. D., Bridgeford, E. W., Varjavand, B. K., Helm, H. S., & Vogelstein, J. T. (2019). GraSPy: Graph Statistics in Python. Journal of Machine Learning Research, 20(158), 1-7.

- [local G](https://doi.org/10.1007/s11749-018-0599-x)

  > Bivand, R.S., Wong, D.W.S. Comparing implementations of global and local indicators of spatial association. TEST 27, 716–748 (2018). https://doi.org/10.1007/s11749-018-0599-x

- [dsb](https://doi.org/10.1038/s41467-022-29356-8)

  > Mulè, M.P., Martins, A.J. & Tsang, J.S. Normalizing and denoising protein expression data from droplet-based single cell profiling. Nat Commun 13, 2099 (2022). https://doi.org/10.1038/s41467-022-29356-8

GitHub Events

Total

Create event: 60
Issues event: 1
Release event: 9
Watch event: 5
Delete event: 45
Issue comment event: 8
Push event: 233
Pull request review comment event: 70
Pull request review event: 86
Pull request event: 101
Fork event: 1

Last Year

Create event: 60
Issues event: 1
Release event: 9
Watch event: 5
Delete event: 45
Issue comment event: 8
Push event: 233
Pull request review comment event: 70
Pull request review event: 86
Pull request event: 101
Fork event: 1

Committers

Last synced: about 2 years ago

All Time

Total Commits: 219
Total Committers: 9
Avg Commits per committer: 24.333
Development Distribution Score (DDS): 0.429

Past Year

Commits: 219
Committers: 9
Avg Commits per committer: 24.333
Development Distribution Score (DDS): 0.429

Top Committers

Name	Email	Commits
Johan Dahlberg	j**g@p**h	125
fbdtemme	f**n@p**m	68
Alvaro Martinez Barrio	A**o@p**h	9
Max Karlsson	m**n@p**m	8
dependabot[bot]	4****]	3
Stefan Petkov	s**v@p**m	2
maxkarlsson	4****n	2
Johan Dahlberg	j**n@u**e	1
Max Karlsson	m**n@p**m	1

Committer Domains (Top 20 + Academic)

pixelgen.com: 3 pixelgen.tech: 2 pixelgenius.pixelgen.com: 1 uppsala-bioinformatics.se: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 2
Total pull requests: 416
Average time to close issues: 24 days
Average time to close pull requests: 4 days
Total issue authors: 2
Total pull request authors: 8
Average comments per issue: 1.5
Average comments per pull request: 0.74
Merged pull requests: 349
Bot issues: 0
Bot pull requests: 16

Past Year

Issues: 2
Pull requests: 122
Average time to close issues: 24 days
Average time to close pull requests: 3 days
Issue authors: 2
Pull request authors: 5
Average comments per issue: 1.5
Average comments per pull request: 0.11
Merged pull requests: 91
Bot issues: 0
Bot pull requests: 3

View more stats

Top Authors

Issue Authors

ambarrio (1)
EitanGronich (1)

Pull Request Authors

johandahlberg (170)
ptajvar (88)
fbdtemme (85)
ambarrio (29)
dependabot[bot] (16)
ludvigla (14)
maxkarlsson (10)
stefanppetkov (4)

Top Labels

Issue Labels

Pull Request Labels

dependencies (16) python (3)

Packages

Total packages: 1
Total downloads:
- pypi 164 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 25
Total maintainers: 3

pypi.org: pixelgen-pixelator

A command-line tool and library to process and analyze data generated from technologies from Pixelgen Technologies.

Homepage: https://github.com/PixelgenTechnologies/pixelator
Documentation: https://software.pixelgen.com
License: MIT
Latest release: 0.21.4
published 6 months ago

Versions: 25
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 164 Last month

Rankings

Dependent packages count: 7.4%

Downloads: 15.7%

Forks count: 30.0%

Average: 32.2%

Stargazers count: 38.9%

Dependent repos count: 68.9%

Maintainers (3)

ambarrio fbdtemme johandahlberg

Last synced: 6 months ago

Dependencies

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145 dependencies

pyproject.toml pypi

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click *
cssselect *
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importlib-resources ^5.12.0
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numpy <1.24.0
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pyarrow *
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scipy *
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environment.yml conda

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python 3.10.*
setuptools >=65.0
virtualenv

pixelgen-pixelator

Science Score: 57.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Pixelator

Documentation

Installation

Installation with pip

Installation with conda / mamba

Installation from source

Using docker

Usage

Contributing

Contact

License

Credits

Citation (CITATIONS.md)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: pixelgen-pixelator

Rankings

Maintainers (3)

Dependencies