recipe bioconductor-crossmeta

Cross Platform Meta-Analysis of Microarray Data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/crossmeta.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-crossmeta/meta.yaml

Implements cross-platform and cross-species meta-analyses of Affymentrix, Illumina, and Agilent microarray data. This package automates common tasks such as downloading, normalizing, and annotating raw GEO data. The user then selects control and treatment samples in order to perform differential expression analyses for all comparisons. After analysing each contrast seperately, the user can select tissue sources for each contrast and specify any tissue sources that should be grouped for the subsequent meta-analyses.

package bioconductor-crossmeta

Versions:

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.15.0-1,  1.15.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0

Depends:

• bioconductor-affxparser >=1.70.0,<1.71.0

• bioconductor-affy >=1.76.0,<1.77.0

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-geoquery >=2.66.0,<2.67.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-oligo >=1.62.0,<1.63.0

• bioconductor-sva >=3.46.0,<3.47.0

• r-base >=4.2,<4.3.0a0

• r-biocmanager >=1.30.4

• r-data.table >=1.10.4

• r-dbi >=1.0.0

• r-dt >=0.2

• r-fdrtool >=1.2.15

• r-matrixstats >=0.51.0

• r-metama >=3.1.2

• r-miniui >=0.1.1

• r-rcurl >=1.95.4.11

• r-reader >=1.0.6

• r-readxl >=1.3.1

• r-rsqlite >=2.1.1

• r-shiny >=1.0.0

• r-shinybs >=0.61

• r-shinyjs >=2.0.0

• r-shinypanel >=0.1.0

• r-shinywidgets >=0.5.3

• r-stringr >=1.2.0

• r-tibble

• r-xml >=3.98.1.17

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-crossmeta

and update with:

conda update bioconductor-crossmeta

or use the docker container:

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

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

Download stats

Link to this page

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