GeoDiff

DOI: 10.18129/B9.bioc.GeoDiff  

Count model based differential expression and normalization on GeoMx RNA data

Bioconductor version: Release (3.17)

A series of statistical models using count generating distributions for background modelling, feature and sample QC, normalization and differential expression analysis on GeoMx RNA data. The application of these methods are demonstrated by example data analysis vignette.

Author: Nicole Ortogero [cre], Lei Yang [aut], Zhi Yang [aut]

Maintainer: Nicole Ortogero <nortogero at nanostring.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GeoDiff")

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("GeoDiff")

 

HTML	R Script	Workflow_WTA
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, Normalization, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0), Biobase
Imports	Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools
LinkingTo	Rcpp, RcppArmadillo, roptim
Suggests	knitr, rmarkdown, dplyr
SystemRequirements
Enhances
URL	https://github.com/Nanostring-Biostats/GeoDiff
BugReports	https://github.com/Nanostring-Biostats/GeoDiff
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GeoDiff_1.6.0.tar.gz
Windows Binary	GeoDiff_1.6.0.zip
macOS Binary (x86_64)	GeoDiff_1.6.0.tgz
macOS Binary (arm64)	GeoDiff_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GeoDiff
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GeoDiff
Bioc Package Browser	https://code.bioconductor.org/browse/GeoDiff/
Package Short Url	https://bioconductor.org/packages/GeoDiff/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive