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W2: Using NGS Analysis Tools

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. First, this workshop introduces the more “universal” aspects of high-throughput sequence analysis—from experimental design to sequencing and alignment methods. Next, this workshop covers common file formats for sequence data and limitations of sequencing technologies. We will […]

W18: Advanced Python

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This workshop will cover some more advanced topics in python including an overview of object-oriented python (this will not be an in-depth course on object-oriented programming), use of the numpy and pandas libraries (python libraries for efficient handling of large numeric and heterogenous datasets, and matplotlib for plotting results. At the end of this workshop, […]

W1b: Intro to Unix command line II

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This workshop (UNIX Command Line II) continues Workshop W1: UNIX Command Line I and uses the Hoffman2 campus computing cluster. The focus is on features that make dealing with large files or large numbers of files or repetitive tasks easier. These include shell variables, substitutions, redirections, pipes, loops, conditionals, subshells, shell functions, and shell scripts. […]

W3: Intro to R and Data Visualization

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

R (www.r-project.org) is a free software environment for statistical computing and graphics. First, this workshop introduces basic concepts, syntax, and usage in R programming, statistical analysis, and visualization techniques. We will conduct hands-on tutorials throughout the session, giving attendees a chance to see R in action. This course is a pre-requisite for several other Collaboratory […]

W37: Applications of Large Language Models

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This 3-day interactive workshop introduces the overarching principles guiding generative modeling and specifically Large-Scale Language Models (LLM), their application in Python for inference, and specific use-cases in Genomics. Experience with Python is necessary, and basic knowledge about ML workflows is preferred. At the end of this workshop, you WILL be comfortable with loading, inferencing and […]

W31: Spatial Transcriptomics

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

Spatial transcriptomics is an emerging field that bridges molecular biology and anatomy. Over the last decade, a battery of assays have been developed that profile gene expression in-situ, i.e, measuring the abundances of mRNA molecules in cells and tissues while retaining information about their spatial locations. This workshop will introduce the basic concepts, major techniques, […]

W36: Mergeomics for Multiomics Integration

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

Mergeomics is a computational tool designed to elucidate the underlying pathways, networks, and key regulators of complex diseases by integrating multi-omics data (genomics, transcriptomics, epigenomics, proteomics, etc). With use of integrative omics concepts and network modeling methods, this tool can uncover disease-associated gene sets and biological pathways across omics layers and can identify key drivers […]

W7: ChIP-seq Analysis

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This workshop aims to provide skills needed to address principles of the assay, quality assessment, sequencing depth, data processing and functional downstream analyses of ChIP-seq datasets. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.

W32: GitHub/Docker

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

Learn how to make your applications ready for production and distribution. This workshop will give you your introduction to setting up version control and containerization for your applications to ensure that changes are tracked and dependencies are documented and automatically installed.  Git and Docker allow developers and users to quickly replicate code and computing environments […]

W16: Library Prep for NGS

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq, ChIP-seq, RNA-seq, Methyl-seq) are explained the first and second day in class. The third day, Quality Control steps of the starting input material and final libraries are performed in the Lab (TapeStation). Purification from Primer Dimers […]