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

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

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

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

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

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