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January 2021

W16: Library Prep for NGS

January 26 @ 1:30 pm - January 28 @ 4:30 pm
ZOOM CA United States + Google Map

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 (using AMPure beads) and Library Submission is also performed on the same day. The third day is optional, sign-up is required.

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February 2021

W22: Advanced Cytoscape

February 2 @ 9:00 am - February 4 @ 12:00 pm
ZOOM CA United States + Google Map

The workshop will cover experimental approaches to protein interaction determination; processing and presentation of interaction data available from online resources, and the role of interaction data in the interpretation of large scale datasets.

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W20: Single-Cell RNA-Seq Analysis with Python

February 9 @ 1:30 pm - February 12 @ 4:30 pm
ZOOM CA United States + Google Map

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 scRNA-seq data and would like to learn about different analytical approaches.  

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W3: Intro to R and Data Visualization

February 16 @ 9:00 am - February 18 @ 12:00 pm
ZOOM CA United States + Google Map

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 workshops. This workshop is geared towards researchers who have little or no experience with R who want to get started with importing data into R…

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W11: Metagenomics Analysis with Python and R

February 16 @ 9:00 am - February 18 @ 12:00 pm
ZOOM CA United States + Google Map

This workshop provides an introduction to the microbiome analyses from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the microbiome data beyond QIIME, including statistical analyses and functional analyses.

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W14: Intro to Modern Statistics with R

February 16 @ 1:30 pm - February 18 @ 3:30 pm
ZOOM CA United States + Google Map

Through this seminar, attendees will walk away knowing when and how to run modern versions of traditional statistical analysis. These tests and the underlying bioinformatical lesson about resampling will be of use to most scientific disciplines. The course makes no assumptions about familiarity with traditional statistics – we will simply go through relatable experimental examples and ask how to test various hypotheses, introducing the relevant methods along the way. There will be homework assignments each night to solidify the concepts…

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W23: DNA Methylation Analysis with R and Unix

February 23 @ 9:00 am - February 25 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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This workshop will introduce the basic principles of DNA methylation and briefly describe available methods for DNA methylation assessment, focusing on bisulfite sequencing (BSseq). 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 by the instructor and run the analysis on Hoffman2 and locally. Attendees need to have a basic knowledge in UNIX commands and R programming for…

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W5a: RNA-seq I Analysis

February 23 @ 1:30 pm - February 25 @ 4:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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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 workshop will be centered on hands-on tutorial that will guide students in processing the data from raw reads through read counts using a real case…

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March 2021

W5b: RNA-Seq II Analysis

March 2 @ 9:00 am - March 3 @ 11:00 am
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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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).

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W8: Variant Calling with GATK

March 2 @ 1:30 pm - March 4 @ 3:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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This workshop uses materials developed by the Broad Institute to teach Variant Discovery with GATK.  Attendees with no prior experience in variant calling are recommended to review all of the materials below before coming to the workshop. This early preparation will allow a focus on the specific issues of running GATK on the UCLA hoffman2 cluster rather than introducing the GATK variant calling pipeline. There will also be a focus on post variant discovery quality control steps as time allows.

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