Biology subjects

Berman, B. P.

Publications and source records attributed to Berman, B. P..

3 recordsLinked to original sources

bioRxiv2017

Enhancer Linking by Methylation/Expression Relationships with the R package ELMER version 2

MotivationDNA methylation has been used to identify functional changes at transcriptional enhancers and other cis-regulatory modules (CRMs) in tumors and other disease tissues. Our R/Bioconductor package ELMER (Enhancer Linking by Methylation/Expression Relationships) provides a systematic approach that reconstructs altered gene regulatory networks (GRNs) by combining enhancer methylation and gene expression data derived from the same sample set.\n\nResultsWe present a completely revised version 2 of ELMER that provides numerous new features including an optional web-based interface and a new Supervised Analysis mode to use pre-defined sample groupings. We show that this approach can identify GRNs associated with many new Master Regulators including KLF5 in breast cancer.\n\nAvailabilityELMER v.2 is available as an R/Bioconductor package at http://bioconductor.org/packages/ELMER/

bioinformatics↗

bioRxiv2017

TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data

BackgroundThe GDC (Genomic Data Commons) data portal provides users with data from cancer genomics studies. Recently, we developed the R/Bioconductor TCGAbiolinks package, which allows users to search, download and prepare cancer genomics data for integrative data analysis. The use of this package requires users to have advanced knowledge of R thus limiting the number of users.\n\nResultsTo overcome this obstacle and improve the accessibility of the package by a wider range of users, we developed TCGAbiolinksGUI that uses shiny graphical user interface (GUI) available through the R/Bioconductor package.\n\nConclusionThe TCGAbiolinksGUI package is freely available within the Bioconductor project at http://bioconductor.org/packages/TCGAbiolinksGUI/. Links to the GitHub repository, a demo version of the tool, a docker image and PDF/video tutorials are available at http://bit.do/TCGAbiolinksDocs.

bioinformatics↗

bioRxiv2017

StateHub-StatePaintR: rules-based chromatin state annotations.

Genome annotation is critical to understand the function of disease variants, especially for clinical applications. To meet this need there are segmentations available from public consortia reflecting varying unsupervised approaches to functional annotation based on epigenetics data, but there remains a need for transparent, reproducible, and easily interpreted genomic maps of the functional biology of chromatin. We introduce a new methodological framework for defining a combinatorial epigenomic model of chromatin state on a web database, StateHub. In addition, we created an annotation tool for bioconductor, StatePaintR, which accesses these models and uses them to rapidly (on the order of seconds) produce chromatin state segmentations in standard genome browser formats. Annotations are fully documented with change history and versioning, authorship information, and original source files. StatePaintR calculates ranks for each state from next-gen sequencing peak statistics, facilitating variant prioritization, enrichment testing, and other types of quantitative analysis. StateHub hosts annotation tracks for major public consortia as a resource, and allows users to submit their own alternative models.

bioinformatics↗