IWTomics

This is the development version of IWTomics; for the stable release version, see IWTomics.

Interval-Wise Testing for Omics Data

Bioconductor version: Development (3.24)

Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.

Author: Marzia A Cremona, Alessia Pini, Francesca Chiaromonte, Simone Vantini

Maintainer: Marzia A Cremona <mac78 at psu.edu>

Citation (from within R, enter citation("IWTomics")):

Seminal Bioconductor project articles:

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("IWTomics")

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("IWTomics")

Introduction to IWTomics	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, GenomeAnnotation, MultipleComparison, Software, StatisticalMethod
Version	1.37.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	GPL (>=2)
Depends	R (>= 3.5.0), GenomicRanges
Imports	parallel, gtable, grid, graphics, methods, IRanges, KernSmooth, fda, S4Vectors, grDevices, stats, utils, tools
System Requirements
URL

Suggests	XVector, knitr
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	IWTomics_1.37.0.tar.gz
Windows Binary (x86_64)	IWTomics_1.37.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	IWTomics_1.37.0.tgz
macOS Binary (sonoma-arm64)	IWTomics_1.37.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IWTomics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IWTomics
Bioc Package Browser	https://code.bioconductor.org/browse/IWTomics/
Package Short Url	https://bioconductor.org/packages/IWTomics/
Package Downloads Report	Download Stats