Package: phenopath 1.37.0

Kieran Campbell

phenopath: Genomic trajectories with heterogeneous genetic and environmental backgrounds

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

Authors:Kieran Campbell

phenopath_1.37.0.tar.gz
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phenopath_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
phenopath/json (API)

# Install 'phenopath' in R:

install.packages('phenopath', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:phenopath-1.37.0(bioc 3.24)phenopath-1.36.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology rnaseq geneexpression bayesian singlecell principalcomponent cpp

4.76 score 58 scripts 464 downloads 9 exports 46 dependencies

Last updated from:23129254ea. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	176
linux-devel-arm64	NOTE	237
linux-devel-x86_64	NOTE	289
source / vignettes	OK	241
linux-release-arm64	NOTE	274
linux-release-x86_64	NOTE	325
macos-release-arm64	NOTE	149
macos-release-x86_64	NOTE	537
macos-oldrel-arm64	NOTE	186
macos-oldrel-x86_64	NOTE	444
windows-devel	NOTE	243
windows-release	NOTE	236
windows-oldrel	NOTE	302
wasm-release	OK	285

Exports:clvm interaction_effects interaction_sds interactions phenopath plot_elbo significant_interactions simulate_phenopath trajectory

Dependencies:abind Biobase BiocGenerics cli cpp11 DelayedArray dplyr farver generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats pillar pkgconfig purrr R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors S7 scales Seqinfo SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

Introduction to PhenoPath

Kieran R Campbell

Rendered fromintroduction_to_phenopath.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2019-01-18
Started: 2017-06-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Fit a CLVM Model	clvm
Get the interaction effect sizes	interaction_effects
Get the interaction standard deviations	interaction_sds
Tidy summary of interactions	interactions
PhenoPath - genomic trajectories with heterogeneous backgrounds	phenopath
Plots the ELBO	plot_elbo
Print a PhenoPath fit	print.phenopath_fit
Significance testing for interaction features	significant_interactions
Simulate from phenopath model	simulate_phenopath
Get the latent PhenoPath trajectory	trajectory