Package: TreeSummarizedExperiment

Type: Package

Title: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Version: 2.1.4

Date: 2021-01-01

Authors@R:

c(person("Ruizhu", "Huang", email = "ruizhuRH@gmail.com",

role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3285-1945")),

person("Felix G.M.", "Ernst", email = "felix.gm.ernst@outlook.com",

role = c("ctb"), comment = c(ORCID = "0000-0001-5064-0928")))

Description: TreeSummarizedExperiment has extended SingleCellExperiment to

include hierarchical information on the rows or columns of the rectangular

data.

Depends:

R(>= 3.6.0),

SingleCellExperiment,

S4Vectors (>= 0.23.18),

Biostrings

License: GPL (>=2)

Encoding: UTF-8

LazyData: true

biocViews: DataRepresentation, Infrastructure

Imports:

methods,

BiocGenerics,

utils,

ape,

rlang,

dplyr,

SummarizedExperiment,

BiocParallel,

IRanges,

treeio

VignetteBuilder: knitr

Suggests:

ggtree,

ggplot2,

BiocStyle,

knitr,

rmarkdown,

testthat

RoxygenNote: 7.1.1

Collate:

'TreeSummarizedExperiment.R'

'aboutLoop.R'

'allClass.R'

'aggTSE.R'

'allGenerics.R'

'changeTree.R'

'classAccessor.R'

'classValid.R'

'coercion.R'

'combine.R'

'data.R'

'deprecate_Fun.R'

'internal_utils.R'

'makeTSE.R'

'tree_addLabel.R'

'tree_asLeaf.R'

'tree_asPhylo.R'

'tree_convertNode.R'

'tree_countLeaf.R'

'tree_countNode.R'

'tree_distNode.R'

'tree_findAncestor.R'

'tree_findChild.R'

'tree_findDescendant.R'

'tree_findSibling.R'

'tree_isLeaf.R'

'tree_joinNode.R'

'tree_matTree.R'

'tree_printNode.R'

'tree_shareNode.R'

'tree_showNode.R'

'tree_toTree.R'

'tree_trackNode.R'

'tree_unionLeaf.R'

'updateObject.R'