Welcome to the new bioconductor.org!

GeoDiff

Count model based differential expression and normalization on GeoMx RNA data


Bioconductor version: Release (3.18)

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>

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

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")
Workflow_WTA HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GeneExpression, Normalization, Software
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
System Requirements
URL https://github.com/Nanostring-Biostats/GeoDiff
Bug Reports https://github.com/Nanostring-Biostats/GeoDiff
See More
Suggests knitr, rmarkdown, dplyr
Linking To Rcpp, RcppArmadillo, roptim
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 GeoDiff_1.8.0.tar.gz
Windows Binary GeoDiff_1.8.0.zip (64-bit only)
macOS Binary (x86_64) GeoDiff_1.8.0.tgz
macOS Binary (arm64) GeoDiff_1.8.0.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