recipe bioconductor-crossmeta

Cross Platform Meta-Analysis of Microarray Data

Homepage:

https://bioconductor.org/packages/3.17/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

(downloads) docker_bioconductor-crossmeta

versions:
1.26.0-01.24.0-01.20.0-01.18.0-01.15.0-11.15.0-01.14.0-01.12.0-01.10.0-1

1.26.0-01.24.0-01.20.0-01.18.0-01.15.0-11.15.0-01.14.0-01.12.0-01.10.0-11.8.0-0

depends bioconductor-affxparser:

>=1.72.0,<1.73.0

depends bioconductor-affy:

>=1.78.0,<1.79.0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-edger:

>=3.42.0,<3.43.0

depends bioconductor-geoquery:

>=2.68.0,<2.69.0

depends bioconductor-limma:

>=3.56.0,<3.57.0

depends bioconductor-oligo:

>=1.64.0,<1.65.0

depends bioconductor-sva:

>=3.48.0,<3.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

>=1.30.4

depends r-data.table:

>=1.10.4

depends r-dbi:

>=1.0.0

depends r-dt:

>=0.2

depends r-fdrtool:

>=1.2.15

depends r-matrixstats:

>=0.51.0

depends r-metama:

>=3.1.2

depends r-miniui:

>=0.1.1

depends r-rcurl:

>=1.95.4.11

depends r-reader:

>=1.0.6

depends r-readxl:

>=1.3.1

depends r-rsqlite:

>=2.1.1

depends r-shiny:

>=1.0.0

depends r-shinybs:

>=0.61

depends r-shinyjs:

>=2.0.0

depends r-shinypanel:

>=0.1.0

depends r-shinywidgets:

>=0.5.3

depends r-stringr:

>=1.2.0

depends r-tibble:

depends r-xml:

>=3.98.1.17

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-crossmeta

and update with::

   mamba update bioconductor-crossmeta

To create a new environment, run:

mamba create --name myenvname bioconductor-crossmeta

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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