Package: phenopath 1.31.0

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

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phenopath.pdf |phenopath.html✨
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-1.31.0(bioc 3.21)phenopath-1.30.0(bioc 3.20)

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

4.63 score 43 scripts 228 downloads 9 exports 62 dependencies

Last updated 2 months agofrom:e66e4a6bec. Checks:OK: 7 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 02 2024
R-4.5-win-x86_64	NOTE	Dec 02 2024
R-4.5-linux-x86_64	NOTE	Dec 02 2024
R-4.4-win-x86_64	OK	Dec 02 2024
R-4.4-mac-x86_64	OK	Dec 02 2024
R-4.4-mac-aarch64	OK	Dec 02 2024
R-4.3-win-x86_64	OK	Dec 02 2024
R-4.3-mac-x86_64	OK	Dec 02 2024
R-4.3-mac-aarch64	OK	Dec 02 2024

Exports:clvm interaction_effects interaction_sds interactions phenopath plot_elbo significant_interactions simulate_phenopath trajectory

Dependencies:abind askpass Biobase BiocGenerics cli colorspace cpp11 crayon curl DelayedArray dplyr fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig purrr R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors scales SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Introduction to PhenoPath

Kieran R Campbell

Rendered fromintroduction_to_phenopath.Rmdusingknitr::rmarkdownon Dec 02 2024.

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