seeker

seeker processes and prepares transcriptome datasets (RNA-seq and microarray) by fetching data and producing standardized sample metadata and gene expression values mapped to Entrez or Ensembl Gene IDs.

Key Features:

• Data fetching and processing: Fetches and processes transcriptome datasets, including RNA-seq and microarray data.
• R-based wrapper: Wraps existing bioinformatics tools within an R framework to coordinate data preparation steps.
• Parallel processing: Implements simple parallelization to accelerate handling of large datasets.
• Detailed logging: Produces comprehensive logs that document each processing step.
• Standardized outputs: Generates sample metadata and gene expression values mapped to standardized identifiers such as Entrez and Ensembl Gene IDs.
• Reproducibility support: Provides a Docker image bundling dependencies alongside the R package to support reproducible execution.

Scientific Applications:

• Differential expression analysis: Prepares expression matrices and sample metadata formatted for input to differential expression workflows.
• Transcriptome data integration: Produces standardized identifiers and outputs that facilitate integration and meta-analysis across studies.
• Downstream transcriptomic analyses: Streamlines initial data preparation for analyses interrogating biological systems using RNA-seq and microarray datasets.

Methodology:

Wraps existing bioinformatics tools within an R framework, implements simple parallel processing and comprehensive logging, and provides a Docker image bundling dependencies.