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

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

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