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

• R Introductory Series (Jan – Feb, 2023)
  • This course introduced the foundational skills necessary to begin to analyze and visualize data in R and was designed for individuals new to R or with limited R experience.
• Data Visualization with R
  •  The purpose of this course was to introduce learners to data visualization with R with a primary focus on ggplot2 and related packages. Course content was developed for those with beginner level experience in R.
• Data Wrangling with R
  • This course was designed for those with beginner level experience to introduce learners to essential R packages and functions needed to explore, clean, transform, and summarize data.
• How to install and setup and R environment

Data Analysis

• 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
  • 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.
• Variant Analysis – Experimental Design, Best Practices, and Workflows (June 30, 2022)
  • Presentation slides:
    • Variant analysis – presentation 1
    • Variant analysis – presentation 2
• Qlucore: Pathway Analysis with Gene Set Enrichment Analysis (GSEA) (April 6)
  • Recommended Resources:
    • GSEA hands-on webinar_Qlucore
    • GSEA in Qlucore
    • GSEA_MSigDB Collections
    • How to do Pathway analysis A
    • MSigDB Hallmark human gene sets UCSD
    • PNAS-2005-Subramanian-GSEA
• Introducing QIIME2, a Powerful Platform for Microbiome Analysis (March 24)
  • Presentation slides: qiime2_overview

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

• Introduction to Unix on Biowulf (Jan – Feb, 2023)
  • Biowulf is the high performance compute cluster at NIH and runs on a Unix-like operating system. This course series introduced the basics of working in Unix command line on Biowulf.
• BTEP Coding Club