recipe bioconductor-consensusde

RNA-seq analysis using multiple algorithms






This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation.

package bioconductor-consensusde

(downloads) docker_bioconductor-consensusde



depends bioconductor-airway:


depends bioconductor-annotationdbi:


depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-biostrings:


depends bioconductor-deseq2:


depends bioconductor-edaseq:


depends bioconductor-edger:


depends bioconductor-ensdb.hsapiens.v86:


depends bioconductor-ensembldb:


depends bioconductor-genomicalignments:


depends bioconductor-genomicfeatures:


depends bioconductor-limma:




depends bioconductor-pcamethods:


depends bioconductor-rsamtools:


depends bioconductor-ruvseq:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene:


depends r-base:


depends r-data.table:

depends r-dendextend:

depends r-rcolorbrewer:



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-consensusde

and update with::

   mamba update bioconductor-consensusde

To create a new environment, run:

mamba create --name myenvname bioconductor-consensusde

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<tag>

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

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