DeepBlueR

DeepBlueR provides programmatic access to the DeepBlue Epigenomics Data Server to retrieve, filter, transform, aggregate, and import large-scale epigenomic datasets into the R/Bioconductor environment for downstream analysis.

Key Features:

• Comprehensive Data Access: Access and query epigenomic datasets from the DeepBlue Epigenomics Data Server with operations to filter, transform, aggregate, and download data via the server API.
• Integration with R/Bioconductor: An R/Bioconductor package enables direct connectivity and data transfer from DeepBlue into the Bioconductor ecosystem.
• Streamlined Data Processing: Support for gathering and transforming epigenomic data from selected experiments for immediate use in R-based analyses.
• Compatibility: Compatible with R version 3.3 and Bioconductor version 3.4.

Scientific Applications:

• DNA methylation analysis: Facilitates retrieval and comparative analysis of DNA methylation datasets across experiments and consortia.
• Histone modification analysis: Enables access to histone modification data for mapping and comparative studies of chromatin marks.
• Chromatin accessibility analysis: Supports analysis of chromatin accessibility datasets to investigate regulatory landscape and open chromatin regions.
• Comparative epigenomics: Enables cross-experiment and cross-sample comparative analyses of epigenetic states.
• Regulatory element identification: Supports identification and characterization of regulatory elements using aggregated epigenomic signals.
• Epigenetics and gene expression/disease studies: Facilitates exploration of the impact of epigenetic changes on gene expression and disease mechanisms.

Methodology:

Operations specify parameters for filtering and transforming datasets via the DeepBlue API and return data in formats compatible with Bioconductor for import into R.