TreeSummarizedExperiment

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 2.20.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: SingleCellExperiment, S4Vectors, Biostrings
• Imports: BiocGenerics, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio
• System requirements: URL
• Install: BiocManager::install("TreeSummarizedExperiment")

When to Use

• Storing rectangular experimental data alongside hierarchical tree structures using the TreeSummarizedExperiment class.
• Aggregating data to different taxonomic levels (e.g., phylum or class) using aggTSE.
• Subsetting data by specific tree nodes or leaves using subsetByNode.
• Storing reference sequence data per feature using the referenceSeq slot.

When NOT to Use

• For standard single-cell RNA-seq without hierarchical relationships, use SingleCellExperiment because the tree-related slots and overhead are unnecessary.
• For purely manipulating or visualizing phylogenetic trees without rectangular assay data, use ape or ggtree directly because they are specialized for tree operations.

Data Requirements

• An assays matrix representing observed data (e.g., counts) with rows as entities and columns as samples.
• rowData and colData data frames for feature and sample annotations.
• Hierarchical structures provided as phylo objects for rowTree and/or colTree.
• Link information mapping assay rows/columns to tree nodes via rowNodeLab or colNodeLab.
• Optional reference sequences as DNAStringSet or DNAStringSetList.