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 logoMarisa Loach avatar Marisa Loachorcid logoFlorian Heyl avatar Florian Heylorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoWendi Bacon avatar Wendi BaconMehmet Tekman avatar Mehmet Tekmanorcid logoMorgan Howells avatar Morgan Howells

Action Items

Item Status Why you should do this
Summary Done ✅ Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic.
Sufficient Editorial Board Members Done ✅ (6 members) Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
Enable Subtopics Done ✅ Subtopics help organize the content and make it easier to navigate.
Annotate Funders Done ✅ (7 funders) By annotating the funders of your topic's materials, you make it easier to write your grant reports later
Learning Pathway CTA Done ✅ By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.

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 quality control with scater ✅ ✅ ✅ ✅
Removing the effects of the cell cycle ✅ ✅ ✅ ✅
Scanpy Parameter Iterator ✅ ✅ ✅ ✅
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 ✅ ✅ ✅ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Understanding Barcodes Understanding Barcodes Jun 6, 2025 1 ✅ ✅ ❌
Pre-processing of 10X Single-Cell RNA Datasets GTN - Preprocessing of 10X scRNA-seq data Jun 6, 2025 4 ✅ ✅ ❌
Clustering 3K PBMCs with Scanpy Clustering 3k PBMC with Scanpy Jun 6, 2025 2 ✅ ✅ ❌
Clustering 3K PBMCs with Seurat Clustering 3k PBMCs with Seurat - Workflow Jun 6, 2025 1 ✅ ✅ ✅
Clustering 3K PBMCs with Seurat Cluster 3k PBMCs with Seurat - Workflow - SCTransform Version Jun 6, 2025 1 ✅ ✅ ✅
Generating a single cell matrix using Alevin Generating a single cell matrix using Alevin Jun 6, 2025 1 ❌ ❌ ❌
Generating a single cell matrix using Alevin LOCKED | Generating a single cell matrix using Alevin Jun 6, 2025 1 ❌ ✅ ✅
Combining single cell datasets after pre-processing Combining datasets after pre-processing Jun 6, 2025 1 ❌ ❌ ❌
Combining single cell datasets after pre-processing LOCKED | Combining single cell datasets after pre-processing Jun 6, 2025 1 ❌ ✅ ✅
Filter, plot and explore single-cell RNA-seq data with Scanpy CS3_Filter, Plot and Explore Single-cell RNA-seq Data Jun 6, 2025 1 ✅ ✅ ❌
Filter, plot and explore single-cell RNA-seq data with Scanpy Filter, Plot and Explore Single-cell RNA-seq Data updated Jun 6, 2025 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) Jun 6, 2025 1 ✅ ✅ ✅
Filter, plot, and explore single cell RNA-seq data with Seurat Seurat Filter, Plot and Exlore tutorial Jun 6, 2025 1 ✅ ❌ ❌
Inferring single cell trajectories with Scanpy Inferring Trajectories with Scanpy Tutorial Workflow Jun 6, 2025 1 ✅ ❌ ❌
Inferring single cell trajectories with Monocle3 AnnData object to Monocle input files Jun 6, 2025 1 ❌ ❌ ❌
Inferring single cell trajectories with Monocle3 Monocle3 workflow Jun 6, 2025 1 ❌ ❌ ❌
Inferring single cell trajectories with Monocle3 Trajectory analysis using Monocle3 - full tutorial workflow Jun 6, 2025 1 ✅ ❌ ❌
Pre-processing of Single-Cell RNA Data CelSeq2: Multi Batch (mm10) Jun 6, 2025 1 ❌ ❌ ❌
Pre-processing of Single-Cell RNA Data CelSeq2: Single Batch (mm10) Jun 6, 2025 1 ❌ ❌ ❌
Downstream Single-cell RNA analysis with RaceID RaceID Workflow Jun 6, 2025 1 ✅ ✅ ❌
Analysis of plant scRNA-Seq Data with Scanpy scRNA Plant Analysis Jun 6, 2025 1 ❌ ❌ ❌
Analysis of plant scRNA-Seq Data with Scanpy scRNA Plant Analysis Jun 6, 2025 1 ✅ ✅ ❌
Bulk RNA Deconvolution with MuSiC MuSiC: Deconvolution Jun 6, 2025 3 ✅ ✅ ✅
Bulk RNA Deconvolution with MuSiC Music: Pre-grouping cell types Jun 6, 2025 1 ✅ ✅ ✅
Comparing inferred cell compositions using MuSiC deconvolution MuSiC-Deconvolution: Compare Jun 6, 2025 1 ❌ ❌ ❌
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 1 - Create pseudobulk and actual proportions Jun 6, 2025 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 2 - Inferring cellular proportions Jun 6, 2025 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 3 - Preprocess Visualisations Jun 6, 2025 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 4 - Compute metrics Jun 6, 2025 1 ✅ ✅ ✅
Pre-processing of 10X Single-Cell ATAC-seq Datasets scATAC-seq Count Matrix Filtering Jun 6, 2025 1 ✅ ❌ ❌
Pre-processing of 10X Single-Cell ATAC-seq Datasets scATAC-seq FASTQ to Count Matrix Jun 6, 2025 1 ✅ ❌ ❌
Single-cell ATAC-seq standard processing with SnapATAC2 Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 Jun 6, 2025 2 ✅ ✅ ✅
Multi-sample batch correction with Harmony and SnapATAC2 Multisample Batch Correction with SnapATAC2 and Harmony Jun 6, 2025 1 ❌ ✅ ✅
Single-cell quality control with scater Single-cell QC with scater Jun 6, 2025 2 ✅ ✅ ❌
Removing the effects of the cell cycle Cell Cycle Regression Workflow Jun 6, 2025 2 ✅ ✅ ❌
Scanpy Parameter Iterator Scanpy Parameter Iterator workflow full (imported from URL) Jun 6, 2025 1 ✅ ❌ ❌
Converting between common single cell data formats AnnData to Cell Data Set (CDS) conversion Jun 6, 2025 1 ✅ ❌ ❌
Converting between common single cell data formats AnnData to Seurat conversion Jun 6, 2025 1 ✅ ❌ ❌
Converting between common single cell data formats AnnData to SingleCellExperiment (SCE) conversion Jun 6, 2025 1 ✅ ❌ ❌
Importing files from public atlases EBI SCXA to AnnData (Scanpy) or Seurat Object Jun 6, 2025 2 ✅ ✅ ❌
Converting NCBI Data to the AnnData Format NCBI to Anndata Jun 6, 2025 2 ✅ ✅ ✅
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution MuSiC-Deconvolution: Data generation | sc | matrix + ESet Jun 6, 2025 1 ❌ ❌ ❌
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution MuSiC-Deconvolution: Data generation | sc | metadata Jun 6, 2025 1 ❌ ❌ ❌
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution MuSiC-Deconvolution: Data generation | bulk | ESet Jun 6, 2025 1 ❌ ❌ ❌
GO Enrichment Analysis on Single-Cell RNA-Seq Data GO Enrichment Workflow Jun 6, 2025 1 ✅ ✅ ❌
Pseudobulk Analysis with Decoupler and EdgeR Pseudobulk with decoupler and edgeR tutorial workflow Jun 6, 2025 2 ✅ ✅ ❌

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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