R packages

An R package to create gene expression atlases from public bulk RNA-seq data


September 8, 2023


In the past decades, there has been an exponential accumulation of RNA-seq data in public repositories. This steep increase paved the way to the creation of gene expression atlases, which consist in comprehensive collections of expression data from public databases, analyzed with a single pipeline for consistency and cross-project comparison. bears is a package that allows you to create your own gene expression atlas for a given species using public data. The package features:

  • Data download from NCBI’s Sequence Read Archive (SRA) or the European Nucleotide Archive (ENA).
  • Sequence quality check and trimming of low-quality sequences and adapters.
  • Removal of rRNA, which are typical problems of libraries that were prepared with the rRNA depletion protocol.
  • Read mapping against a reference genome.
  • Transcriptome assembly.
  • Quantification of gene- and transcript-level transcript abundance with alignment-based and alignment-free methods.