Chalk Talk

Gladstone Conference Room A/B 1650 Owens St, San Francisco, CA

SPEAKER: Sara Sawyer, PhD. Professor of Molecular, Cellular, and Developmental Biology at the BioFrontiers Institute, University of Colorado Boulder.

Introduction to Cytoscape and Network Biology for Biologists

Mission Hall 1406 550 16th Street, San Francisco, CA

The course will introduce the basic concepts of biological network analysis and provide practical instruction on commonly used tools and databases with a focus on Cytoscape to analyze and visualize biological networks. The course will comprise theoretical and practical sessions where course participants will learn how to perform different biological network analyses and how to […]

UCSC Genome Browser Workshop

Main Session in Byers Auditorium (9am-12pm), Hands-on Workshop in Mission Hall 1407 1-5pm 600 16th St, CA

The UCSC Genome Browser is a powerful web-based tool for interacting with genome assemblies of many organisms. This workshop will introduce you to the wealth of data contained in the browser and related databases, and will allow you to integrate and compare results of your genomic and transcriptomic experiments. The main morning session, held in […]

Introduction to Cytoscape and Network Biology for Computer Scientists

Mission Hall, Room 1401/1402 550 16th Street, San Francisco, CA

The course will introduce the basic concepts of biological network analysis and provide practical instruction on commonly used tools and databases with a focus on Cytoscape to analyze and visualize biological networks. The course will comprise theoretical and practical sessions where course participants will learn how to perform computational analyses of biological networks and how […]

Intermediate Cytoscape: Networks and Omics Data Visualization

Mission Hall, Room 1407 550 16th Street, San Francisco, CA

This course is a complement to “Introduction to Network Biology and Cytoscape” from the previous day. Following a brief review of the key concepts of network analysis, we will embark on a deep dive into data visualization and advanced Cytoscape features. We will work through three prepared use cases demonstrating various omics data types and […]

Intro to R data analysis

Mission Hall, Room 1400 550 16th Street, San Francisco, CA

The high-level language of R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This workshop will help you get started with analyzing your datasets and creating graphs for visualization. No background in statistics or computing necessary. *Bring your laptop with RStudio and R installed.

Intro to RNA-seq analysis

Mission Hall, Room 1407 550 16th Street, San Francisco, CA

Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. To quantify the expression levels, RNA-seq has become one of the most popular experimental methods. This workshop will provide an introduction to a typical bulk RNA-seq protocol and focus on the data analysis steps […]

Intermediate R data visualization

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The high-level language of R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This hands-on workshop will be taught as a two-part webinar. It is designed for folks who have some experience in using R and are looking to take their R skills to the next level. We shall […]

Batch Correction with Bulk RNA-Seq

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Bulk RNA-seq has become routine for unbiased transcript/gene expression quantification in samples across multiple conditions. There is currently data for literally hundreds of thousands of samples on public databases like the Gene Expression Omnibus (GEO). We may be tempted to include data from some of these samples in our own analyses to either enrich or provide […]

Recurring

Webinar: Introduction to R for Data Analysis

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The scripting language of R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This workshop will help you get started with analyzing your datasets and creating graphs for visualization. We'll do hands-on exercises to demystify data analysis using R. From our previous experience in teaching this workshop, we know […]

Webinar: Introduction to Unix Command Line

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Knowing how to use the command line of your computer can save you a lot of time. In this workshop, you will learn how to navigate the Unix terminal. The only thing you need is a Mac or Linux laptop (you can use Windows if you can’t access a Linux machine). Topics to be covered […]

High dimensional data integration

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Biological processes like gene regulation are complex involving multiple modalities. It is becoming more common to query biological processes using multiple orthogonal and related assays to get a more complete understanding. For example, one may assay expression of genes using RNA-seq and chromatin state using Atac-seq in the samples associated with the underlying conditions of […]

Webinar: Intermediate R RNA Seq Analysis

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The learning objectives for this workshop include: How to go from a matrix of raw gene expression counts to differentially expressed genes. How to analyze experimental designs that go beyond 2-group comparisons using edgeR’s generalized linear modeling capabilities. Ways to test specific hypotheses using a joint model fit. Prerequisites: A minimum of 4 to 6 […]

Introduction to Cytoscape and Network Biology for Biologists

Zoom Only

Join this course for an introduction to the basic concepts of biological network analysis and practical instruction on commonly used tools and databases, with a focus on Cytoscape to analyze and visualize biological networks. The course will comprise theoretical and practical sessions in which you will learn how to perform different biological network analyses and […]

Introduction to R Data Analysis

Zoom Only

The scripting language R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This workshop will help you get started using R to analyze your datasets and create graphs for visualization. You'll do hands-on exercises to demystify data analysis using R. This workshop is designed for those who have no […]

Intermediate Cytoscape: Networks and Omics Data Visualization

Zoom Only

This course is a complement to “Introduction to Network Biology and Cytoscape.” Following a brief review of the key concepts of network analysis, you will embark on a deep dive into data visualization and advanced Cytoscape features. You will work through three prepared use cases demonstrating various omics data types and strategies. You are encouraged […]

Introduction to Unix Command Line

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Knowing how to use the command line of your computer can save you a lot of time. In this workshop, you will learn how to navigate the Unix terminal. The only thing you need is a Mac or Linux laptop (you can use Windows if you can’t access a Linux machine). Topics to be covered […]

Python Fundamentals Part 1

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This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application.    Part 1 Topics: Running Python […]

UCSC Genome Browser Workshop

Zoom Only

The UCSC Genome Browser is a powerful web-based tool for interacting with genome assemblies of many organisms. This workshop will introduce you to the wealth of data contained in the browser and related databases, and will allow you to integrate and compare results of your genomic and transcriptomic experiments. Prior experience with the Browser is not […]

Advanced Command Line

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Knowing how to use the command line of your computer can save you a lot of time. In this advanced workshop, you will learn how to navigate the Unix terminal, process files, set permissions, etc. The only thing you need is a Mac or Linux laptop (you can use Windows if you can’t access a Linux […]

Statistics of Enrichment Analysis

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Gene set or pathway enrichment methods allow researchers to assign functional or mechanistic significance to results from high-throughput assays like RNA-sequencing. In this workshop, you’ll learn the theory behind some of these methods, and how to interpret the associated results. REGISTER HERE

Introduction to Cytoscape and Network Biology for Biologists

Zoom Only

Join this course for an introduction to the basic concepts of biological network analysis and practical instruction on commonly used tools and databases, with a focus on Cytoscape to analyze and visualize biological networks. The course will comprise theoretical and practical sessions in which you will learn how to perform different biological network analyses and […]

Introduction to Pathway Analysis and Visualization

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This workshop is an introduction to functional enrichment analysis and effective visualization. You will learn about different enrichment analysis tools and methods, and how to use them. You will also learn how to visualize data on pathways and GO terms resulting from enrichment analysis. No programming experience required. Visit the workshop site for more details and materials. […]

Intermediate Cytoscape: Networks and Omics Data Visualization

Zoom Only

This course is a complement to “Introduction to Network Biology and Cytoscape.” Following a brief review of the key concepts of network analysis, you will embark on a deep dive into data visualization and advanced Cytoscape features. You will work through three prepared use cases demonstrating various omics data types and strategies. You are encouraged […]

Hypothesis Testing

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When you attempt to make discoveries, you test new hypotheses using experimental data and hope that a skeptical and discerning person would start to believe your claims. Hypothesis testing, a branch of statistics, is a step you can rely on to bolster your claims. In this workshop, you will gain a fundamental understanding of common […]

Introduction to RNA-Seq Analysis

Zoom Only

Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. RNA-Seq has become one of the most popular experimental methods to quantify gene expression levels. This 2-day hands-on workshop will provide an introduction to a typical bulk RNA-Seq protocol and focus on the data […]

Working with Biomedical Graph Databases

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Scientific databases are a critical resource for modern biomedical researchers and practitioners. Graph databases are a specialized type of database that offer distinct advantages for storing and representing biomedical knowledge. Major NIH initiatives are funding the development of new biomedical graph databases to support advanced queries and reasoning not possible with traditional relational databases. Learn […]

Single Cell RNA-Seq Analysis

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This 4-session workshop will focus on the analysis of single-cell RNA-Seq data, starting from raw count matrices and progressing to network analysis of single-cell datasets. You’ll analyze data using R and Cytoscape. Attendance at all four sessions is required.  Register here! October 22, 10am–12pm: Loading data, quality control, normalization, feature selection, dimensionality reduction October 22, 2–4pm: Dimensionality […]

Advanced Cytoscape Using R

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In this course, you’ll learn about the integration of Cytoscape into programmatic workflows and pipelines using R. Following a brief review of the goals and capabilities of Cytoscape in network analysis, you’ll learn how to translate these into scriptable use cases for practical applications. The bulk of the course will be a hands-on demonstration of […]

Whole Genome Sequence Analysis

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When you are working with whole genome sequencing data, finding the information you need can be a daunting challenge. This course offers both theoretical and hands-on training so you can learn the main tools used to do alignment, variant calling, annotation, and visualization. You’ll learn how to go from raw FASTQ reads to annotated variants […]

Introduction to Statistics and Experimental Design

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Why do we perform experiments? What conclusions would we like to be able to draw from these experiments? Who are we trying to convince? How does the “magic” of statistics help us reach conclusions? This talk is open to anyone interested in designing experiments to test hypotheses (e.g., the effect of a drug treatment, gene […]

Intermediate R for Data Visualization

Zoom Only

The high-level language of R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This workshop is designed for folks who have some experience using R and are looking to take their R skills to the next level. You’ll learn how to generate high-quality and publication-ready data visualizations using R […]

Intermediate RNA-Seq Analysis Using R

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RNA-Seq is a powerful tool to interrogate cellular functions. In this intermediate workshop you’ll learn  the skills you need to get the most out of your RNA-Seq data through analysis in R. This is a 2-day workshop, December 6th and 7th @ 2-4pm.  Attendance at both sessions is required.   By the end of the […]

Intermediate Cytoscape: Networks and Omics Data Visualization

Zoom Only

This course is a complement to “Introduction to Network Biology and Cytoscape.” Following a brief review of the key concepts of network analysis, you’ll embark on a deep dive into data visualization and advanced Cytoscape features. Work through three prepared use cases demonstrating various omics data types and strategies. You’re also encouraged to bring your […]

Unix Command Line

Zoom Only

Knowing how to use the command line of your computer can save you a lot of time. In this workshop, you’ll learn how to navigate the Unix terminal. For this workshop, you’ll need a Mac or Linux laptop (you can use Windows if you can’t access a Linux machine). Topics to be covered include: File […]

Introduction to Statistics and Experimental Design

Zoom Only

Why do we perform experiments? What conclusions would we like to be able to draw from these experiments? Who are we trying to convince? How does the “magic” of statistics help us reach conclusions? This workshop is open to anyone interested in learning more about experimental design, biological and technical aspects to consider, confounding factors, […]

Recurring

Introduction to RNA-Seq Analysis

Zoom Only

Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. RNA-seq has become one of the most popular experimental methods to quantify gene expression levels. This 2-day hands-on workshop will provide an introduction to a typical bulk RNA-seq protocol and focus on the data […]

Recurring

Introduction to RNA-Seq Analysis

Zoom Only

Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. RNA-seq has become one of the most popular experimental methods to quantify gene expression levels. This 2-day hands-on workshop will provide an introduction to a typical bulk RNA-seq protocol and focus on the data […]

Intermediate RNA-Seq Analysis Using R

Zoom Only

RNA-Seq is a powerful tool to interrogate cellular functions. In this intermediate workshop you’ll learn  the skills you need to get the most out of your RNA-Seq data through analysis in R. By the end of the workshop, you'll know how to: Go from a matrix of raw gene expression counts to differentially expressed genes […]

Recurring

Single Cell RNA-Seq Analysis

Zoom Only

This three-session workshop will focus on the analysis of single-cell RNA-Seq data, starting from raw count matrices and progressing to network analysis of single-cell datasets. You’ll analyze data using R. Attendance at all three sessions is required. April 15, 2022 • 10am–12pm: Loading data, quality control, normalization, feature selection, dimensionality reduction April 15, 2022 • 1–3pm: Dimensionality […]

Recurring

Single Cell RNA-Seq Analysis

Zoom Only

This three-session workshop will focus on the analysis of single-cell RNA-Seq data, starting from raw count matrices and progressing to network analysis of single-cell datasets. You’ll analyze data using R. Attendance at all three sessions is required. April 15, 2022 • 10am–12pm: Loading data, quality control, normalization, feature selection, dimensionality reduction April 15, 2022 • 1–3pm: Dimensionality […]

Recurring

Single Cell RNA-Seq Analysis

Zoom Only

This three-session workshop will focus on the analysis of single-cell RNA-Seq data, starting from raw count matrices and progressing to network analysis of single-cell datasets. You’ll analyze data using R. Attendance at all three sessions is required. April 15, 2022 • 10am–12pm: Loading data, quality control, normalization, feature selection, dimensionality reduction April 15, 2022 • 1–3pm: Dimensionality […]

Statistics of Enrichment Analyses Methods

Zoom Only

Gene set or pathway enrichment methods allow researchers to assign functional or mechanistic significance to results from high-throughput assays like RNA-sequencing. In this workshop, you’ll learn the theory behind some of these methods, and how to interpret the associated results. Intermediate: This is an intermediate workshop in both the Biostats series and the Pathway Analysis series. The demos session will […]

Introductory Machine Learning for Biologists

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Machine learning is becoming increasingly important not only in data science, but also in bioinformatics. Machine learning gives you the opportunity to find hidden patterns in your data and draw predictive conclusions. In this workshop, you’ll learn key machine learning concepts and categories, and get hands-on practice with simple examples. See how machine learning can […]

Advanced Cytoscape Automation

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In this course, you’ll learn how to integrate  Cytoscape into programmatic workflows and pipelines using R or Python. Following a brief review of the goals and capabilities of Cytoscape in network analysis, you’ll learn how to translate these capabilities into scriptable use cases for practical applications. Gain hands-on experience accessing and controlling Cytoscape from R/Python […]