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

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

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

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