phenopath

This is the development version of phenopath; for the stable release version, see phenopath.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Genomic trajectories with heterogeneous genetic and environmental backgrounds

Bioconductor version: Development (3.24)

PhenoPath infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them.

Author: Kieran Campbell

Maintainer: Kieran Campbell <kieranrcampbell at gmail.com>

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

Kieran Campbell. phenopath: Genomic trajectories with heterogeneous genetic and environmental backgrounds. doi:10.18129/B9.bioc.phenopath, R package version 1.37.0, https://bioconductor.org/packages/phenopath.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("phenopath")

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("phenopath")

Vignette Title	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, GeneExpression, ImmunoOncology, PrincipalComponent, RNASeq, SingleCell, Software
Version	1.37.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
License	Apache License (== 2.0)
Depends
Imports	Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr
System Requirements
URL

Suggests	knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me	splatter
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	phenopath_1.37.0.tar.gz
Windows Binary (x86_64)	phenopath_1.37.0.zip
macOS Binary (big-sur-x86_64)	phenopath_1.37.0.tgz
macOS Binary (sonoma-arm64)	phenopath_1.37.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/phenopath
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/phenopath
Package Short Url	https://bioconductor.org/packages/phenopath/
Package Downloads Report	Download Stats