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

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 May 13, 2025 1 ✅ ✅ ❌
Pre-processing of 10X Single-Cell RNA Datasets GTN - Preprocessing of 10X scRNA-seq data May 13, 2025 4 ✅ ✅ ❌
Clustering 3K PBMCs with Scanpy Clustering 3k PBMC with Scanpy May 13, 2025 2 ✅ ✅ ❌
Clustering 3K PBMCs with Seurat Clustering 3k PBMCs with Seurat - Workflow May 13, 2025 1 ✅ ✅ ✅
Clustering 3K PBMCs with Seurat Cluster 3k PBMCs with Seurat - Workflow - SCTransform Version May 13, 2025 1 ✅ ✅ ✅
Generating a single cell matrix using Alevin Generating a single cell matrix using Alevin May 13, 2025 1 ❌ ❌ ❌
Generating a single cell matrix using Alevin LOCKED | Generating a single cell matrix using Alevin May 13, 2025 1 ❌ ✅ ✅
Combining single cell datasets after pre-processing Combining datasets after pre-processing May 13, 2025 1 ❌ ❌ ❌
Combining single cell datasets after pre-processing LOCKED | Combining single cell datasets after pre-processing May 13, 2025 1 ❌ ✅ ✅
Filter, plot and explore single-cell RNA-seq data with Scanpy CS3_Filter, Plot and Explore Single-cell RNA-seq Data May 13, 2025 1 ✅ ✅ ❌
Filter, plot and explore single-cell RNA-seq data with Scanpy Filter, Plot and Explore Single-cell RNA-seq Data updated May 13, 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) May 13, 2025 1 ✅ ✅ ✅
Filter, plot, and explore single cell RNA-seq data with Seurat Seurat Filter, Plot and Exlore tutorial May 13, 2025 1 ✅ ❌ ❌
Inferring single cell trajectories with Scanpy Inferring Trajectories with Scanpy Tutorial Workflow May 13, 2025 1 ✅ ❌ ❌
Inferring single cell trajectories with Monocle3 AnnData object to Monocle input files May 13, 2025 1 ❌ ❌ ❌
Inferring single cell trajectories with Monocle3 Monocle3 workflow May 13, 2025 1 ❌ ❌ ❌
Inferring single cell trajectories with Monocle3 Trajectory analysis using Monocle3 - full tutorial workflow May 13, 2025 1 ✅ ❌ ❌
Pre-processing of Single-Cell RNA Data CelSeq2: Multi Batch (mm10) May 13, 2025 1 ❌ ❌ ❌
Pre-processing of Single-Cell RNA Data CelSeq2: Single Batch (mm10) May 13, 2025 1 ❌ ❌ ❌
Downstream Single-cell RNA analysis with RaceID RaceID Workflow May 13, 2025 1 ✅ ✅ ❌
Analysis of plant scRNA-Seq Data with Scanpy scRNA Plant Analysis May 13, 2025 1 ❌ ❌ ❌
Analysis of plant scRNA-Seq Data with Scanpy scRNA Plant Analysis May 13, 2025 1 ✅ ✅ ❌
Bulk RNA Deconvolution with MuSiC MuSiC: Deconvolution May 13, 2025 3 ✅ ✅ ✅
Bulk RNA Deconvolution with MuSiC Music: Pre-grouping cell types May 13, 2025 1 ✅ ✅ ✅
Comparing inferred cell compositions using MuSiC deconvolution MuSiC-Deconvolution: Compare May 13, 2025 1 ❌ ❌ ❌
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 1 - Create pseudobulk and actual proportions May 13, 2025 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 2 - Inferring cellular proportions May 13, 2025 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 3 - Preprocess Visualisations May 13, 2025 1 ✅ ✅ ✅
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 4 - Compute metrics May 13, 2025 1 ✅ ✅ ✅
Pre-processing of 10X Single-Cell ATAC-seq Datasets scATAC-seq Count Matrix Filtering May 13, 2025 1 ✅ ❌ ❌
Pre-processing of 10X Single-Cell ATAC-seq Datasets scATAC-seq FASTQ to Count Matrix May 13, 2025 1 ✅ ❌ ❌
Single-cell ATAC-seq standard processing with SnapATAC2 Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 May 13, 2025 2 ✅ ✅ ✅
Multi-sample batch correction with Harmony and SnapATAC2 Multisample Batch Correction with SnapATAC2 and Harmony May 13, 2025 1 ❌ ✅ ✅
Single-cell quality control with scater Single-cell QC with scater May 13, 2025 2 ✅ ✅ ❌
Removing the effects of the cell cycle Cell Cycle Regression Workflow May 13, 2025 2 ✅ ✅ ❌
Scanpy Parameter Iterator Scanpy Parameter Iterator workflow full (imported from URL) May 13, 2025 1 ✅ ❌ ❌
Converting between common single cell data formats AnnData to Cell Data Set (CDS) conversion May 13, 2025 1 ✅ ❌ ❌
Converting between common single cell data formats AnnData to Seurat conversion May 13, 2025 1 ✅ ❌ ❌
Converting between common single cell data formats AnnData to SingleCellExperiment (SCE) conversion May 13, 2025 1 ✅ ❌ ❌
Importing files from public atlases EBI SCXA to AnnData (Scanpy) or Seurat Object May 13, 2025 2 ✅ ✅ ❌
Converting NCBI Data to the AnnData Format NCBI to Anndata May 13, 2025 2 ✅ ✅ ✅
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution MuSiC-Deconvolution: Data generation | sc | matrix + ESet May 13, 2025 1 ❌ ❌ ❌
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution MuSiC-Deconvolution: Data generation | sc | metadata May 13, 2025 1 ❌ ❌ ❌
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution MuSiC-Deconvolution: Data generation | bulk | ESet May 13, 2025 1 ❌ ❌ ❌
GO Enrichment Analysis on Single-Cell RNA-Seq Data GO Enrichment Workflow May 13, 2025 1 ✅ ✅ ❌
Pseudobulk Analysis with Decoupler and EdgeR Pseudobulk with decoupler and edgeR tutorial workflow May 13, 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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