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April 2021

W3: Intro to R and Data Visualization

April 20 @ 9:00 am - April 22 @ 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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W16: Library Prep for NGS

April 20 @ 1:30 pm - April 22 @ 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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W15: Bacterial Genomics

April 27 @ 1:30 pm - April 29 @ 4:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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The workshop will mainly focus on teaching the fundamentals of bacterial genomics and basic bioinformatics analysis. As a sample data Vibrio cholerae genome will be used as the practice dataset, and workshop participants will try to reproduce the expected results. The workshop will start with detailed instructions on how to quality control the raw sequence data and the assemble of a genome. Next, basic statistics will be explained to learn how to check the quality of assembledgenome (e.g., N50, #…

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May 2021

W20: Single-Cell RNA-Seq Analysis with Python

May 4 @ 1:30 pm - May 7 @ 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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W11: Metagenomics Analysis with Python and R

May 11 @ 9:00 am - May 13 @ 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

May 11 @ 1:30 pm - May 13 @ 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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W6: BS-DNA Methylation Analysis with Hoffman2 and R

May 18 @ 9:00 am - May 20 @ 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 (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 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

May 18 @ 1:30 pm - May 20 @ 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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W5b: RNA-Seq II Analysis

May 25 @ 9:00 am - May 27 @ 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

May 26 @ 1:30 pm - May 27 @ 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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