Bioconductor 3.3 packages
R
bioconductor
Wrap up of new packages in the Bioconductor 3.3 release
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