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 […]

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 […]

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.

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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

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 […]

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. […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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, […]

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 […]

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 […]

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 […]

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 […]

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 […]

Join this introduction to functional enrichment analysis and effective visualization. You’ll learn about different enrichment analysis tools and methods, and how to use them. You’ll also learn how to visualize data in pathways and using GO terms resulting from enrichment analysis. No programming experience required. This is an introductory workshop. No prior experience is required. […]

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 […]

More often than not, biological experiments involve repeated measures. Examples include responses measured in cellular assays, where the repeated measures may occur over multiple experimental batches, multiple plates, or multiple wells within a plate. Observations of mouse behavior over consecutive trials would be another example of experiments involving repeated measures. The distinctions between biological and […]