Bioconductor 3.3 has just been released. You can find the complete list of new packages (and changes to existing packages) here but here are a few I thought might be interesting based on the description. I might have more to say once I’ve had time to try a few out.

  • debrowser – Interactive plots and tables for differential expression
  • DEFormats – convert between differential expression formats
  • EBSEA – exon based differential expression
  • EmpiricalBrownsMethod – combining dependent p-values
  • Linnorm – normalisation for parametric tests, simulation of RNA-seq data
  • multiClust – feature selection and clustering analysis for transcriptomic data
  • RGraph2js – interactive network visualisations with D3
  • tximport – import and summarise transcript-level estimates

Single-cell

These packages are specific to single-cell RNA-seq analysis. A couple of them I am already familiar with, particularly scater.

  • cellity - identifying low-quality cells
  • celTree - model the relationship between individual cells over time or space.
  • scater - tools for analysis of single-cell RNA-seq data (particularly QC)
  • scde - single-cell differential expression
  • scran - normalisation, cell-cycle assignment, gene detection