treeclimbR
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see treeclimbR.
An algorithm to find optimal signal levels in a tree
Bioconductor version: 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("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 | ||
| 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 (x86_64) | 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 |