recipe bioconductor-geodiff

Count model based differential expression and normalization on GeoMx RNA data

Homepage

https://bioconductor.org/packages/3.14/bioc/html/GeoDiff.html

License

MIT + file LICENSE

Recipe

/bioconductor-geodiff/meta.yaml

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.

package bioconductor-geodiff

Versions

1.0.0-1,  1.0.0-0

Depends

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-geomxtools >=2.0.0,<2.1.0

• bioconductor-nanostringnctools >=1.2.0,<1.3.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=10.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=10.3.0

• r-base >=4.1,<4.2.0a0

• r-lme4

• r-matrix

• r-plyr

• r-rcpp >=1.0.4.6

• r-rcpparmadillo

• r-robust

• r-roptim

• r-testthat

• r-withr

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-geodiff

and update with:

conda update bioconductor-geodiff

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-geodiff:<tag>

(see bioconductor-geodiff/tags for valid values for <tag>)

Download stats

Link to this page

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