Single Cell — Editorial Board Home

This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.

Editorial Board

orcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoFlorian Heyl avatar Florian Heylorcid logoMarisa Loach avatar Marisa Loachorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoPavankumar Videm avatar Pavankumar Videm

Action Items

Item Status Why you should do this
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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
An introduction to scRNA-seq data analysis ✅ ✅ ✅
Understanding Barcodes ✅ ✅ ✅ ✅
Plates, Batches, and Barcodes ✅ ✅ ✅ ✅
Single-cell Formats and Resources ✅ ✅ ✅ ✅
Trajectory analysis ✅ ✅ ✅ ✅
Automated Cell Annotation ✅ ✅ ✅ ✅
Pre-processing of 10X Single-Cell RNA Datasets ✅ ✅ ✅ ✅
Clustering 3K PBMCs with Scanpy ✅ ✅ ✅ ✅
Clustering 3K PBMCs with Seurat ✅ ✅ ✅ ✅
Generating a single cell matrix using Alevin ✅ ✅ ✅ ✅
Combining single cell datasets after pre-processing ✅ ✅ ✅ ✅
Filter, plot and explore single-cell RNA-seq data with Scanpy ✅ ✅ ✅ ✅
Filter, plot, and explore single cell RNA-seq data with Seurat ✅ ✅ ✅ ✅
Inferring single cell trajectories with Scanpy ✅ ✅ ✅ ✅
Inferring single cell trajectories with Monocle3 ✅ ✅ ✅ ✅
Generating a single cell matrix using Alevin and combining datasets (bash + R) ✅ ✅ ✅ ✅ ✅
Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) ✅ ✅ ✅ ✅ ✅
Filter, plot, and explore single cell RNA-seq data with Seurat (R) ✅ ✅ ✅ ✅ ✅
Inferring single cell trajectories with Scanpy (Python) ✅ ✅ ✅ ✅ ✅
Inferring single cell trajectories with Monocle3 (R) ✅ ✅ ✅ ✅ ✅
Pre-processing of Single-Cell RNA Data ✅ ✅ ✅ ✅
Downstream Single-cell RNA analysis with RaceID ✅ ✅ ✅ ✅
Analysis of plant scRNA-Seq Data with Scanpy ✅ ✅ ✅ ✅
Bulk RNA Deconvolution with MuSiC ✅ ✅ ✅ ✅
Comparing inferred cell compositions using MuSiC deconvolution ✅ ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution ✅ ✅ ✅ ✅
Pre-processing of 10X Single-Cell ATAC-seq Datasets ✅ ✅ ✅ ✅
Single-cell ATAC-seq standard processing with SnapATAC2 ✅ ✅ ✅ ✅
Multi-sample batch correction with Harmony and SnapATAC2 ✅ ✅ ✅
Single Cell Proteomics data analysis with bioconductor-scp ✅ ✅
Single-cell quality control with scater ✅ ✅ ✅ ✅
Removing the effects of the cell cycle ✅ ✅ ✅ ✅
Scanpy Parameter Iterator ✅ ✅ ✅ ✅
Batch Correction and Integration with Seurat or Scanpy ✅ ✅ ✅
Converting between common single cell data formats ✅ ✅ ✅ ✅
Importing files from public atlases ✅ ✅ ✅ ✅
Converting NCBI Data to the AnnData Format ✅ ✅ ✅ ✅
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution ✅ ✅ ✅ ✅
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution ✅ ✅ ✅ ✅
GO Enrichment Analysis on Single-Cell RNA-Seq Data ✅ ✅ ✅ ✅
Pseudobulk Analysis with Decoupler and EdgeR ✅ ✅ ✅ ✅
Spatial transcriptomics analysis of a primary dermal melanoma section from Xenium ✅ ✅ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Understanding Barcodes Understanding Barcodes Nov 3, 2026 1 ✅ ✅ ❌
Pre-processing of 10X Single-Cell RNA Datasets GTN - Preprocessing of 10X scRNA-seq data Nov 3, 2026 4 ✅ ✅ ❌
Clustering 3K PBMCs with Scanpy Clustering 3k PBMC with Scanpy Nov 3, 2026 2 ✅ ✅ ❌
Clustering 3K PBMCs with Seurat Clustering 3k PBMCs with Seurat - Workflow Nov 3, 2026 1 ✅ ✅ ✅
Clustering 3K PBMCs with Seurat Cluster 3k PBMCs with Seurat - Workflow - SCTransform Version Nov 3, 2026 1 ✅ ✅ ✅
Generating a single cell matrix using Alevin Generating a single cell matrix using Alevin Nov 3, 2026 1 ❌ ❌ ❌
Generating a single cell matrix using Alevin LOCKED | Generating a single cell matrix using Alevin Nov 3, 2026 1 ❌ ✅ ✅
Combining single cell datasets after pre-processing Combining datasets after pre-processing Nov 3, 2026 1 ❌ ❌ ❌
Combining single cell datasets after pre-processing LOCKED | Combining single cell datasets after pre-processing Nov 3, 2026 1 ❌ ✅ ✅
Filter, plot and explore single-cell RNA-seq data with Scanpy CS3_Filter, Plot and Explore Single-cell RNA-seq Data Nov 3, 2026 1 ✅ ✅ ❌
Filter, plot and explore single-cell RNA-seq data with Scanpy Filter, Plot and Explore Single-cell RNA-seq Data updated Nov 3, 2026 1 ✅ ❌ ❌
Filter, plot and explore single-cell RNA-seq data with Scanpy Filter plot and explore single-cell RNA-seq data with Scanpy (imported from uploaded file) Nov 3, 2026 1 ✅ ✅ ✅
Filter, plot, and explore single cell RNA-seq data with Seurat Seurat Filter, Plot and Exlore tutorial Nov 3, 2026 1 ✅ ❌ ❌
Inferring single cell trajectories with Scanpy Inferring Trajectories with Scanpy Tutorial Workflow Nov 3, 2026 1 ✅ ❌ ❌
Inferring single cell trajectories with Monocle3 AnnData object to Monocle input files Nov 3, 2026 1 ❌ ❌ ❌
Inferring single cell trajectories with Monocle3 Monocle3 workflow Nov 3, 2026 1 ❌ ❌ ❌
Inferring single cell trajectories with Monocle3 Trajectory analysis using Monocle3 - full tutorial workflow Nov 3, 2026 1 ✅ ❌ ❌
Pre-processing of Single-Cell RNA Data CelSeq2: Multi Batch (mm10) Nov 3, 2026 1 ❌ ❌ ❌
Pre-processing of Single-Cell RNA Data CelSeq2: Single Batch (mm10) Nov 3, 2026 1 ❌ ❌ ❌
Downstream Single-cell RNA analysis with RaceID RaceID Workflow Nov 3, 2026 1 ✅ ✅ ❌
Analysis of plant scRNA-Seq Data with Scanpy scRNA Plant Analysis Nov 3, 2026 1 ❌ ❌ ❌
Analysis of plant scRNA-Seq Data with Scanpy scRNA Plant Analysis Nov 3, 2026 1 ✅ ✅ ❌
Bulk RNA Deconvolution with MuSiC MuSiC: Deconvolution Nov 3, 2026 3 ✅ ✅ ✅
Bulk RNA Deconvolution with MuSiC Music: Pre-grouping cell types Nov 3, 2026 1 ✅ ✅ ✅
Comparing inferred cell compositions using MuSiC deconvolution MuSiC-Deconvolution: Compare Nov 3, 2026 1 ❌ ❌ ❌
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 1 - Create pseudobulk and actual proportions Nov 3, 2026 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 2 - Inferring cellular proportions Nov 3, 2026 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 3 - Preprocess Visualisations Nov 3, 2026 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 4 - Compute metrics Nov 3, 2026 1 ✅ ✅ ✅
Pre-processing of 10X Single-Cell ATAC-seq Datasets scATAC-seq Count Matrix Filtering Nov 3, 2026 2 ✅ ✅ ❌
Pre-processing of 10X Single-Cell ATAC-seq Datasets scATAC-seq FASTQ to Count Matrix Nov 3, 2026 2 ✅ ✅ ❌
Single-cell ATAC-seq standard processing with SnapATAC2 Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 Nov 3, 2026 3 ✅ ✅ ✅
Multi-sample batch correction with Harmony and SnapATAC2 Multisample Batch Correction with SnapATAC2 and Harmony Nov 3, 2026 1 ❌ ✅ ✅
Single-cell quality control with scater Single-cell QC with scater Nov 3, 2026 2 ✅ ✅ ❌
Removing the effects of the cell cycle Cell Cycle Regression Workflow Nov 3, 2026 2 ✅ ✅ ❌
Scanpy Parameter Iterator Scanpy Parameter Iterator workflow full (imported from URL) Nov 3, 2026 1 ✅ ❌ ❌
Batch Correction and Integration with Seurat or Scanpy Batch Correction - Scanpy Nov 3, 2026 1 ✅ ✅ ✅
Batch Correction and Integration with Seurat or Scanpy Batch Correction - Seurat Nov 3, 2026 1 ✅ ✅ ✅
Converting between common single cell data formats AnnData to Cell Data Set (CDS) conversion Nov 3, 2026 1 ✅ ❌ ❌
Converting between common single cell data formats AnnData to Seurat conversion Nov 3, 2026 1 ✅ ❌ ❌
Converting between common single cell data formats AnnData to SingleCellExperiment (SCE) conversion Nov 3, 2026 1 ✅ ❌ ❌
Importing files from public atlases EBI SCXA to AnnData (Scanpy) or Seurat Object Nov 3, 2026 2 ✅ ✅ ❌
Converting NCBI Data to the AnnData Format NCBI to Anndata Nov 3, 2026 2 ✅ ✅ ✅
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution MuSiC-Deconvolution: Data generation | sc | matrix + ESet Nov 3, 2026 1 ❌ ❌ ❌
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution MuSiC-Deconvolution: Data generation | sc | metadata Nov 3, 2026 1 ❌ ❌ ❌
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution MuSiC-Deconvolution: Data generation | bulk | ESet Nov 3, 2026 1 ❌ ❌ ❌
GO Enrichment Analysis on Single-Cell RNA-Seq Data GO Enrichment Workflow Nov 3, 2026 1 ✅ ✅ ❌
Pseudobulk Analysis with Decoupler and EdgeR Pseudobulk with decoupler and edgeR tutorial workflow Nov 3, 2026 2 ✅ ✅ ❌
Spatial transcriptomics analysis of a primary dermal melanoma section from Xenium Normalising_clustring_and_spatial_melanoma_without_scaling_xenium_workflow Nov 3, 2026 1 ✅ ✅ ❌
Spatial transcriptomics analysis of a primary dermal melanoma section from Xenium Quality_control_and_filtering_melanoma_xenium_workflow Nov 3, 2026 1 ✅ ✅ ❌
Spatial transcriptomics analysis of a primary dermal melanoma section from Xenium full_melanoma_without_scaling_xenium_workflow Nov 3, 2026 1 ✅ ✅ ❌

Your topic's Workflow Testing Results

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Learning Pathways using materials from this Topic

Image of cells in different coloured clusters
Applying single-cell RNA-seq analysis

Gone is the pre-annotated, high quality tutorial data - now you have real, messy data to deal with. You have decisions to make and parameters to decide. This learning pathway challenges you to replicate a published analysis as if this were your own dataset. You will be introduced to a few more tools available for scRNA-seq in Galaxy. Finally, if...

intermediate single-cell
XY plot of actual versus inferred proportions, with coloured dots representing clusters and largely falling in a 1-1 slope
Bioinformatics Projects: Using deconvolution to get new insights from old bulk RNA-seq data

Are you an educator looking for project ideas for students to practice independent enquiry and research skills? Are you a student looking for a project idea? Look no more - here, you will find a learning pathway of tutorials that can guide you through the skills to find old data and transform it into new results! To be clear, we...

advanced single-cell
Image of cells in different coloured clusters
Introduction to Galaxy and Single Cell RNA Sequence analysis

This learning path aims to teach you the basics of Galaxy and analysis of Single Cell RNA-seq data. You will learn how to use Galaxy for analysis, and an important Galaxy feature for iterative single cell analysis. You’ll tbe guided through the general theory of single analysis and then perform a basic analysis of 10X chromium data. For support throughout...

beginner single-cell
Image of cells in different coloured clusters
Applying single-cell RNA-seq analysis in Coding Environments

Gone is the pre-annotated, high quality tutorial data - now you have real, messy data to deal with. You have decisions to make and parameters to decide. This learning pathway challenges you to replicate a published analysis as if this were your own dataset. You will perform this analysis in coding environments hosted on Galaxy, instead of Galaxy’s button-based tool...

advanced single-cell
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Events using materials from this Topic

TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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