metapod
This is the released version of metapod; for the devel version, see metapod.
Meta-Analyses on P-Values of Differential Analyses
Bioconductor version: Release (3.23)
Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("metapod")):
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")
BiocManager::install("metapod")
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("metapod")| Meta-analysis strategies | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialPeakCalling, MultipleComparison, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | |
| Imports | Rcpp |
| System Requirements | C++11 |
| URL | https://github.com/LTLA/metapod |
| Bug Reports | https://github.com/LTLA/metapod/issues |
See More
| Suggests | testthat, knitr, BiocStyle, rmarkdown |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | csaw, mumosa, scp, scran, DGEAR |
| Suggests Me | TSCAN |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | metapod_1.20.0.tar.gz |
| Windows Binary (x86_64) | metapod_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | metapod_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | metapod_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/metapod |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/metapod |
| Bioc Package Browser | https://code.bioconductor.org/browse/metapod/ |
| Package Short Url | https://bioconductor.org/packages/metapod/ |
| Package Downloads Report | Download Stats |