e-learning
Importing files from public atlases
Abstract
Public single cell datasets seem to accumulate by the second. Well annotated, quality datasets are slightly trickier to find, which is why projects like the Single Cell Expression Atlas (SCXA) exist - to curate datasets for public use. Here, we will guide you through transforming data imported from the SCXA repository into the input file required for the Filter, Plot, Explore tutorial and we will also show how to use the public atlases for your own research.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How do I use the EBI Single Cell Expression Atlas and Human Cell Atlas?
- How can I reformat and manipulate the downloaded files to create the correct input for downstream analysis?
Learning Objectives
- You will retrieve raw data from the EBI Single Cell Expression Atlas and Human Cell Atlas.
- You will manipulate the metadata and matrix files.
- You will combine the metadata and matrix files into an AnnData or Seurat object for downstream analysis.
Licence: Creative Commons Attribution 4.0 International
Keywords: Single Cell, data import, data management
Target audience: Students
Resource type: e-learning
Version: 6
Status: Active
Prerequisites:
- Combining single cell datasets after pre-processing
- Generating a single cell matrix using Alevin
- Introduction to Galaxy Analyses
Learning objectives:
- You will retrieve raw data from the EBI Single Cell Expression Atlas and Human Cell Atlas.
- You will manipulate the metadata and matrix files.
- You will combine the metadata and matrix files into an AnnData or Seurat object for downstream analysis.
Date modified: 2025-01-14
Date published: 2023-11-14
Contributors: Björn Grüning, Helena Rasche, Julia Jakiela, Mehmet Tekman, Pablo Moreno, Pavankumar Videm, Saskia Hiltemann, Wendi Bacon
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