BTEP Video Archive of Past Classes

BTEP Single Cell Half Day (March 23rd)

• Mike Kelly presentation
  • Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=88cab9860935550e0c344855932e8449
  • Slides
• Kimia Dadkhah presentation, Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=53b6172258525c8e30a363c668dbf4f0
• Abdalla Abdelmaksoud presentation, Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=82614165eeb7a3abeda632e0963d3032
• Stefan Cordes presentation, Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=a4ab6fe37bb9a5cfedab34dbe01b4032

  BTEP Coding Club

  The BTEP Coding club is a new initiative to provide more tailored bioinformatics training to the NCI community. Each month we will feature a 1-hour demo / tutorial of a bioinformatics tool, software, skill, or platform. We welcome suggestions from the NCI community. Email us at ncibtep@nih.gov if there is a specific topic you would like to see featured.
  
  Course documentation: https://bioinformatics.ccr.cancer.gov/docs/btep-coding-club/
  
  
  • March 15th: VLOOKUP in excel and the R programming equivalent Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=979fd07f613f74e9e7fae19ee1a14d83

  Partek Flow Training

  • March 8th, Single cell RNA sequencing analysis with Partek Flow, Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=ce7fe9d4b9f3eb3419434ae731a42a2f

  Introduction to Unix on Biowulf (Jan – Feb)

  This course series introduces scientists to working on Biowulf, the Unix-based and high-performance compute system at NIH. Biowulf staff installs and maintains hundreds of tools for working with large datasets such as those generated from high-throughput sequencing. Course documentation: https://btep.ccr.cancer.gov/docs/unix-on-biowulf-2023/
  • Lesson 1, Getting connected to Biowulf Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=032d972b0179679e782aa5e91c768424
  • Lesson 2, Overview of Biowulf environment and navigating Unix file systems Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=451ce4c03ea6b33cea1c5555c69df27b
  • Lesson 3, File/directory permissions, copying files/directories, listing directory content, and removing files Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=555c3a0deafe31672b2e7352bb214e5c
  • Lesson 4, Moving, renaming, and removing files/directories Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=653c656a2f1bcb27dc56c472ad307c70
  • Lesson 5, Working with interactive sessions and bioinformatics applications on Biowulf Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=7e107abddd45232f8b6078313c97c80b
  • Lesson 6, Submitting shell scripts to the Biowulf batch system Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=096447ad2fcb8b328b770bc1e7e52df1
  • Lesson 7, Downloading data from the web, viewing file content, and searching for patterns in files Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=0327e14b365f345c713102af1036a019

  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 and RStudio IDE Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=372a37975aedba342158cd79d161c167
  • Lesson 2, R Basics Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=3bec2ee683cf0bdf8e3ee6db6d8a6875
  • Lesson 3, Data Frames Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=264936cfa4972bbb93fd6a323fd0961f
  • Lesson 4, Data Frames Cont’d / Data Wrangling Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=964b300de17bc972656c865348d6ca2e
  • Lesson 5, Data Wrangling with the Tidyverse Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e3f0d88fa03ee1dc29a65f055ca3af66
  • Lesson 6, Introduction to data visualization with ggplot2 Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=de715222acfeb2dd315fb549759de16a
  • Lesson 7, Data Visualization with ggplot2 Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=fc92813bb3a34138b8616c051585b66f

  Bulk RNA-Seq Data Analyses: Learn About Expression Counts with Qlucore (Jan 25)

  We will go over the  different types of expression counts – raw counts, FPKM, RPKM, TPM, and CPM to help you make better decisions with your data. Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=0b57e53057895b1662f6d8040d82f762
  Slides are here: Expression counts for RNAseq Jan 2023

  Introduction to Bioinformatics Resources for NCI CCR Scientists (Jan 12)

  Learn about the: (1) NIH Bioinformatics Calendar, (2) Training Opportunities, (3) Upcoming Events, (4) New BTEP Website Resources, (5) Biowulf, (6) Next-Gen Seq Analysis Tools (Partek Flow, Qlucore, Qiagen IPA), (7) Workflows, (8) Cloud Resources, (9) NCI Sequencing Cores, (10) NIH Training Resources.
  Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=69e3b859e87d766b9361524e12288034

Microbiome Analysis with QIIME 2

• 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

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

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

• 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)

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

Bioinformatics Resources for CCR Scientists (July 26)

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

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

Data Wrangling with R (June 7 – July 7)

• Lesson 1, June, 7^th: 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
• Lesson 2, June 9^th: 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
• 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
• 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
• 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
• Lesson 6, June 23^rd: 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 5^th: 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 7^th: 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)

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

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

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

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

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)

• 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)

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

R Introductory Series (Jan – Feb)

• 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)