path2path
This is the development version of path2path; to use it, please install the devel version of Bioconductor.
Directional Pathway-by-Pathway Interaction Maps from Genome-Scale Perturb-Seq
Bioconductor version: Development (3.24)
Builds a directional pathway-by-pathway interaction map from genome-scale Perturb-seq differential-expression statistics by two stacked runs of preranked gene set enrichment analysis: once per perturbation over genes, then once per readout pathway over perturbations. Entry (j,k) of the resulting matrix measures whether perturbations targeting pathway j's members produce a coordinated transcriptional response in pathway k. The package includes target exclusion, effective-size filters, overlap masking, Stage 2 p-values with false-discovery-rate control, and a whole-pipeline permutation calibration with generalized-Pareto tail estimation.
Maintainer: Jun Li <jun.li at nd.edu>
citation("path2path")):Jun Li. path2path: Directional Pathway-by-Pathway Interaction Maps from Genome-Scale Perturb-Seq. doi:10.18129/B9.bioc.path2path, R package version 0.99.4, https://bioconductor.org/packages/path2path.
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("path2path")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("path2path")| path2path: directional pathway maps from Perturb-seq | HTML | R Script |
| Reference Manual |
Details
| biocViews | CRISPR, DifferentialExpression, GeneExpression, GeneSetEnrichment, GeneTarget, KEGG, NetworkInference, Pathways, SingleCell, Software, Transcriptomics, WholeGenome |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | fgsea, msigdbr, data.table, BiocParallel, withr, methods, stats, utils, grDevices, graphics |
| System Requirements | |
| URL | https://github.com/jli-stat/path2path |
| Bug Reports | https://github.com/jli-stat/path2path/issues |
See More
| Suggests | ggplot2, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, SummarizedExperiment, R.utils |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | path2path_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | path2path_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/path2path |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/path2path |
| Package Short Url | https://bioconductor.org/packages/path2path/ |
| Package Downloads Report | Download Stats |