Package: pixelgen-pixelator
PixelatorDocumentation|Installation|Usage|Contributing|Contact|License|CreditsPixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) assays
and analyze PXL data.It provides thepixelatorcommandline tool to process FASTQ files and generate PXL files and reports
and can be used as a python library for further downstream processing.© 2023 - Pixelgen Technologies ABDocumentationMore information about pixelator is available on thePixelgen Technologies Software documentation site.InstallationPixelgen 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 pipOur software pixelator is available on PyPi aspixelgen-pixelatorand can be installed with pip.
It is recommended to install pixelator in a separate virtual environment.pipinstallpixelgen-pixelatorInstallation with conda / mambaA conda package is available on the bioconda channel and can be installed with conda or mamba.condainstall-cbiocondapixelatorormambainstall-cbiocondapixelatorInstallation from sourceYou can also install pixelator from source by cloning the repository.gitclonehttps://github.com/pixelgentechnologies/pixelator.gitcdpixelator
pipinstall.Using dockerThepixelatorcommand-line tool can be run with docker images available on
theGitHub container registry.dockerpullghcr.io/pixelgentechnologies/pixelator:latest
dockerrunghcr.io/pixelgentechnologies/pixelator:latestpixelator--helpYou can also use the containers provided by the biocontainers project onquay.io.UsageOur 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.ContributingContribution are welcome!
Please check out thecontributing guidelinesfor more information.ContactFor feature requests or bug reports, please use the GitHubissues.
For questions, comments, or suggestions you can use the GitHubdiscussions.You can also email the development team atdevelopers@pixelgen.com.LicensePixelator is licensed under theMITlicense.CreditsPixelator is developed and maintained by thedevelopersatPixelgen 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: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023.https://doi.org/10.1101/2023.06.05.543770.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 allcode contributors!A non-exhaustive list of contributors follows:Filip Karlsson (@fika-pixelgen)Max Karlsson (@maxkarlsson)