Computational Biology Core Tools


Here you can find documentation from workshops we conducted at Brown, as well as documentation for our software packages, tutorials, and best practices.

Software


Maintainers: Ashok Ragavendran

A bioinformatics workflow engine that streamlines the most common analysis pipelines. Key features include: 1) Provision of standardized workflows 2) A module for automating SRA downloads and 3) External tools are made available as CONDA packages alongwith the tool.

Maintainers: August Guang

Wrappers for the SeqAn library for use in R with Rcpp.

Maintainers: Andrew Leith

Software for Automating Jupyter Deployment on AWS.

Maintainers: August Guang

A comprehensive quality control R package for Next Generation Sequencing FASTQ data.

RefChef is a reference management tool used to: (1) document the exact steps undertaken in the retrieval of genomic references; (2) maintain the associated metadata; (3) provide a mechanism for automatically reproducing retrieval and creation of an exact copy of genomic references.

This site describes the acquisition and use of the nmrdock docker image containing a variety of tools for analyzing NMR data both from the command line and via GUI. The site contains screenshots and video in addition to the standard narrative documentation..

Workshops


Instructors: Andrew Leith

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

Instructors: 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.

Instructors: 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.

Instructors:

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

Instructors: 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.

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.

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

Instructors: August Guang

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

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.

Tutorials


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

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

Documentation


Documentation templates and best-practices for Brown’s Computational Biology Core.