- recipe bioconductor-consensusde
RNA-seq analysis using multiple algorithms
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/consensusDE.html
- License:
GPL-3
- Recipe:
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¶
- versions:
1.20.0-0,1.18.0-0,1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-1,1.20.0-0,1.18.0-0,1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-1,1.2.1-0,1.0.0-0- depends bioconductor-airway:
>=1.22.0,<1.23.0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-deseq2:
>=1.42.0,<1.43.0- depends bioconductor-edaseq:
>=2.36.0,<2.37.0- depends bioconductor-edger:
>=4.0.0,<4.1.0- depends bioconductor-ensdb.hsapiens.v86:
>=2.99.0,<2.100.0- depends bioconductor-ensembldb:
>=2.26.0,<2.27.0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-org.hs.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-pcamethods:
>=1.94.0,<1.95.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-ruvseq:
>=1.36.0,<1.37.0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene:
>=3.2.0,<3.3.0- depends r-base:
>=4.3,<4.4.0a0- depends r-data.table:
- depends r-dendextend:
- depends r-rcolorbrewer:
- 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-consensusde and update with:: mamba update bioconductor-consensusde
To create a new environment, run:
mamba create --name myenvname bioconductor-consensusde
with
myenvnamebeing 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-consensusde:<tag> (see `bioconductor-consensusde/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-consensusde/README.html)
