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Workshops and tutorials

Here you can find the material from CCV Workshops and Tutorials.

CCV Workshops and Tutorials


Advanced Slurm

Maintainers: Helen Kershaw

This workshop is for people who are already familiar with SLURM, but would like to use SLURM's more powerful features. It covers dependent jobs, job arrays and scripting.

CCV-Con Slide Archive

Maintainers: Fernando Gelin · Mary McGrath · Paul Stey

This repo houses links to the publically available slides from presentations at the CCV-Con Conference at Brown University.

Version Control with Git

Maintainers: Helen Kershaw

A practical introduction to version control using Git

Getting Started on Oscar

Maintainers: Helen Kershaw

An introduction to Oscar, Brown’s research computing cluster

File Transfer Basics

Maintainers: Helen Kershaw

An overview of methods for moving files onto and off of Oscar. Topics covered include: Linux command line tools for file transfer (scp, rsync, sftp), GUI-based file transfer applications, mounting Oscar’s filesystem using CIFS, and using Globus on Oscar.

A Beginner's guide to using Slurm on Oscar

Maintainers: Helen Kershaw

A primer on submitting jobs to the job scheduler on Oscar. Some basic familiarity with Unix/Linux systems is assumed. Participants will learn the basics of Slurm for resource allocation, how to submit jobs on Oscar, and how to check for common errors.

Basic Bash

Maintainers: Helen Kershaw

This workshop will cover basic shell scripting in Bash: variables, loops, pipes and more so participants can learn to automate work with Bash

Introduction to Programming, Web Scraping, and Data Cleaning in Python

Maintainers: Andras Zsom · Ashley Lee

The goal of this workshop is to increase data fluency of the Brown community. In the first two weeks of the workshop, we learn Python basics. In the third week, we use web scraping to collect data from the web. Web scraping allows us to automate data collection from websites of varying underlying formats. In the fourth week, attendees learn to clean and process the scraped data using the pandas library.

Computational Biology Core Workshops and Tutorials


Command-Line Bioinformatics Primer

Maintainers: Andrew Leith

Introduction to command line tools that are used in bioinformatics and computational biology.

Introduction to Jupyter and Conda

Maintainers: Andrew Leith

This repository contains various tutorials for installing and configuring Jupyter and Conda, the tools used in the Computational Biology Core's workshops.

CBC Workshop Directory

Maintainers:

This page hosts the user directory for the current CBC workshop; when there is no scheduled workshop, it is left empty.

Analyses of RNA-seq and ChiP-seq with R/Bioconductor

Maintainers: Andrew Leith

This workshop is designed to expand upon the Bioconductor training provided in the first Bioconductor workshop; it is an intermediate-level lecture that presupposes some knowledge of R like that found in our 'Fundamentals of R' workshop.

R/Bioconductor Workshop for Genomic Data Analysis

Maintainers: Andrew Leith

This workshop is designed to introduce attendees to Bioconductor and a variety of its use cases; it is an intermediate-level lecture that presupposes some knowledge of R like that found in our 'Fundamentals of R' workshop.

Single-Cell RNA-seq Workshop

Maintainers: Andrew Leith

This workshop serves as an introduction to the tools associated with 10x-based single-cell analysis in R; it is an intermediate-level lecture that presupposes some knowledge of R like that found in our 'Fundamentals of R' workshop.

Fundamentals of R Workshop

Maintainers: Joselynn Wallace

This workshop serves as an introduction to the R programming language for those with little to no experience in its use.

RNA-seq QC and Exploratory Data Analysis Using Bioconductor Workshop

Maintainers: Andrew Leith · Levi Waldron

This workshop is designed to introduce the process of conducting exploratory data analysis in an RNA-seq analysis workflow. It is the first part of a series of two workshops that combine to form the full analysis workflow.

Analyses of metagenomics data with R/Bioconductor

Maintainers: Kellyanne Duncan · Damien Cabral

This workshop is designed to introduce the QIIME and dada2 pipelines for analyzing metagenomics data. A full video of this workshop can be found at the following URLs: https://www.youtube.com/watch?v=LUS62N7tSUU https://www.youtube.com/watch?v=nWeRN2lKIto https://www.youtube.com/watch?v=wV5_z7rR6yw

Visualization in R with tidyverse

Maintainers: August Guang

This workshop is designed to introduce ggplot2 and the tidyverse paradigm for transforming and visualization data in R.

Differential Expression Analysis Using Bioconductor Workshop

Maintainers: Andrew Leith · Levi Waldron

This workshop is designed to introduce the process of differential expression and ontology analysis in an RNA-seq analysis workflow. It is the second part of a series of two workshops that combine to form the full analysis workflow.

Data Science, Computation and Visualization (DSCoV)


Keras Tutorial

Maintainers: Drew Linsley

Deep learning with Keras/Tensorflow

Tidying, transforming and visualizing data with tidyverse in R

Maintainers: August Guang

This workshop is designed to introduce ggplot2 and the tidyverse paradigm for transforming and visualization data in R.

Basics of Data Exploration and Visualization with Vega

Maintainers: Mary McGrath

Vega is an interactive grammar of graphics for creating, saving, and sharing visualizations. In this workshop, we’ll explore a dataset with DataVoyager, create an interactive flight map with Vega, and show how to use Vega with JavaScript, Julia, Python, and R.

Solving the Two-Language Problem with Julia

Maintainers: Paul Stey

The Julia language aims to give its users the rare combination of exceptional performance and expressiveness. Its syntax is similar to MATLAB or Python, but its performance is on the order of C, Fortran, or C++. This tutorial provides an introduction to Julia, explores its many features, and demonstrates its advantages for data science and technical computing more broadly. No prior experience with Julia is required.

Getting Started with Virtual Reality

Maintainers: Ben Knörlein

This workshop will provide an introduction to Virtual Reality and how it can easily be applied to research. We will demonstrate 3 programs that can be used to visualize and interact with data in VR: Paraview (scientific visualization), A-Frame (web visualization), and Unity3D (game development platform)

Cloud computing with GCP

Maintainers: Isabel Restrepo

This workshop provides an introduction to Google Cloud Platform. We will gain familirity with Google Cloud Console and the basics of interacting and using Google's Compute Engine