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AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.

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This summary is machine-generated.

The AnVILWorkflow R package simplifies accessing large-scale genomics data and analysis tools on the AnVIL platform. This bioinformatics tool empowers researchers by enabling easy execution of complex genomic workflows directly within R.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Advancements in sequencing technologies generate vast biological datasets.
  • The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) offers cloud-based access to genomics data and tools.
  • Executing complex bioinformatics workflows on AnVIL can be challenging for researchers lacking extensive bioinformatics expertise.

Purpose of the Study:

  • To introduce the AnVILWorkflow R package for simplifying AnVIL workflow execution.
  • To enable researchers to conveniently run bioinformatics workflows from an R environment.
  • To lower the barrier for utilizing AnVIL's resources for genomics data analysis.

Main Methods:

  • Development of the AnVILWorkflow R package.
  • Implementation of intuitive functions for cloud environment setup, data formatting, workflow submission, and results retrieval.
  • Demonstration of utility through use cases including bulk RNA-seq, metagenomics, and digital pathology image processing.

Main Results:

  • AnVILWorkflow simplifies the execution of bioinformatics workflows on AnVIL.
  • The package facilitates seamless integration of R and non-R tools for reproducible analysis.
  • Researchers can access scalable computing resources without direct management overhead.
  • User-friendly browsing of data and workflows is provided.

Conclusions:

  • AnVILWorkflow significantly lowers the barrier for researchers to leverage AnVIL's capabilities.
  • The package empowers a broader research community to utilize advanced genomics tools and datasets.
  • It is particularly beneficial for exploratory analyses and bulk processing using established workflows.
  • The AnVILWorkflow R package is available via Bioconductor and GitHub.