Overview of PhenoPath | The PhenoPath model | Mean-field variational inference | Example on simulated data | Simulating data | Fit PhenoPath model | Examining results | Advanced | Using an SummarizedExperiment as input | Initialisation of latent space | Controlling variational inference | Technical | References
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:
phenopath_1.37.0.tar.gz
phenopath_1.37.0.zip(r-4.7)phenopath_1.37.0.zip(r-4.6)phenopath_1.37.0.zip(r-4.5)
phenopath_1.37.0.tgz(r-4.6-x86_64)phenopath_1.37.0.tgz(r-4.6-arm64)phenopath_1.37.0.tgz(r-4.5-x86_64)phenopath_1.37.0.tgz(r-4.5-arm64)
phenopath_1.37.0.tar.gz(r-4.7-arm64)phenopath_1.37.0.tar.gz(r-4.7-x86_64)phenopath_1.37.0.tar.gz(r-4.6-arm64)phenopath_1.37.0.tar.gz(r-4.6-x86_64)
phenopath_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
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')) |
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.
immunooncologyrnaseqgeneexpressionbayesiansinglecellprincipalcomponentcpp
Last updated from:23129254ea. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 197 | ||
| linux-devel-arm64 | NOTE | 275 | ||
| linux-devel-x86_64 | NOTE | 327 | ||
| source / vignettes | OK | 290 | ||
| linux-release-arm64 | NOTE | 263 | ||
| linux-release-x86_64 | NOTE | 356 | ||
| macos-release-arm64 | NOTE | 181 | ||
| macos-release-x86_64 | NOTE | 345 | ||
| macos-oldrel-arm64 | NOTE | 199 | ||
| macos-oldrel-x86_64 | NOTE | 446 | ||
| windows-devel | NOTE | 220 | ||
| windows-release | NOTE | 214 | ||
| windows-oldrel | NOTE | 220 | ||
| wasm-release | OK | 137 |
Exports:clvminteraction_effectsinteraction_sdsinteractionsphenopathplot_elbosignificant_interactionssimulate_phenopathtrajectory
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArraydplyrfarvergenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpurrrR6RColorBrewerRcpprlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
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 |
