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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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) | path2path_0.99.4.zip |
| macOS Binary (big-sur-x86_64) | path2path_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | path2path_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/path2path |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/path2path |
| Bioc Package Browser | https://code.bioconductor.org/browse/path2path/ |
| Package Short Url | https://bioconductor.org/packages/path2path/ |
| Package Downloads Report | Download Stats |