- recipe bioconductor-edger
Empirical Analysis of Digital Gene Expression Data in R
- Homepage:
- License:
GPL-3.0-or-later
- Recipe:
- Links:
Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.
- package bioconductor-edger¶
- versions:
4.0.16-1
,4.0.2-0
,3.42.4-0
,3.40.0-1
,3.40.0-0
,3.36.0-2
,3.36.0-1
,3.36.0-0
,3.34.0-0
,4.0.16-1
,4.0.2-0
,3.42.4-0
,3.40.0-1
,3.40.0-0
,3.36.0-2
,3.36.0-1
,3.36.0-0
,3.34.0-0
,3.32.1-0
,3.32.0-0
,3.30.0-0
,3.28.0-1
,3.28.0-0
,3.26.5-0
,3.26.0-0
,3.24.3-0
,3.24.1-0
,3.22.5-0
,3.20.7-0
,3.20.1-0
,3.20.0-0
,3.18.1-0
,3.16.5-0
,3.14.0-1
,3.14.0-0
,3.12.1-1
,3.12.1-0
,3.12.0-0
,3.10.5-0
- depends bioconductor-limma:
>=3.58.0,<3.59.0
- depends bioconductor-limma:
>=3.58.1,<3.59.0a0
- depends libblas:
>=3.9.0,<4.0a0
- depends libgcc-ng:
>=12
- depends liblapack:
>=3.9.0,<4.0a0
- depends libstdcxx-ng:
>=12
- depends r-base:
>=4.3,<4.4.0a0
- depends r-locfit:
- depends r-rcpp:
- requirements:
- additional platforms:
linux-aarch64
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-edger and update with:: mamba update bioconductor-edger
To create a new environment, run:
mamba create --name myenvname bioconductor-edger
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-edger:<tag> (see `bioconductor-edger/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-edger/README.html)