Resources

Resources provided by the Computational Biology Core. Includes database subscriptions and licenses. Additionally, we provide various open source software, workshops, and tutorials in Bioinformatics and Data Science.

Software

bioflows

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.


RSeqAn

Maintainers: August Guang


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


JupyterFleet

Maintainers: Andrew Leith


Software for Automating Jupyter Deployment on AWS.


qckitfastq

Maintainers: August Guang


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


RefChef

Maintainers: Andrew Leith, Fernando Gelin


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.


NMRdock

Maintainers: Andrew Leith, Kyle East


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

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.


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.


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.


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.


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.


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.


Tutorials

Documentation

RefChef

The Computational Biology Core keeps genome references in Brown’s supercomputer Oscar. Oscar users can incorporate those genome references in their analyses. Click the link below for a list of Genome References available on Oscar. Contact us if you there’s a genome reference you need added to that list.



RefChef View

  

Ingenuity Pathway Analysis

IPA is a software application that enables biologists and bioinformaticians to identify the biological mechanisms, pathways, and functions most relevant to their experimental datasets or genes of interest. It allows researchers to graphically view, analyze, and query data in a comprehensive and seamless manner to understand molecular interactions, biological functions and disease on multiple levels. For more details go to qiagen IPA website and also access their webinars. Access to IPA free for the entire Brown community through September 2019.

Only one concurrent users will be allowed at a time, so use the scheduler below to reserve analysis time.

To request access to IPA please use the request button below. After registration, Ingenuity Systems will send each registrant, via e-mail, their individual password and login instructions. Please note, the first time you login to your IPA account, it may take a few minutes to load the application. Additionally, please disable all pop-up blockers prior to signing in as they may prevent the application from loading.


Use the calendar to see what times are available to access IPA. Click below to schedule your IPA session or to request access. Please restrict yourself to at most two consecutive slots for any given time.


Request Access to IPA   Schedule a session