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 logoWendi Bacon avatar Wendi Baconorcid logoFlorian Heyl avatar Florian Heylorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMarisa Loach avatar Marisa LoachMehmet 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 ✅ (8 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.
Review Feedback Received Ongoing 🔁 Review all feedback received for the Single Cell topic and create GitHub issues or PRs where needed.
Review open Pull Requests Ongoing 🔁 View all open PRs in the Single Cell topic and review, comment and merge!
Review open GitHub Issues Ongoing 🔁 View all open issues related to the Single Cell topic and comment, fix, or ask others for help!

Topic Materials

Material Contributions v2 help Pre-requisites help 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 Sep 3, 2025 1
Pre-processing of 10X Single-Cell RNA Datasets GTN - Preprocessing of 10X scRNA-seq data Sep 3, 2025 4
Clustering 3K PBMCs with Scanpy Clustering 3k PBMC with Scanpy Sep 3, 2025 2
Clustering 3K PBMCs with Seurat Clustering 3k PBMCs with Seurat - Workflow Sep 3, 2025 1
Clustering 3K PBMCs with Seurat Cluster 3k PBMCs with Seurat - Workflow - SCTransform Version Sep 3, 2025 1
Generating a single cell matrix using Alevin Generating a single cell matrix using Alevin Sep 3, 2025 1
Generating a single cell matrix using Alevin LOCKED | Generating a single cell matrix using Alevin Sep 3, 2025 1
Combining single cell datasets after pre-processing Combining datasets after pre-processing Sep 3, 2025 1
Combining single cell datasets after pre-processing LOCKED | Combining single cell datasets after pre-processing Sep 3, 2025 1
Filter, plot and explore single-cell RNA-seq data with Scanpy CS3_Filter, Plot and Explore Single-cell RNA-seq Data Sep 3, 2025 1
Filter, plot and explore single-cell RNA-seq data with Scanpy Filter, Plot and Explore Single-cell RNA-seq Data updated Sep 3, 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) Sep 3, 2025 1
Filter, plot, and explore single cell RNA-seq data with Seurat Seurat Filter, Plot and Exlore tutorial Sep 3, 2025 1
Inferring single cell trajectories with Scanpy Inferring Trajectories with Scanpy Tutorial Workflow Sep 3, 2025 1
Inferring single cell trajectories with Monocle3 AnnData object to Monocle input files Sep 3, 2025 1
Inferring single cell trajectories with Monocle3 Monocle3 workflow Sep 3, 2025 1
Inferring single cell trajectories with Monocle3 Trajectory analysis using Monocle3 - full tutorial workflow Sep 3, 2025 1
Pre-processing of Single-Cell RNA Data CelSeq2: Multi Batch (mm10) Sep 3, 2025 1
Pre-processing of Single-Cell RNA Data CelSeq2: Single Batch (mm10) Sep 3, 2025 1
Downstream Single-cell RNA analysis with RaceID RaceID Workflow Sep 3, 2025 1
Analysis of plant scRNA-Seq Data with Scanpy scRNA Plant Analysis Sep 3, 2025 1
Analysis of plant scRNA-Seq Data with Scanpy scRNA Plant Analysis Sep 3, 2025 1
Bulk RNA Deconvolution with MuSiC MuSiC: Deconvolution Sep 3, 2025 3
Bulk RNA Deconvolution with MuSiC Music: Pre-grouping cell types Sep 3, 2025 1
Comparing inferred cell compositions using MuSiC deconvolution MuSiC-Deconvolution: Compare Sep 3, 2025 1
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 1 - Create pseudobulk and actual proportions Sep 3, 2025 1
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 2 - Inferring cellular proportions Sep 3, 2025 1
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 3 - Preprocess Visualisations Sep 3, 2025 1
Evaluating Reference Data for Bulk RNA Deconvolution Music Stage 4 - Compute metrics Sep 3, 2025 1
Pre-processing of 10X Single-Cell ATAC-seq Datasets scATAC-seq Count Matrix Filtering Sep 3, 2025 1
Pre-processing of 10X Single-Cell ATAC-seq Datasets scATAC-seq FASTQ to Count Matrix Sep 3, 2025 1
Single-cell ATAC-seq standard processing with SnapATAC2 Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 Sep 3, 2025 2
Multi-sample batch correction with Harmony and SnapATAC2 Multisample Batch Correction with SnapATAC2 and Harmony Sep 3, 2025 1
Single-cell quality control with scater Single-cell QC with scater Sep 3, 2025 2
Removing the effects of the cell cycle Cell Cycle Regression Workflow Sep 3, 2025 2
Scanpy Parameter Iterator Scanpy Parameter Iterator workflow full (imported from URL) Sep 3, 2025 1
Converting between common single cell data formats AnnData to Cell Data Set (CDS) conversion Sep 3, 2025 1
Converting between common single cell data formats AnnData to Seurat conversion Sep 3, 2025 1
Converting between common single cell data formats AnnData to SingleCellExperiment (SCE) conversion Sep 3, 2025 1
Importing files from public atlases EBI SCXA to AnnData (Scanpy) or Seurat Object Sep 3, 2025 2
Converting NCBI Data to the AnnData Format NCBI to Anndata Sep 3, 2025 2
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution MuSiC-Deconvolution: Data generation | sc | matrix + ESet Sep 3, 2025 1
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution MuSiC-Deconvolution: Data generation | sc | metadata Sep 3, 2025 1
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution MuSiC-Deconvolution: Data generation | bulk | ESet Sep 3, 2025 1
GO Enrichment Analysis on Single-Cell RNA-Seq Data GO Enrichment Workflow Sep 3, 2025 1
Pseudobulk Analysis with Decoupler and EdgeR Pseudobulk with decoupler and edgeR tutorial workflow Sep 3, 2025 2

Your topic's Workflow Testing Results

Coming Soon™

Learning Pathways using materials from this Topic

Statistics for your Learning Pathways
Stats powered by Plausible Analytics

Events using materials from this Topic

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

Statistics For Your Materials

Stats powered by Plausible Analytics