Listed below are the video recordings of past BTEP events (classes, seminars, workshops).
Videos are hosted on various servers and may play slightly differently.
Some videos may be downloaded for local viewing.
Recorded Videos of Recent BTEP Classes
Online Classes 2023
Introduction to Unix on Biowulf (September 7 – September 28)
Course documentation: https://bioinformatics.ccr.cancer.gov/docs/unix-on-biowulf-september-2023/index.html- Lesson 1, September 7, 2023: Overview of Unix and Biowulf and getting connected to Biowulf
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=f553d0c31d41fffe56af4c13f58da84b
- Lesson 2, September 14, 2023: Navigating the Biowulf directory structure, downloading files from the web, and viewing file content
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=ea7ee90b07049e93d1659b2c453d1742
- Lesson 3, September 21, 2023: Working with files and directories, interactive sessions, and exploring Next Generation Sequencing data
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=2b02b4f8acd2dfb7654d839042ea04af - Lesson 4, September 28, 2023: Working with bioinformatics applications on Biowulf and submitting shell as well as swarm scripts to the Biowulf batch system
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=15e40b308b36b0d84f47186bcc68ce42
Python Introductory Series (August 15 – August 29)
Course documentation: https://bioinformatics.ccr.cancer.gov/docs/pies-2023/- Lesson 1, Short introduction to Python, signing onto Biowulf, and starting Jupyter Lab (August 15)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=28b10cbe0179993cd0008f1300a1a9ed - Lesson 2, Python data types, data structures, variable assignment, conditionals, and for loop (August 17)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=41f35ca8d9d251425edd765389b47c32 - Lesson 3, Data wrangling using Pandas (August 22)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=0749d0a1a34b9dbcc3abfbb6b34292ff - Lesson 4, Data visualization using Seaborn (August 29)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=f6dc3393c95acb10a4ffb2a3b1be6a29
Toward Reproducibility with R on Biowulf (July 6 – July 27)
Course documentation: https://bioinformatics.ccr.cancer.gov/docs/reproducible-r-on-biowulf/index.html- Lesson 1, Introduction to Biowulf, Unix, and R (July 6)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=cafa2009842d2c5cf37612b3afee9700 - Lesson 2, Getting Started with R on Biowulf (July 13)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=fbe16cc71e59b3b0a0ccec6b5eed6cf8 - Lesson 3, R Project Management and renv (July 20)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=117505a491e692d053bd4e576f2a2065 - Lesson 4, Submitting R Scripts via command line (July 27)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=652038d995032a8a286298f3a2202b8f
Analyzing your data WITHOUT coding experience: CCR Bioinformatics Licensed Software (June 15)
- Event documentation: https://bioinformatics.ccr.cancer.gov/docs/analyzing-data-without-coding-event/
- Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e3e6f8eb90d93b2c970bb41a64ff872b
Introduction to Bioinformatics Summer Series (June 13 – July 27)
Course documents: https://bioinformatics.ccr.cancer.gov/docs/intro-to-bioinformatics-ss2023/- Lesson 1, Introduction to Bioinformatics Resources (Jun 13)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=be190580b29b47bd48d25d259d9edf29 - Lesson 2, Central Dogma: Analyzing DNA, RNA and Proteins (Jun 29)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=309b53e4b2ebe7f0d120269e6ad5cf4d - Lesson 3, Keeping your Data FAIR: Organizing, Managing, and Sharing Your Data (Jun 27)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=5655241f0503d51b2c01733c82d6486e - Lesson 4, Introduction to High Performance Computing at NIH: Biowulf (Jul 11)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=2f47ba2dd36bd207b35f248ee75a90a9 - Lesson 5, Introduction to R and Python Programming Languages (Jul 18)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=fd2d3c3eb1aa016b9878c354a97eeb0e - Lesson 6, Managing Bioinformatics Projects with Jupyter Notebook(Jul 25)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=e2088e2a42bcd5f78516e1f0a3b11e65
Introduction to Biowulf (May 16 – June 6)
This course series introduces the basics of working on the Biowulf high performance computing cluster.Course documents: https://bioinformatics.ccr.cancer.gov/docs/biowulf-introduction-summer-2023/
- Lesson 1, overview and getting connected to Biowulf
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=28cce463487aa61dd97b62d732c2caed - Lesson 2, navigating Biowulf directories, downloading from the web, and viewing file content
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=cbde92bcc4237094ad2a10e07fd71823 - Lesson 3, moving files, deleting, interactive session, and working with NGS data
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=75d85718cde0d0d457a2490ccc8a9b46 - Lesson 4, Biowulf bioinformatics applications and submitting jobs to the Biowulf batch system
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=2d793194cc55025a49847d7b30b43a71
Data visualization with R (Apr 11 – Apr 27)
In this course series, the audience will learn how to visualize data using the ggplot2 package from R.- Lesson 1, course overview and introduction to plot types
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=6d16336b8f2f4c154afa56801f87b8dc
- Lesson 2, Getting Started with ggplot2
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=186af7d91366197ae4b2149085bb14bb
- Lesson 3, Scatter plots and Non-data elements of ggplot2 customization
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=605c3eda4ddba86c53f012002f165139 - Lesson 4, Bar plots, histograms, and box-and-whiskers plots
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=89915f44b77aa4ba07e3aafbd0311549 - Lesson 5, Heatmap
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=6e6e6a14ea0a8208b40d2e8cd9ea9e18 - Lesson 6, Combining multiple plots to create a figure panel
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c65a62529f75c1cf85617243caa3cf4f
BTEP Distinguished Speakers Seminar Series
- Trey Ideker, AI Models of Cancer and Precision Medicine, March 30
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4f455040f2aac674e84cba882633601d - Brandi Davis-Dusenbery, Power of Connection: How the Cancer Research Data Commons enables researchers to connect data, computational tools, and collaborators to accelerate discovery, May 4
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=787d03f670e64dad649b959c5d521993
Single Cell Annotation Seminar Series
- Rahul Satija, (Azimuth) Annotation of Cell Types in Single Cell Analysis of Cancer, April 6 (no recording available)
- Fabian Theis, Learning and Transferring Cellular State in Single Cell Atlases, May 25
Recording Link:https://cbiit.webex.com/cbiit/ldr.php?RCID=14c28085057da628401be41867deefa9 - Chuan Xu, CellTypist v2.0: Automatic Cell Type Harmonization and Integration in Single Cell Data, June 1
Recording Link:https://cbiit.webex.com/cbiit/ldr.php?RCID=bcc5d2dbe4c472e75ab90d457ae80cad - Mallar Bhattacharya, Single Cell Annotation with SingleR: Macrophage-fibroblast crosstalk in lung fibrosis, June 22
Recording Link: https://cbiit.webex.com/cbiit/ldr.php?RCID=1a0d93304e94ce444a75f7d4ead54857
BTEP Single Cell Half Day (March 23rd)
- Mike Kelly presentation
- 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 - April 19th: Documenting Data Analysis with Jupyter Lab
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=a7ef0bb5b6b339d2c3fe5752179a235a - May 17th: Functional Enrichment Analysis with clusterProfiler
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=3dddfe4378bda5cad5da02b4fb1fd19e - June 21st: Interactive and Batch Jobs on Biowulf
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=3ba419f176468f7a931c4b0a888d952d - July 19th: A Beginner’s Guide to Troubleshooting R Code
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=f59495791096b429040e658218b5fbc8 - August 16th: ComplexHeatmap and EnhancedVolcano
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=a9524ece0edec5811960c308bda1a1c1 - September 20th: Differential Alternative Splicing Analysis using rMATS
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=2c43e6143c47b193d57113eacab5e676
Partek Flow Training
- March 8th, Single cell RNA sequencing analysis with Partek Flow, Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=ce7fe9d4b9f3eb3419434ae731a42a2f
- April 12th, 10x Visium spatial transcriptomics analysis with Partek Flow
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=b6a0cf341297bb50ab28253c5d0feebe
Sample dataset: <https://www.10xgenomics.com/resources/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-0-0
Sample dataset: https://www.10xgenomics.com/resources/datasets/mouse-brain-serial-section-1-sagittal-posterior-1-standard-1-0-0 - May 3rd, ChIP sequencing analysis
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=bc9d1f7961d805b8c7dd8cd9c9479088
- June 14th, Bulk RNA sequencing analysis
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=89e7e3f2f1c94684632967315c9fed22
- September 13, Basic single cell RNA sequencing analysis
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=3af6ad96ae7b0da3753611ed85ceacbc
- September 27, Advanced single cell RNA sequencing analysis: cell type classification and comparison of gene expression among treatment groups, CITE-seq, and spatial transcriptomics
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=a9e4ea60bf8674f5298e640270d35757
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://bioinformatics.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://bioinformatics.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 - Lesson 8, Introduction to Bioconductor and RMarkdown
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c4777e4ce0bb8f81079c7a3e320d24c3
Qlucore
- Qlucore v 3.9: New features – Violin Plots, Statistical Tests, and Using Plot Labels and Colors Effectively Archived (Jun 7) Recording Link
- Bulk RNA-Seq Data Analyses: Learn About Expression Counts (Jan 25) Recording Link
- Slides are here: Expression counts for RNAseq Jan 2023
Introduction to Bioinformatics Resources for NCI CCR Scientists
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 Jan 12: https://cbiit.webex.com/cbiit/ldr.php?RCID=69e3b859e87d766b9361524e12288034
- Recording Link May 11: https://cbiit.webex.com/cbiit/ldr.php?RCID=0a004c341bb0da8b43029a4cb1e0ecc0
Online Classes 2022
Microbiome Analysis with QIIME 2
Course materials: https://bioinformatics.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
Greg Caporaso: Toward Fully Reproducible Microbiome Multi-omics Bioinformatics with QIIME 2 (Oct 19th)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c44af836ce9dd1631b58ccc285880a56Bioinformatics for Beginners: RNA-Seq Data Analysis (Sept 27th – Dec 13th)
Course materials: https://bioinformatics.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.comCreating Publication Ready RNA-Seq Graphs in Partek Flow (Aug 24)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=3d5ea2c9c65a811972d0ff1f884e2ddaBioinformatics 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 VERSIONVariant Analysis – Experimental Design, Best Practices, and Workflows (June 30)
Recording link: https://cbiit.webex.com/recordingservice/sites/cbiit/recording/8cd6adf4dacc103a83be00505681c451Presentation slides:
Qlucore: Bulk RNA-Seq Data Analysis (June 29)
Recording link: https://cbiit.webex.com/webappng/sites/cbiit/recording/c788382fd9e1103ab7f6005056818fceData Wrangling with R (June 7 – July 7)
Course Materials: https://bioinformatics.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
- 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
- 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 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=b5b1948aab3093124275d06fa55b08aeQlucore: Import and analyze public data from SRA, GEO and TCGA (May 11)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c8e8e8ff837caeb2d4d3839bc180b9bbTraining: 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=d081980970fce4cb50dd20d3f4f3e172Single Cell RNA-Seq Analysis with Partek Flow (April 13)
Recording Link: https://cbiit.webex.com/cbiit/ldr.php%3FRCID%3D02b734d9f2b8466bf996ccc5d52d0c02Qlucore: Pathway Analysis with Gene Set Enrichment Analysis (GSEA) (April 6)
Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=8cfdd939b601f0402b312ba2f8e85262Recommended Resources:
- GSEA hands-on webinar_Qlucore.pdf
- GSEA in Qlucore.pdf
- GSEA_MSigDB Collections.pdf
- How to do Pathway Analysis A.pdf
- MSigDB Hallmark human gene sets UCSD.pdf
- PNAS-2005-Subramanian-GSEA.pdf
Data Visualization with R (April 5 – May 10)
Course Materials: https://bioinformatics.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_overviewQlucore: 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=e5cdeb4d9a3720b6807ab767d78c4e40R 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://bioinformatics.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=95300876cd21dcdf724b34450edf02b7Recorded Videos of Other BTEP Events
Distinguished Speaker Series
- Melissa Haendel (University of Colorado, Anschutz), Realizing Data Interoperability Across Basic Research, Clinical Care, and Patients April 21, 2022 https://cbiit.webex.com/cbiit/ldr.php?RCID=42fa0d8d30fa5d0b53d50d534b060065
- Karen Miga (UC Santa Cruz), Expanding Studies of Centromere Structure and Function in the Era of T2T Genomics November 4, 2021 https://cbiit.webex.com/cbiit/ldr.php?RCID=4b56f90d35d1f5cf59fcb6e773cffd83
- Yi Xing (University of Pennsylvania), Computational Tools to Study mRNA Isoform Variation in Cancer October 26, 2021 https://cbiit.webex.com/cbiit/ldr.php?RCID=4b04bb2437cb047bd4d3034bbaab1ccc
- Neville Sanjana (New York University), New Functional Approaches in Human Cancer Models October 14, 2021 https://cbiit.webex.com/cbiit/ldr.php?RCID=0cae5d425e4f4517cd9fbf854f904b50
- Adam Phillippy (NHGRI), Discoveries from the First Truly Complete Sequence of a Human Genome September 16, 2021 https://cbiit.webex.com/cbiit/ldr.php?RCID=14e5a64b30e9de41e645697e3ff8b5b1
- Michael Schatz (Johns Hopkins University), Long Read Sequencing for Cancer Genomics and Beyond June 10, 2021 https://cbiit.webex.com/cbiit/ldr.php?RCID=a4947355a005414697ff567bc92a03d3
- Elana J. Fertig (Johns Hopkins University), Uncovering Hidden Sources of Transcriptional Dysregulation from Inter and Intra-Tumor Heterogeneity May 13, 2021 https://web.microsoftstream.com/video/8d0d79cf-cebc-4815-9bd4-f6bf0b389567
- Christina Leslie (Memorial Sloan Kettering Cancer Center), Decoding Chromatin States in T Cell Dysfunction and Modeling Gene Regulation March 18, 2021 https://cbiit.webex.com/cbiit/ldr.php?RCID=22aff9b1e11e4298bcbe689e80dd0706
- Stephanie Hicks (Johns Hopkins University), Scalable Statistical Methods and Software for Single-Cell Data Science January 28, 2021 https://cbiit.webex.com/cbiit/ldr.php?RCID=50a812337de243a9bfca430ae5d8c1a8
- Peng Jiang (NCI), Data-driven Approaches to Identify the Regulators of the Anticancer Immune Response July 9, 2020 https://nci.rev.vbrick.com/#/videos/a2b07301-c087-432f-b258-117b9f981d05
- Istvan Albert (Pennsylvania State University), Bioinformatics Recipes: Creating and Sharing Reproducible Data Analysis Workflows April 23, 2020 https://cbiit.webex.com/cbiit/ldr.php?RCID=d212f383485e4b0341264e14995dbc7b
- Sridhar Hannenhalli (NCI), To Function or Not to Function February 6, 2020 https://cbiit.webex.com/cbiit/ldr.php?RCID=ec72d1923ffe18a82b63ed348b75be0c
- Ben Langmead (Johns Hopkins University), Marshaling Public Data for Lean and Powerful Splicing Studies January 16, 2020 https://cbiit.webex.com/cbiit/ldr.php?RCID=da15d3aface8f25f7f478b9a813f6499
- Max Leiserson (UMD), Methods for Characterizing the Activity of Mutational Processes in Cancer November 19, 2019 https://btep.ccr.cancer.gov/wp-content/uploads/Max-Leiserson-BTEP.mp4?_=1
- Steven Salzberg (JHU), Distinguished Speakers Seminar Series October 24, 2019 https://videocast.nih.gov/summary.asp?live=34578
NGS Analysis
- Alex Emmons (BTEP), Introducing QIIME2, a Powerful Platform for Microbiome Analysis March 24, 2022 https://cbiit.webex.com/cbiit/ldr.php?RCID=2ad95564340a539395ff3c62e1126ae3
- BTEP bulk RNA-Seq Weeks: Qiagen Ingenuity Pathway Analysis (IPA) Date https://cbiit.webex.com/cbiit/ldr.php?RCID=c564ed2d03014ff2bdac5fe2765b7ff1
- Variant Annotation, Visualization and Impact Analysis using AVIA Date https://cbiit.webex.com/cbiit/ldr.php?RCID=838671822befaaf2bf504f85a5fb897b
Programming
- Data Visualization with R (April 5 – May 10, 2022)
Lesson 6, May 10, 2022 – Combining multiple plots to create a figure panel
https://cbiit.webex.com/cbiit/ldr.php?RCID=890e966d5e6520052426214db0345d96
Lesson 5, May 6, 2022 – Visualizing clusters with heatmaps
https://cbiit.webex.com/cbiit/ldr.php?RCID=4183dc8595b722b9eed9aa32a0e016ef
Lesson 4, April 26, 2022 – Visualizing summary statistics with histograms, bar plots, and box plots
https://cbiit.webex.com/cbiit/ldr.php?RCID=83a227f93612bdc27637783e586d7025
Lesson 3, April 19, 2022 – Scatter plots and ggplot2 customization
https://cbiit.webex.com/cbiit/ldr.php?RCID=ee0789d3b2cb5cc40c77f0d9e8bb3790
Lesson 2, April 12, 2022 – Basics of ggplot2
https://cbiit.webex.com/cbiit/ldr.php?RCID=c2bacdc4f78ef005f1356fb2d8b798c4
Lesson 1, April 5, 2022 – Introduction to plot types
https://cbiit.webex.com/cbiit/ldr.php?RCID=5bfc45c875be766b41f8a9948487a822 - R Introductory Series (February 1 – February 22, 2022)
Lesson 4, February 22, 2022 – Visualize Data in Graphs, Plots and Charts with R (ggplot2)
https://cbiit.webex.com/cbiit/ldr.php?RCID=f2ef31106aef2a6fb9979377dfd0f563
Lesson 3, February 15, 2022 – Working with Tabular Data in R (tidy verse)
https://btep.ccr.cancer.gov/wp-content/uploads/R-class-Lesson-3-2022-02-15-13-04-05.mp4/
Lesson 2, February 8, 2022 – Data Frames and Data Wrangling
https://btep.ccr.cancer.gov/events/r-introductory-series-2022/r-class-lesson-2-2022-02-08-13-03-58-2/
Lesson 1, February 1, 2022 – Introduction to R (Why Learn R?, Getting Started with R and RStudio, R Basics)
https://cbiit.webex.com/cbiit/ldr.php?RCID=db2be53e42f365c74246c02dfc41867b - Publishing your data analysis story with Jupyter Notebook
December 9, 2021
https://cbiit.webex.com/cbiit/ldr.php?RCID=2a90c0bd794b63a972cf8d7aa4c501b6 - Getting to know R
November 18, 2021
https://cbiit.webex.com/recordingservice/sites/cbiit/recording/playback/b5f1f8622ac7103aaf5f0050568ccf8b - BTEP, Coursera Study Groups: R or Python, Which Should I Learn ?
October 28, 2021
https://cbiit.webex.com/cbiit/ldr.php?RCID=8a3ff4f83125f7946acec6c0f6804dc2 - Bioconductor: Tools and Data Resources for Analysis of High-Throughput Biological Data
December 16, 2020
https://cbiit.webex.com/cbiit/ldr.php?RCID=da0be85f3b8141588e48357d52c94675
Single Cell
- Virtual Single Cell Town Hall: Single-Cell RNA-Seq Data Analysis Date https://nci.rev.vbrick.com/#/webcasts/singlecellpart2
- Virtual Single Cell Town Hall: Experimental Design for Optimal Results in Single-Cell RNA-Seq Date https://nci.rev.vbrick.com/#/webcasts/singlecellpart1
Commercial Software
- Partek Flow: Bulk and Single Cell Gene Expression Visualization
May 18, 2022
https://cbiit.webex.com/cbiit/ldr.php?RCID=b5b1948aab3093124275d06fa55b08ae - Qlucore: Import and analyze public data from SRA, GEO and TCGA
May 11, 2022
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, 2022
https://cbiit.webex.com/cbiit/ldr.php?RCID=d081980970fce4cb50dd20d3f4f3e172 - Single Cell RNA-Seq Analysis with Partek Flow
April 13, 2022
https://cbiit.webex.com/cbiit/ldr.php%3FRCID%3D02b734d9f2b8466bf996ccc5d52d0c02 - Qlucore: Pathway Analysis with Gene Set Enrichment Analysis (GSEA)
April 6, 2022
https://cbiit.webex.com/cbiit/ldr.php?RCID=8cfdd939b601f0402b312ba2f8e85262 - Qlucore: Single Cell Data, from 10x Output to Clustering, Cluster ID and Statistical Analysis in a Visual Qlucore Platform
February 23, 2022
https://cbiit.webex.com/cbiit/ldr.php?RCID=e5cdeb4d9a3720b6807ab767d78c4e40 - Partek Flow: Variant DNA-Seq Data Analysis
January 19, 2022
https://cbiit.webex.com/cbiit/ldr.php?RCID=95300876cd21dcdf724b34450edf02b7