Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.

ABSTRACT:

Objective

Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server.

Materials and methods

We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a

SUBMITTER: Almugbel R 

PROVIDER: S-EPMC6381817 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature