leapR
This is the development version of leapR; for the stable release version, see leapR.
Layered enrichment analysis of pathways R
Bioconductor version: Development (3.24)
leapR is a package that identifies pathways that are enriched across diverse 'omics experiments. It leverages any tabular expression data (proteomics, transcriptomics) using the `SummarizedExperiment` object. It works with any pathway in the .gct file format.
Author: Sara Gosline [aut, cre]
, Jason McDermott [aut], Jeremy Jacobson [aut], Vincent Danna [ctb], National Institutes of Health [fnd]
Maintainer: Sara Gosline <sara.gosline at pnnl.gov>
citation("leapR")):
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("leapR")
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("leapR")| leapR | HTML | R Script |
| leapR | HTML | R Script |
| leapR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Pathways, Proteomics, Software, Transcriptomics |
| Version | 1.1.2 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | stats, gplots, readr, tibble, gplots, methods, ggplot2, dplyr, stringr, tidyr, SummarizedExperiment, BiocStyle, BiocFileCache |
| System Requirements | |
| URL | https://pnnl.github.io/leapR/ |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
| 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 | leapR_1.1.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | leapR_1.1.2.tgz |
| macOS Binary (sonoma-arm64) | leapR_1.1.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/leapR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/leapR |
| Bioc Package Browser | https://code.bioconductor.org/browse/leapR/ |
| Package Short Url | https://bioconductor.org/packages/leapR/ |
| Package Downloads Report | Download Stats |