QCB Collaboratory

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https://qcb.ucla.edu/collaboratory/schedule-of-workshops/
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W21: Image Processing for Microscopy

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

The analysis of imaging datasets is both exciting and challenging. New and increasingly powerful techniques try to maximize the information derived from multi-dimensional imaging datasets. Yet, every dataset can be a unique analysis challenge, and packages may not always work out-of-the-box. In this workshop, we will explore some popular computational tools to extract quantitative information […]

W26: Protein Structure with AlphaFold

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

The goal of the workshop is to enable the participants to submit and rationally evaluate results of the AlphaFold protein structure predictions. The class will cover the basic principles of the structural biology of proteins, protein structure visualization (in pymol) and protein structure prediction. The participants will have opportunity to generate AlphaFold predictions for a […]

W6: BS-DNA Methylation Analysis with Hoffman2 and R

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

This workshop will introduce the basic principles of DNA methylation and briefly describe available methods for DNA methylation assessment, focusing on bisulfite sequencing (BS-Seq). We will cover the principles of BSseq preprocessing, alignment and methylation calling, differential methylation analysis, annotation and visualization. Attendees will have the opportunity to work on real DNA methylation data provided […]

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 […]

W5a: RNA-seq I Analysis

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

RNA-seq I aims to provide an introduction and the basics tools to process raw RNA-seq data on a cluster machine (Hoffman2). The workshop can serve also as a starting point to develop a gene expression project. This workshop is divided in three days that will cover major steps of processing RNA-seq. To facilitate learning, the […]

W5b: RNA-Seq II Analysis

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

RNA-seq II aims to provide tools for analysis of gene expression data from read counts to biology using R. To facilitate learning, the workshop will use a real case study based approach appropriate for Illumina read data (same as RNA-seq I).

W24: Cancer Genomics

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

As we step into the era of precision medicine, the need for extensive genomic data analysis is more pressing than ever. With the advent of high-throughput technologies, a plethora of genomic, transcriptomic, and epigenomic datasets from cancer patients have been sequenced, providing a wealth of data for systematic bioinformatics analysis. This workshop is tailored to […]

W20: Single-Cell RNA-Seq Analysis with R

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

This workshop aims to introduce the basic concepts and algorithms for single-cell RNA-seq analysis. It will help participants obtain a better idea of how to use scRNA-seq technology, from considerations in experimental design to data analysis and interpretation. This workshop can serve researchers who are interested in designing an scRNA-seq study or who have acquired […]