treeclimbR

An algorithm to find optimal signal levels in a tree


Bioconductor version: Release (3.19)

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

Author: Ruizhu Huang [aut] , Charlotte Soneson [aut, cre]

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

Citation (from within R, enter citation("treeclimbR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("treeclimbR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("treeclimbR")
treeclimbR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, Software, StatisticalMethod
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends R (>= 4.4.0)
Imports TreeSummarizedExperiment(>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang
System Requirements
URL https://github.com/csoneson/treeclimbR
Bug Reports https://github.com/csoneson/treeclimbR/issues
See More
Suggests knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package treeclimbR_1.0.0.tar.gz
Windows Binary treeclimbR_1.0.0.zip
macOS Binary (x86_64) treeclimbR_1.0.0.tgz
macOS Binary (arm64) treeclimbR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/treeclimbR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/treeclimbR
Bioc Package Browser https://code.bioconductor.org/browse/treeclimbR/
Package Short Url https://bioconductor.org/packages/treeclimbR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive