The Center for Computation and Visualization remains committed to supporting the computing needs of the Brown Research Community during this difficult time. COVID-19 Updates

Software and applications

Here are some of our software projects and applications.

CCV Open Source Software and Applications


Computational Biology Core Software and Applications


RSeqAn

Maintainers: August Guang

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

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.

qckitfastq

Maintainers: August Guang

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

JupyterFleet

Maintainers: Andrew Leith

Software for Automating Jupyter Deployment on AWS.

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.

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..