IHWpaper
This is the released version of IHWpaper; for the devel version, see IHWpaper.
Reproduce figures in IHW paper
Bioconductor version: Release (3.23)
This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package.
Author: Nikos Ignatiadis [aut, cre]
Maintainer: Nikos Ignatiadis <nikos.ignatiadis01 at gmail.com>
citation("IHWpaper")):Nikos Ignatiadis. IHWpaper: Reproduce figures in IHW paper. doi:10.18129/B9.bioc.IHWpaper, R package version 1.40.0, https://bioconductor.org/packages/IHWpaper.
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")
BiocManager::install("IHWpaper")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("IHWpaper")| "Various: BH explanation / visualization" | HTML | R Script |
| "NMeth paper: Explaining tdr" | HTML | R Script |
| "Various: Grenander Estimator as applied to IHW (vs ECDF)" | HTML | R Script |
| "Stats paper: hQTL analysis with IHW-Benjamini-Yekutieli" | HTML | R Script |
| "NMeth paper: IHW-Bonferroni simulations" | HTML | R Script |
| "Various: Real data examples: 1-fold weight function" | HTML | R Script |
| "NMeth paper: Real data examples" | HTML | R Script |
| "NMeth paper: Simulation Figures" | HTML | R Script |
| "NMeth paper: Stratified Histograms" | HTML | R Script |
| "Various: tdr and pvalue rejection regions" | HTML | R Script |
| "Various: Weights vs Independent Filtering" | HTML | R Script |
| Reference Manual |
Details
| biocViews | ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3), IHW |
| Imports | Rcpp, stats, splines, methods, utils, DESeq2, SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase, BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot |
| System Requirements | |
| URL |
See More
| Suggests | testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IHWpaper_1.40.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/IHWpaper |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/IHWpaper |
| Package Short Url | https://bioconductor.org/packages/IHWpaper/ |
| Package Downloads Report | Download Stats |