This lesson continues with the second workshop on reproducible science, focusing on additional open source tools for researchers and data scientists, such as the R programming language for data science, as well as associated tools like RStudio and R Markdown. Additionally, users are introduced to Python and iPython notebooks, Google Colab, and are given hands-on tutorials on how to create a Binder environment, as well as various containers in Docker and Singularity.

This lesson provides a quick tour of some data repositories and how to download and manipulate data from them.

This lecture provides an introduction to the application of genetic testing in neurodevelopmental disorders.

This is a hands-on tutorial on PLINK, the open source whole genome association analysis toolset. The aims of this tutorial are to teach users how to perform basic quality control on genetic datasets, as well as to identify and understand GWAS summary statistics. 

This is a tutorial on using the open-source software PRSice to calculate a set of polygenic risk scores (PRS) for a study sample. Users will also learn how to read PRS into R, visualize distributions, and perform basic association analyses. 

This is a tutorial introducing participants to the basics of RNA-sequencing data and how to analyze its features using Seurat. 

This tutorial demonstrates how to perform cell-type deconvolution in order to estimate how proportions of cell-types in the brain change in response to various conditions. While these techniques may be useful in addressing a wide range of scientific questions, this tutorial will focus on the cellular changes associated with major depression (MDD). 

Similarity Network Fusion (SNF) is a computational method for data integration across various kinds of measurements, aimed at taking advantage of the common as well as complementary information in different data types. This workshop walks participants through running SNF on EEG and genomic data using RStudio.

The Allen Mouse Brain Atlas is a genome-wide, high-resolution atlas of gene expression throughout the adult mouse brain. This tutorial describes the basic search and navigation features of the Allen Mouse Brain Atlas.

The Allen Developing Mouse Brain Atlas is a detailed atlas of gene expression across mouse brain development. This tutorial describes the basic search and navigation features of the Allen Developing Mouse Brain Atlas.

This tutorial demonstrates how to use the differential search feature of the Allen Mouse Brain Atlas to find gene markers for different regions of the brain, as well as to visualize this gene expression in three-dimensional space. Differential search is also available for the Allen Developing Mouse Brain Atlas and the Allen Human Brain Atlas.

This lesson provides a demonstration of GeneWeaver, a system for the integration and analysis of heterogeneous functional genomics data.

This tutorial shows how to use the UCSC genome browser to find a list of genes in a given genomic region.

This tutorial shows how to find all the single nucleotide polymorphisms (SNPs) upstream from genes using the UCSC Genome Browser.

This tutorial demonstrates how to find all the single nucleotide polymorphisms (SNPs) in a gene using the UCSC Genome Browser.

The Saved Sessions feature of the Browser has been around for quite some time, but many of our users have not made full use of it. This feature offers a great way to keep track of your thinking on a particular topic.

The Track Collection Builder is a new tool in the UCSC Genome Browser that provides a way to create grouped collections of sub-tracks with native tracks, custom tracks, or hub tracks of continuous value graphing data types.

This tutorial demonstrates the visibility controls on the Genome Browser, showing the effect on BED tracks, wiggle tracks, and Conservation tracks. It also discusses supertracks and composite tracks.

This tutorial describes the isPCR tool and demonstrates how to use it for predicting the size and location of PCR products and visualizing the genomic location on the genome. The tool operates on DNA templates for all organisms, and on human and mouse DNA/RNA. It also demonstrates how to use the Browser to obtain DNA sequences from the genome.