GeoDiff
This is the released version of GeoDiff; for the devel version, see GeoDiff.
All Bioconductor versions of GeoDiff
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14
Count model based differential expression and normalization on GeoMx RNA data
Bioconductor version: 3.23 · Package version: 1.18.0
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: Maddy Griswold [cre], Lei Yang [aut], Zhi Yang [aut]
Maintainer: Maddy Griswold <mgriswold at nanostring.com>
Citation
From within R, enter citation("GeoDiff"):
Lei Yang, Zhi Yang. GeoDiff: Count model based differential expression and normalization on GeoMx RNA data. doi:10.18129/B9.bioc.GeoDiff, R package version 1.18.0, https://bioconductor.org/packages/GeoDiff.
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("GeoDiff")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.18.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/Nanostring-Biostats/GeoDiff |
| Bug Reports | https://github.com/Nanostring-Biostats/GeoDiff |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| Downloads rank | 1454 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, Normalization, Software |
| Package Short Url | https://bioconductor.org/packages/GeoDiff/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GeoDiff")| Workflow_WTA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | GeoDiff_1.18.0.tar.gz |
| Windows binary (x86_64) | GeoDiff_1.18.0.zip |
| macOS binary (arm64) | GeoDiff_1.18.0.tgz |
| macOS binary (x86_64) | GeoDiff_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GeoDiff |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GeoDiff |
| Package Downloads Report | Download Stats |
Dependencies
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