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>
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
| Linking To | Rcpp, RcppArmadillo, roptim |
| Suggests | knitr, rmarkdown, dplyr |
| System Requirements | |
| Enhances | |
| URL | https://github.com/Nanostring-Biostats/GeoDiff |
| Bug Reports | https://github.com/Nanostring-Biostats/GeoDiff |
See More
| 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 |