single-cell

Tutorials covering single-cell

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Single Cell

Lesson Slides Hands-on Recordings Input dataset Workflows
An introduction to scRNA-seq data analysis
Bulk RNA Deconvolution with MuSiC
transcriptomics deconvolution
Converting between common single cell data formats
data management data import sc_formats
Generating a single cell matrix using Alevin
paper-replication MIGHTS
Generating a single cell matrix using Alevin and combining datasets (bash + R)
10x paper-replication MIGHTS jupyter-notebook
Pre-processing of 10X Single-Cell ATAC-seq Datasets
10x epigenetics
Pre-processing of 10X Single-Cell RNA Datasets
10x
Clustering 3K PBMCs with Scanpy
10x
Combining single cell datasets after pre-processing
paper-replication MIGHTS
Comparing inferred cell compositions using MuSiC deconvolution
transcriptomics deconvolution
Filter, plot and explore single-cell RNA-seq data with Scanpy (Python)
paper-replication MIGHTS jupyter-notebook
Filter, plot, and explore single cell RNA-seq data with Seurat (R)
paper-replication MIGHTS rmarkdown-notebook jupyter-notebook
Importing files from public atlases
data import data management sc_formats
Removing the effects of the cell cycle
Drop-seq
Single-cell ATAC-seq standard processing with SnapATAC2
10x epigenetics single-cell
Single-cell ATAC-seq standard processing with SnapATAC2
10x epigenetics single-cell
Understanding Barcodes
single-cell
Understanding Barcodes
single-cell
Analysis of plant scRNA-Seq Data with Scanpy
plants paper-replication 10x
Clustering 3K PBMCs with Seurat
10x
Converting NCBI Data to the AnnData Format
data management data import sc_formats
Evaluating Reference Data for Bulk RNA Deconvolution
transcriptomics deconvolution
Filter, plot and explore single-cell RNA-seq data with Scanpy
paper-replication MIGHTS
Filter, plot, and explore single cell RNA-seq data with Seurat
paper-replication MIGHTS
Inferring single cell trajectories with Scanpy (Python)
paper-replication MIGHTS jupyter-notebook
Multi-sample batch correction with Harmony and SnapATAC2
10x epigenetics
Plates, Batches, and Barcodes
Scanpy Parameter Iterator
single-cell
Scanpy Parameter Iterator
single-cell
Batch Correction and Integration with Seurat or Scanpy
10x
Inferring single cell trajectories with Monocle3 (R)
paper-replication MIGHTS rmarkdown-notebook jupyter-notebook
Inferring single cell trajectories with Scanpy
paper-replication MIGHTS
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
data management deconvolution
Single-cell Formats and Resources
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
transcriptomics data management deconvolution
Inferring single cell trajectories with Monocle3
paper-replication MIGHTS
Trajectory analysis
Automated Cell Annotation
GO Enrichment Analysis on Single-Cell RNA-Seq Data
single-cell GO enrichment
GO Enrichment Analysis on Single-Cell RNA-Seq Data
single-cell GO enrichment
Pseudobulk Analysis with Decoupler and EdgeR
transcriptomics pseudobulk

Contributors

This material was contributed to by:

orcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice Batutorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzDavid López avatar David Lópezorcid logoDaniel Blankenberg avatar Daniel BlankenbergMenna Gamal avatar Menna GamalMehmet Tekman avatar Mehmet TekmanCarlos Chee Mendonça avatar Carlos Chee MendonçaDonny Vrins avatar Donny Vrinsorcid logoAnthony Bretaudeau avatar Anthony BretaudeauSimon Bray avatar Simon Brayorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMarius van den Beek avatar Marius van den Beekorcid logoMorgan Howells avatar Morgan Howellsorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoHelena Rasche avatar Helena RascheCamila Goclowski avatar Camila Goclowskiorcid logoMartin Čech avatar Martin Čechorcid logoJulia Jakiela avatar Julia Jakielaorcid logoMohua Das avatar Mohua Dasorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoArmin Dadras avatar Armin DadrasJonathan Manning avatar Jonathan Manningorcid logoGraham Etherington avatar Graham Etheringtonorcid logoMarisa Loach avatar Marisa Loachorcid logoNate Coraor avatar Nate CoraorPablo Moreno avatar Pablo Morenoorcid logoFlorian Heyl avatar Florian Heylorcid logoMatthias Bernt avatar Matthias Berntorcid logoTeresa Müller avatar Teresa Müllerorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoLucille Delisle avatar Lucille Delisleorcid logoWendi Bacon avatar Wendi Baconorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamienieckaorcid logoGraeme Tyson avatar Graeme TysonGildas Le Corguillé avatar Gildas Le Corguilléorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoTimon Schlegel avatar Timon Schlegel

Funding

These individuals or organisations provided funding support for the development of this resource

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UFR
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de.KCD
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DASH UK
This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.
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EPSRC/OU
The research internship was supported through EPSRC Training Grant DTP 2020-2021 Open University
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BioFAIR
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EOSC-Life
EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
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ELIXIR Europe
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de.NBI