ExperimentSubset

The 'ExperimentSubset' package in R addresses challenges in subsetting data matrices within Experiment objects like SummarizedExperiment or SingleCellExperiment. These objects are widely used in genomics for high-throughput data storage and analysis. The package provides efficient classes for storing and retrieving subsets of assays based on rows or columns, eliminating the need to create additional objects and improving data provenance. The classes inherently maintain the relationship between subsetted and parent assays.

Topic

RNA-Seq;Workflows;Data submission, annotation and curation

Detail

  • Operation: Data retrieval;Feature selection;Filtering

  • Software interface: Library

  • Language: R

  • License: The MIT License

  • Cost: Free

  • Version name: 1.12.0

  • Credit: National Library of Medicine (NLM), the Informatics Technology for Cancer Research (ITCR).

  • Input: -

  • Output: -

  • Contact: Irzam Sarfraz irzam9095@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects.
  • Sarfraz I, et al. ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects. ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects. 2021; 37:3058-3060. doi: 10.1093/bioinformatics/btab179
  • https://doi.org/10.1093/BIOINFORMATICS/BTAB179
  • PMID: 33715007
  • PMC: PMC9940906

Download and documentation

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