Register now for an upcoming seminar on January 22, 2025, “Revealing Tumor-Promoting Signals in Breast Cancer Subtypes: A NIDAP Analysis of Single-Cell Data”. This one-hour talk will feature guest speaker and NIDAP developer, Josh Meyer, who will take you through an analysis of a publicly available BRCA single-cell atlas (link) to identify changes in the tumor microenvironment across breast cancer subtypes. By the end of this session, attendees will be able to:
- Understand the structure and capabilities of the CCBR Single-Cell RNA-seq Workflow on NIDAP, including cell filtering, clustering, batch correction, visualization (e.g. UMAP, t-SNE, violin plot, etc.), cell annotation, differential expression, and pathway analysis.
- Access training resources and support for using this single-cell workflow, as well as additional NIDAP workflows (Bulk RNA-seq, Digital Spatial Profiling, and Visium) to analyze your own data.
Learn more about this session here, or register now.
What is NIDAP? NIDAP is an innovative, cloud-based, collaborative data aggregation and analysis platform that hosts user-friendly bioinformatics workflows and component analysis and visualization tools developed by the NCI developer community based on open source tools and makes them immediately available to biologist end-users across NIH. CCR researchers can access NIDAP on the NIH network at nidap.nih.gov.
Visit the NIDAP website.
Why use NIDAP? NCI researchers have access to several cloud platforms, software suites, and related bioinformatics platforms. What advantages does NIDAP offer? The primary benefits of NIDAP include:
- Expandability & Flexibility – Workflows can be rearranged or created bespoke for specific analysis needs. Researchers may also be interested in popular CCBR workflows including bulk RNA-Seq, scRNA-Seq, and digital spatial profiling (DSP). See more info here.
- Reproducibility – Results are reproducible and portable by anyone once extracted to GitHub.
- Education – Users can learn both the biology and the code behind an analysis to the depth they desire with trainings and access to CCR Collaborative Bioinformatic Resource (CCBR) expert collaboration.
- Security – Users can work independently or collaboratively with PII/PHI in a secure environment.
What do we mean by single-cell analysis? Single-cell analysis includes methods for genomic, transcriptomic, proteomic, and metabolomic investigations at the level of a single cell. These methods provide a higher resolution of information compared to traditional approaches that investigate populations of cells (e.g., bulk RNA-seq). Examples of methods that fall under single cell analysis include single-cell transcriptomics (scRNA-Seq), single-cell proteomics, single-cell genomics (scDNA-Seq), single-cell epigenomics (scATAC-Seq, scChIP-Seq), and single-cell metabolomics. Single-cell spatial analysis adds a spatial dimension to these methods, allowing scientists to better understand aspects of cellular location, organization, and interaction.
What workflows are available on NIDAP? As mentioned above, users can create workflows specific to their analysis needs using NIDAP. This can be done independently or with the help of CCBR experts. NIDAP contains workflows including single-cell RNA-Seq, Bulk RNA-seq, spatial analysis (DSP & Visium), and workflows for single-cell spatial transcriptomics and proteomics (e.g., MAWA, SPAC).
The best place to learn more about these workflows is by navigating to the NIDAP SharePoint site and selecting a desired workflow.
Where can you learn more about single cell analysis and NIDAP? Learn more about the CCBR single-cell workflow on NIDAP here.
Interested in a hands-on tutorial? See training information available on our NIDAP training site here or sign up for a dedicated training session: Sign Up for a NIDAP Hands-on Workshop.
Who can you contact for help or more information? For questions about the workflows or additional support, contact CCR Support at NCICCBRNIDAP@mail.nih.gov. You can also attend weekly consultation sessions on Thursdays 3-5 PM in-person at the NIH Bethesda Campus, Building 37, Room 3041 or virtually on Microsoft Teams (Meeting Link). Additional bioinformatics support and consultation can be requested using the CCBR Project Help Form.
– NIDAP Team