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Galaxy Single-cell Community: Year in Review

The Galaxy Single-cell Community provides a 2023 review!

swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)

🚀Embarking on a cosmic journey, the Galaxy Single-cell Community has clustered together to unveil a constellation of tools, making strides in RNA-stellar discoveries and creating out-of-this-world workflows. With a commitment to battling work duplication across the multiverse, this community is boldly charting a course for global domination, proving that when it comes to bioinformatics, the Galaxy is the limit!✨

Tools & Workflows

The past year has been a spectacular journey in advancing tools and workflows within the Galaxy Single-cell Community. Breaking free from the confines of scRNA-seq, we've expanded our horizons to include tools for analyzing data from other modalities such as single-cell ATAC-seq and CITE-Seq. Dive into our updated scRNA-seq analysis tools, now featuring more downstream analysis options for trajectory analysis. We've even thrown in advanced analysis tools for estimating cell type proportions from bulk RNA-seq data!

RNA STARSolo just got a makeover to version 2.7.10b, boasting a revamped UI, Velocyto-like UMI counting, and nifty alternatives for quantifying single nuclei data. Analyzing single-cell ATAC-seq data on Galaxy is now a breeze with the introduction of the EpiScanpy tool suite, built on the renowned Scanpy toolkit. Plus, we've added some powerful tools from the Sinto toolkit for preprocessing scATAC-seq data on Galaxy. And that's not all! The MuSiC tool suite in Galaxy now unveils deconvolution tools for discovering cell type composition in bulk RNA-seq using cell types within scRNA-seq. Multi-faceted comparisons are now at your fingertips with the MuSiC Compare tool.

Seurat fans, rejoice! Updates have rolled in, offering additional functionalities and optional CITE-seq capabilities at runtime.

Community Infrastructure

Our efforts in community building have seen the unification of single-cell subdomains into https://singlecell.usegalaxy.eu/, the creation of the Single Cell Community of Practice hub page (https://galaxyproject.org/projects/singlecell/), and a user-focused Matrix channel. Testing brilliant widgets, automated updates, and the latest addition of automated help request updates onto Matrix channels have made community collaboration a breeze.

Global Connections

Down under, the Australian BioCommons launched their Single Cell and Spatial Omics Analysis Infrastructure Roadmap for Australia, complementing our endeavors to unite across timezones. Collaboration, including international tool adventures across three continents, proves that team work does, in fact, make the dream work.


Get ready for a thrilling journey through the Single Cell Training's latest updates! The Case Study Reloaded tutorial, fueled by three remote-working undergrads, introduces parallel trajectory analysis in R, Python, and the Galaxy GUI.

Sustainability shines as we've revamped numerous tutorials with hands-on and video re-recordings. New tools bring new tutorials, such as Pre-processing of 10X Single-Cell ATAC-seq Datasets and Comparing inferred cell compositions using MuSiC deconvolution.

Tackling user hurdles, our data ingest and conversion tutorials in the Changing data formats & preparing objects section await exploration.

Dive into the unique Tips, tricks & other hints section, offering analysis options like parameter iteration for swift optimization or Removing the effects of the cell cycle for precise clustering analysis.

And don't miss our inaugural Learning Pathway, guiding Galaxy novices to becoming single-cell analysis experts!

Fighting Work Duplication

Our mission: No more work duplication! We've consolidated single-cell instances and are diligently preventing tool and infrastructure duplication, creating smoother pathways across servers. We value efficiency here at single-cell, so we'd like to thank ChatGPT (free version) for adding in Galaxy puns to this post, as per our request.

What a Year!

What's next on our list? World domination or global collaboration? You decide. Stay tuned for another exciting year with the Galaxy Single-cell Community!