pubCounteR

pubCounteR screens publications for experimentally-derived gene lists within a user-defined biological context to facilitate the biological interpretation of gene lists.

Key Features:

• Literature screening: Screens publications using a user-defined set of keywords representing a specific biological context.
• Gene list retrieval: Identifies experimentally-derived gene lists from published literature.
• R package implementation: Provides functionality as an R package for integration into bioinformatics workflows.

Scientific Applications:

• Omics data interpretation: Aids biological interpretation of gene lists generated from genomics, transcriptomics, epigenomics, metabolomics, and proteomics datasets.
• Candidate gene validation: Supports validation of candidate genes hypothesized or shown to be responsible for biological effects.

Methodology:

pubCounteR screens publications by matching a user-defined set of keywords against published literature to identify experimentally-derived gene lists within the specified biological context.