Bioconductor 3.11 wrap-up

My wrap-up of the Bioconductor 3.11 release

Luke Zappia


April 29, 2020

The Bioconductor 3.11 release was yesterday. Here is my wrap-up of new packages and updates. This is only the things I found interesting based on the release and they don’t come with any particular endorsement. If there is something else you are looking for have a look at the release notes here.

New packages

  • {basilisk} - installs a self-contained Python instance that is maintained by the R installation
  • {BiocDockerManager} - management of Bioconductor Docker images
  • {CiteFuse} - suite of methods for working with CITE-seq data
  • {clustifyr} - classify cells in scRNA-seq data using external references
  • {cmapR} - interface for the Broad Institute Connectivity Map resource of gene perturbation expression profiles
  • {ctgGEM} - streamlines building of cell-state hierarchies from single-cell gene expression data
  • {distinct} - differential testing of distributions
  • {dittoSeq} - user friendly visualisation of bulk and single-cell RNA-seq data including consideration of colour blindness
  • {Dune} - merges pairs of clusters to increase ARI and improve reproducibility
  • {frenchFISH} - Poisson models for DNA copy number from FISH data (bonus points for the excellent name)
  • {GeneTonic} - Shiny app for looking at enrichment results from expression data (another great name)
  • {HIPPO} - scRNA-seq feature selection and clustering
  • {ISEEu} - extensions for the {iSEE} shiny app
  • {mitch} - multi-contrast enrichment analysis
  • {peco} - predicting cell-cycle progression using scRNA-seq data
  • {scClassify} - multi-scale classification of scRNA-seq data using cell hierarchies
  • {scHOT} - testing changes in higher-order structure of gene expression such as across (pseudo) time or space
  • {scry} - count-based feature selection and dimensionality reduction for small count data
  • {scTHI} - identify active ligand-receptor pairs in scRNA-seq data
  • {SingleCellSignalR} - clustering of scRNA-seq data and inference of cell-cell interactions
  • {sparseMatrixStats} - high-performance functions for row and column operations on sparse matrices, inspired by {matrixStats}
  • {tidybulk} - tidy wrappers for bulk RNA-seq analysis


  • {BASiCS} - many updates and release of version 2
  • {batchelor} - support of arbitrary design matrices and extension of MNN integration to cluster centroids
  • {DropletUtils} - down sampling of batches, writing to 10x format, removal of chimeric reads, demultiplexing of cell hashing experiments
  • {edgeR} - integration of the limma voom-lmFit pipeline, support for {SummarizedExperiment} objects
  • {iSEE} - support of extensions such as those in {ISEEu}
  • {limma} - changeLog() function can be used with any package, improved treatment of NA values
  • {missMethyl} - bug fixes and fract.counts argument
  • {PCAtools} - functions for choosing the ideal number of components to retain
  • {scater} - multi-feature set UMAP and various new arguments
  • {scran} - new functions for sub-clustering and cluster bootstrapping, wrappers for graph-based clustering, updates to marker identification functions
  • {SummarizedExperiment} - support for assays with more than four dimensions, changes to assay getters and setters to check dimnames
  • {tximeta} - functions for splitting {SummarizedExperiment} objects and conversion to DGEList
  • {tximport} - improved support for importing Alevin output

Workflow packages