Microbiome Analysis with QIIME 2

Course materials: https://btep.ccr.cancer.gov/docs/qiime2/

Lesson 2 (Oct 24th): Getting Started with QIIME 2 (Data import)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=d7fca7b1d6b3441c445770782762c712

Lesson 3 (Oct 26th): Creating a feature table (Trimming and denoising)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=354bc1bfb92d6288a0c00ed0a7a1c777

Lesson 4 (Oct 31st): Feature table filtering, taxonomic classification, and phylogeny

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=b6ca607256a4e8c461487b40362fc51c

Lesson 5-6 (Nov 7th): Alpha and Beta diversity

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=b667466d9ae5f273cf273b6ecc7f93d1

Lesson 7 (Nov 9th): Course Wrap-Up

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4d90e55b0adaebe54bff0ed5030783f3

Greg Caporaso: Toward Fully Reproducible Microbiome Multi-omics Bioinformatics with QIIME 2 (Oct 19th)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c44af836ce9dd1631b58ccc285880a56

Bioinformatics for Beginners: RNA-Seq Data Analysis (Sept 27th – Dec 13th)

Course materials: https://btep.ccr.cancer.gov/docs/b4b/

Lesson 1 (Sept 27th): Introduction to Unix and the Shell

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e19e1849d27f8b3f04aed4321ced7d2c

Lesson 2 (Sept 29th): Navigating file systems with Unix

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=dea8f906e57eca037127a54c3b7e93b7

Lesson 3 (Oct 4th): Introduction to Biowulf 

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4a04321c200300b362ca7a5ff80c59f8

Lesson 4 (Oct 6th): Useful Unix 

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4b159fc6f848ba715346fbb80e0af75e

Lesson 5 (Oct 11th):  Working on Biowulf

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=78a0cae7bb4a4827d3b810f9429a323e

Lesson 6 (Oct 13th): Downloading data from the SRA

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=9c52e2e33df72d435d66fe8f21d33f0e

Lesson 7 (Oct 18th): Review; Downloading RNA-Seq Data

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=752ff24fd25f93a7b69ec295404e04a5

Lesson 8 (Oct 20th): Introduction to RNA sequencing

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=cc07b2529a448e51faf326399fa0d7f4

Lesson 9 (Oct 25th): RNA sequencing: Getting to know reference genomes and annotations

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=efd124edc61536dadac4ea2d631c4fe0

Lesson 10 (Oct 27th): RNA sequencing: FASTQ files and assessing sequencing data quality

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=0b98531157512a78e8f4f2cce1c7d03e

Lesson 11 (Nov 1st): RNA sequencing: Aggregating FASTQC reports and trimming

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=832b386b16123baca2fd8398feb9497e

Lesson 12 (Nov 3rd): RNA sequencing: Review of reference genomes, annotations, FASTQ files, assessing sequencing data quality and trimming

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=593764eda003f31b2766c2bef5f6c74c

Lesson 13 (Nov 8th): RNA sequencing: Alignment of sequencing data to reference genome, part 1

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4d877f2bc99d5ded9515f0ef4f5bb1ca

Lesson 13 (Nov 10th): RNA sequencing: Alignment of sequencing data to reference genome, part 2

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c96bec102980bab422beb4dfbb2b27c8

Lesson 14 (Nov 15th): Visualizing genomic data using the Integrative Genome Viewer

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=16f17a6a3f0854a24c238409d1ec584b

Lesson 15 (Nov 17th): Finding Differentially Expressed Genes

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=88929fd74383ddfa010c3a568fec200e

Lesson 16 (Nov 29th): Classification based RNA sequencing analysis

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=97819965be99b59d53e59e26009b0072

Lesson 17 (Dec 1st): Introduction to gene ontology and pathway analysis

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=5c6a9f415202606a12515f5bbb5c26b1

Lesson 18 (Dec 6th): Functional Annotation Analysis with DAVID

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e40b65d867f24c06718ce1cfd8689f07

Lesson 19 (Dec 8th): Introduction to Qiagen Ingenuity Pathway Analysis

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e2fb05d4f0479a491b6fc3fcb13490bd

Lesson 20 (Dec 13th): Course Wrap-up

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=69b4b4550053c2260a37253ad93ca83c

Qiagen Pathway Analysis for Beginners: Generating a Gene Network from Experimental Data (August 31)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e141aefc6a798f6510fbae29ad98ea41

Qiagen IPA upcoming webinars and trainings

Previously recorded webinars and trainings for IPA

For questions, email Qiagen technical support: ts-bioinformatics@qiagen.com

Creating Publication Ready RNA-Seq Graphs in Partek Flow (Aug 24)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=3d5ea2c9c65a811972d0ff1f884e2dda

Bioinformatics Resources for CCR Scientists (July 26)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=9d83c3a41b5c017de966f39178ea6b03

Presentation slides: Presentation Intro to Bioinformatics Resources FINAL VERSION

Variant Analysis – Experimental Design, Best Practices, and Workflows (June 30)

Recording link: https://cbiit.webex.com/recordingservice/sites/cbiit/recording/8cd6adf4dacc103a83be00505681c451

Presentation slides:
Variant analysis – presentation 1
Variant analysis – presentation 2

Chat history: chat history

Qlucore: Bulk RNA-Seq Data Analysis (June 29)

Recording link: https://cbiit.webex.com/webappng/sites/cbiit/recording/c788382fd9e1103ab7f6005056818fce

Data Wrangling with R (June 7 – July 7)

Course Materials: https://btep.ccr.cancer.gov/docs/data-wrangle-with-r/

Lesson 1, June, 7th: Introduction to R, RStudio, and the Tidyverse

This will be a no coding introduction to R, RStudio, and the Tidyverse. In this lesson, we will review some of the advantages of using R for data analysis and will get you acquainted with the RStudio environment. The help session will be devoted to getting everyone connected to the course on DNAnexus.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=5544470024885f1aa54c26fc5c9ff6cf

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/chat_672022_class.txt

Lesson 2, June 9th: Getting started with R.

Lesson 2 will focus on some of the basics of R programming including naming and assigning R objects, recognizing and using R functions, understanding data types and classes, becoming familiar with the R programming syntax.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=b2f4a57b5ed8665cbdba3d77c669a104

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/chat_692022_class.txt

Lesson 3, June 14: Importing and reshaping data

In lesson 3, we will learn how to import simple and complex data and how to avoid common mistakes. We will also learn how to reshape data, for example, from wide to long format, with tidyr.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=109d6971e46be8b6b60314851618b0bd

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/chat_6142022_class.txt

Lesson 4, June 16: Data Visualization with ggplot2

Lesson 4 will be a brief reprieve from data wrangling. In this lesson, we will learn the basics of plotting with ggplot2.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=fe980430c8ce0bb712f41ad40feb591b

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/chat_6162022_class.txt

Lesson 5, June 21st: Introducing dplyr and the pipe

In Lesson 5, we will learn how to improve code interpretability with the pipe (%>%) from the magrittr package. We will also learn how to merge and filter data frames.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=8b8544f8e907940d3ad20140758a876e

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/chat_6212022_class.txt

Lesson 6, June 23rd: Continue data wrangling with dplyr.

In Lesson 6, we will continue to wrangle data using dplyr. This lesson will focus on functions such as group_by(), arrange(), summarize(), and mutate().

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=cfd33a9e5ee40128be58079472311e74

Lesson 7, July 5th: Lesson Review

In Lesson 7 we will review many of the important concepts we learned throughout the course.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=31ffede1577700afeba4ea74b90a20e8

Lesson 8, July 7th: Working with your own data.

Lesson 8 will be a BYOD (bring your own data) class. You will have two hours to work on your own data and get help accordingly. If you do not have your own data, we will provide a data set and practice questions for you to test your wrangling skills.

Partek Flow: Bulk and Single Cell Gene Expression Visualization (May 18)

Recording link:  https://cbiit.webex.com/cbiit/ldr.php?RCID=b5b1948aab3093124275d06fa55b08ae

Qlucore: Import and analyze public data from SRA, GEO and TCGA (May 11)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c8e8e8ff837caeb2d4d3839bc180b9bb

Training: Access GEO, SRA, ArrayExpress, TCGA, GTEx and more with Qiagen IPA Land Explorer (April 20)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=d081980970fce4cb50dd20d3f4f3e172

Single Cell RNA-Seq Analysis with Partek Flow (April 13)

Recording Link: https://cbiit.webex.com/cbiit/ldr.php%3FRCID%3D02b734d9f2b8466bf996ccc5d52d0c02

Qlucore: Pathway Analysis with Gene Set Enrichment Analysis (GSEA) (April 6)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=8cfdd939b601f0402b312ba2f8e85262

Recommended Resources:

  1. GSEA hands-on webinar_Qlucore.pdf
  2. GSEA in Qlucore.pdf
  3. GSEA_MSigDB Collections.pdf
  4. How to do Pathway Analysis A.pdf
  5. MSigDB Hallmark human gene sets UCSD.pdf
  6. PNAS-2005-Subramanian-GSEA.pdf

Data Visualization with R (April 5 – May 10)

Course Materials: https://btep.ccr.cancer.gov/docs/data-visualization-with-r/

Lesson 1, April 5: Introduction to plot types

Why R for data visualization? We will introduce the various plot types that will be generated throughout the course and will showcase related plots that you will be able to create in the future using the foundational skills gained.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=5bfc45c875be766b41f8a9948487a822

Lesson 2, April 12: Basics of ggplot2

In lesson 2 of the Data Visualization with R series we will focus on the basics of ggplot2, including the grammar of graphics philosophy and its application. This lesson will provide a hands on introduction to the ggplot2 syntax, geom functions, mapping and aesthetics, and plot layering.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c2bacdc4f78ef005f1356fb2d8b798c4

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/data_visualization_r_lesson2_chat.txt

Lesson 3, April 19:  Scatter plots and ggplot2 customization

In lesson 3 of the Data Visualization with R series we will continue the discussion on the grammar of graphics, with a focus on ggplot2 plot customization including axes labels, coordinate systems, axes scales, and themes. This hands on lesson will showcase these features of plot building through the generation of increasingly complex scatter plots using data included with a base R installation as well as RNASeq data.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=ee0789d3b2cb5cc40c77f0d9e8bb3790

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/data_visualization_r_lesson3_chat.txt

Lesson 4, April 26: Visualizing summary statistics with histograms, bar plots, and box plots

In lesson 4 of the Data Visualization with R series we will learn to generate plots that will help with visualization of summary statistics including a bar plot with error bars, histogram, as well as the box and whiskers plot.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=83a227f93612bdc27637783e586d7025

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/data_visualization_r_lesson4_thursday_chat.txt

Lesson 5, May 3: Visualizing clusters with heatmaps

In lesson 5 of the Data Visualization with R series we will introduce the heatmap and dendrogram as tools for visualizing clusters in data.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4183dc8595b722b9eed9aa32a0e016ef

Lesson 6, May 10: Combining multiple plots to create a figure panel

Chat history: data_visualization_r_lesson6

In lesson 6 of the Data Visualization with R series we will focus on generating sub plots and multi plot figure panels using ggplot2 associated packages. This will allow us to meet any figure limitations that scientific journals may have.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=890e966d5e6520052426214db0345d96

Chat history: https://btep.ccr.cancer.gov/wp-content/uploads/data_visualization_r_lesson6_tuesday_chat.txt

Introducing QIIME2, a Powerful Platform for Microbiome Analysis (March 24)

QIIME2 is a powerful microbiome analysis platform with a wide array of tools that can be used throughout all stages of your microbiome workflow, from raw data to statistical evaluation and visualization.

This course will provide an overview of QIIME2, which will include an introduction to the core plugins and methods available with a base QIIME2 installation, tools for reproducibility and visualization, features available for community support and help, and additional learning opportunities.

Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=2ad95564340a539395ff3c62e1126ae3

Link to Slides: qiime2_overview

Qlucore: Single Cell Data, from 10x Output to Clustering, Cluster ID and Statistical Analysis in a Visual Qlucore Platform (February 23)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e5cdeb4d9a3720b6807ab767d78c4e40

R Introductory Series (Jan – Feb)

This course will include a series of lessons for individuals new to R or with limited R experience. The purpose of this course is to introduce the foundational skills necessary to begin to analyze and visualize data in R. This course is not designed for those with intermediate R experience and is not tailored to any one specific type of analysis.

Course documentation: https://btep.ccr.cancer.gov/docs/rintro/

Lesson 1,  Introduction to R: Why Learn R?, Getting Started with R and RStudio, R Basics

Recording: https://cbiit.webex.com/cbiit/ldr.php?RCID=db2be53e42f365c74246c02dfc41867b

Lesson 2,  Data Frames and Data Wrangling

Recording: https://btep.ccr.cancer.gov/events/r-introductory-series-2022/r-class-lesson-2-2022-02-08-13-03-58-2/

Lesson 3,  Working with Tabular Data in R

Recording: https://btep.ccr.cancer.gov/wp-content/uploads/R-class-Lesson-3-2022-02-15-13-04-05.mp4

Lesson 4,  Visualize Data in Graphs, Plots and Charts with R

Recording: https://cbiit.webex.com/cbiit/ldr.php?RCID=f2ef31106aef2a6fb9979377dfd0f563

Partek Flow: Variant DNA-Seq Data Analysis (January 19)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=95300876cd21dcdf724b34450edf02b7