GeoDiff

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see GeoDiff.

Count model based differential expression and normalization on GeoMx RNA data

Bioconductor version: 3.20

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, Normalization, Software

Version 1.12.0

In Bioconductor since BioC 3.14 (R-4.1) (3.5 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

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_1.12.0.tar.gz

Windows Binary (x86_64) GeoDiff_1.12.0.zip (64-bit only)

macOS Binary (x86_64) GeoDiff_1.12.0.tgz

macOS Binary (arm64) GeoDiff_1.12.0.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/

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