genoset

genoset extends the RangedSummarizedExperiment class in Bioconductor to store runs of segmented genomic data across samples using an RleDataFrame and to provide rapid summarization of arbitrary row sets and genomic regions.

Key Features:

• RleDataFrame class: Stores runs of data across multiple samples along the genome and enables rapid summarization of arbitrary row sets or specified genomic regions.
• Extension of RangedSummarizedExperiment: Adds APIs and methods built on the Bioconductor RangedSummarizedExperiment class specifically tailored for segmented genomic data.
• Efficient computation for large-scale datasets: Designed to perform swift summarization and computation over large high-throughput genomic datasets.
• Bioconductor interoperability: Integrates with the Bioconductor ecosystem, ensuring compatibility and interoperability with the 934 packages in Bioconductor.

Scientific Applications:

• Region-level summarization for gene expression: Summarizes genomic regions for analyses such as region-level gene expression studies.
• Support for variant calling workflows: Provides region- and segment-level summaries useful in variant calling and downstream genomic analyses.
• High-throughput genomic data analysis: Applicable to large-scale analyses that require efficient aggregation of segmented genomic signals across samples.

Methodology:

Implemented in the R programming language and integrated with the Bioconductor framework; development includes formal initial review and continuous automated testing.