phenopath

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see phenopath.

Genomic trajectories with heterogeneous genetic and environmental backgrounds

Bioconductor version: 3.14

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")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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 1.18.0

In Bioconductor since BioC 3.6 (R-3.4) (6.5 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

Package Archives

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

Source Package phenopath_1.18.0.tar.gz

Windows Binary phenopath_1.18.0.zip

macOS 10.13 (High Sierra) phenopath_1.18.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/phenopath

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/phenopath

Bioc Package Browser https://code.bioconductor.org/browse/phenopath/

Package Short Url https://bioconductor.org/packages/phenopath/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive