Bioconductor - GeoDiff
Bioconductor 3.22
Software Packages
GeoDiff
GeoDiff
This is the
released
version of GeoDiff; for the devel version, see
GeoDiff
Count model based differential expression and normalization on GeoMx RNA data
DOI:
10.18129/B9.bioc.GeoDiff
Bioconductor version:
Release (3.22)
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
Citation (from within R, enter
citation("GeoDiff")
):
Installation
To install this package, start R (version "4.5") 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
1.16.0
In Bioconductor since
BioC 3.14 (R-4.1) (4.5 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
Bug Reports
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_1.16.0.tar.gz
Windows Binary (x86_64)
GeoDiff_1.16.0.zip
macOS Binary (x86_64)
GeoDiff_1.16.0.tgz
macOS Binary (arm64)
GeoDiff_1.16.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/GeoDiff
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/GeoDiff
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