Training
Educational materials
New state of the art biomedical technologies such as single-cell and spatial approaches are not common at all institutions of higher education. In those cases, faculty members may not have the opportunity to be exposed to the use and analysis techniques for such data. Significant barriers towards making effective use of such data include the lack of available training incorporating sufficient explanatory and prerequisite background material as well as mentoring support to assist those learning unfamiliar topics.
Training modules
HuBMAP has created several self-paced training modules to fill this gap, which focus on introducing the HuBMAP project, including the technologies/assays used by HuBMAP, the HuBMAP metadata, and example use cases. These modules demonstrate how HuBMAP data could be incorporated into research projects, graduate student theses, and classroom teaching. See the training modules.
Hands-on learning
We also recognize the advantages and effectiveness of hands-on training. To provide opportunities for those who prefer a hands-on approach to learning, we offer hackathons and workshops.
Training modules
Introduction to Single-Cell RNA-Seq (scRNA-seq) Data Analysis
This module will teach you to become proficient in single cell RNA-seq data analysis from HuBMAP. After completing it, you should be able to
- Import HuBMAP preprocessed data into an anndata object with the Python library scanpy.
- Filter cell outliers based on the number of genes expressed for raw data.
- Normalize and log transform raw data.
- Generate clusters and visualize via UMAP dimensional reduction.
- Find cluster-specific marker genes with scanpy.
Super Venn and Venn Diagram to compare the marker genes of the scRNA-seq clusters
This module will teach you to become proficient in generating a Super Venn Diagram to compare the marker genes of all the clusters from HuBMAP's scRNA-seq data analysis and in generating a classical Venn Diagram to compare the marker genes for two clusters from HuBMAP's scRNA-seq data analysis.
After completing it, you should be able to
- Define the lists of marker genes for the clusters from a HuBMAP scRNA-seq data analysis.
- Generate a Super Venn Diagram to compare the marker genes from the clusters of the scRNA-seq data analysis.
- Generate a classical Venn Diagram to compare the marker genes from two clusters that share genes in common from the scRNA-seq data analysis.
- Obtain the list of unique and common genes between two clusters that share genes in common.
Protein-Protein Interaction Networks with the STRING Database
This module will teach you to become proficient in using Python's stringdb library to generate protein-protein interaction networks from a list of marker genes for a cluster from HuBMAP's scRNA-seq data analysis. After completing it, you should be able to
- Define the lists of marker genes for the clusters from a HuBMAP scRNA-seq data analysis with scanpy.
- Map the list of marker genes for cluster 0 to the STRING DB IDs application programming interface (API).
- Make sense of cluster-specific marker genes by generating physical and funtional protein-protein interaction networks with the STRING API.
Gene Ontology Enrichment Analysis
This module will teach you to become proficient in performing gene ontology enrichment analysis for marker genes from HuBMAP's scRNA-seq using the Python goatools library. After completing it, you should be able to
- Define the list of marker genes for a cluster of interest from a HuBMAP data analysis
- Perform Gene Ontology Enrichment Analysis (GOEA) for a cluster of interest from a HuBMAP data analysis
Hackathons
HuBMAP Data Portal Workspaces
September 20 - October 4, 2024
All meetings are virtual.
Workspaces are a new feature on the HuBMAP Data Portal that enable lightweight exploration of public HuBMAP data and user-provided data using Python and R in a Jupyter Lab environment hosted by HuBMAP at no cost. The goal of this Hackathon is for members of the single-cell and spatial biology communities to test how the Workspaces functionality can facilitate their research, and to develop their own Jupyter Notebooks that can be made available as public templates for exploration of HuBMAP data.
Workshops
Data Exploration of HuBMAP data on Bridges-2: HuBMAP’s scRNA-seq Data Analysis, Venn diagrams, and Gene Ontology Enrichment Analysis (GOEA)
March 20 - 21, 2024
Ana G. Mendez University
This comprehensive, two-day workshop was hosted at the Universidad Ana G. Mendez and offered to members of PR-INBRE Bioinformatics Community of Practice (BiCoP). The workshop was designed for professionals and enthusiasts seeking to deepen their understanding of data exploration and analysis with Python, single-cell RNA Sequencing Data Analysis of data from HuBMAP, Venn diagrams and Gene Ontology Enrichment Analysis (GOEA).