ncibtep@nih.gov

Bioinformatics Training and Education Program

Class Documents

Most BTEP courses include detailed course materials including lesson content, additional resources, and lesson associated data. These course materials are listed here so that learners can easily return to and review concepts taught in class and/or reproduce code. These materials are also meant to serve as stand alone tutorials for those unable to attend a given course.

Note: not all classes include detailed course material. Other course materials including presentation slides and handouts can also be found here.

Programming Languages

Data Analysis

  • From Theory to Practice: An Introduction to Microbiome Analysis with Nephele
    • This content was from a 2-day workshop on microbiome analysis with Nephele. Day 1 covered the various ways to study the microbiome including important concepts and best practices in microbial community analysis, while Day2 provided hands-on experience with Nephele, NIAID’s free application for microbiome analysis. 
  • Getting Started with scRNA-Seq
    • This content was from a mini series, designed to help attendees learn more about single cell RNA-Seq, from applicable technologies to data analysis. This was not a course. While content from each seminar is complementary, each seminar was designed independently.
  • Microbiome Analysis with QIIME2
    • This course was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME2 platform. Course topics included how to format data and metadata, import data, demultiplex sequences, trim sequences, denoise and classify sequences, and conduct basic analyses including measures of alpha and beta diversity.
  • Bioinformatics for Beginners: RNA-Seq 2025
    • This course was designed to teach the basic skills needed for bioinformatics, including working on the Unix command line. This course primarily focused on RNA-Seq analysis. All steps of the RNA-Seq workflow, from raw data to differential expression and gene ontology analysis, were covered.
  • Bioinformatics for Beginners: RNA-Seq 2026
    • This course introduced fundamental skills needed for bioinformatics, including working on Unix command line. It also introduced experimental and analytical considerations for bulk RNA sequencing and focused on interpreting as well as further analysis of results generated from a pre-built pipeline. Topics discussed included QC, trimming, alignment, expression estimation, differential expression and pathway analysis.
  • Variant Analysis – Experimental Design, Best Practices, and Workflows (June 30, 2022)
  • Qlucore: Pathway Analysis with Gene Set Enrichment Analysis (GSEA) (April 6)
  • Introducing QIIME2, a Powerful Platform for Microbiome Analysis (March 24)

Data Management, Sharing and Transfer

CCR Bioinformatics Resources

  • BTEP – Bioinformatics Resources for CCR Scientists
    • These pages list and describe the main resources available to CCR scientists for carrying out bioinformatic analysis on their data.
      • These resources include:
        1. Places to obtain training and assistance – BTEP Resources
        2. Information about data delivered by the NCI sequencing facilities
        3. High performance compute facilites – Biowulf/Helix
        4. Using Globus to transfer large files
        5. Commercial Software licensed by NCI for use by CCR scientists
        6. Open source resources developed by the scientific community
        7. Info about network storage facilities

Other