- recipe bioconductor-easyrnaseq
Count summarization and normalization for RNA-Seq data
- Homepage:
https://bioconductor.org/packages/3.17/bioc/html/easyRNASeq.html
- License:
Artistic-2.0
- Recipe:
Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
- package bioconductor-easyrnaseq¶
- versions:
2.36.0-0,2.34.0-0,2.30.0-0,2.28.0-0,2.24.1-0,2.22.0-0,2.20.0-1,2.18.2-0,2.16.0-0,2.36.0-0,2.34.0-0,2.30.0-0,2.28.0-0,2.24.1-0,2.22.0-0,2.20.0-1,2.18.2-0,2.16.0-0,2.14.0-0- depends bioconductor-biobase:
>=2.60.0,<2.61.0- depends bioconductor-biocfilecache:
>=2.8.0,<2.9.0- depends bioconductor-biocgenerics:
>=0.46.0,<0.47.0- depends bioconductor-biocparallel:
>=1.34.0,<1.35.0- depends bioconductor-biomart:
>=2.56.0,<2.57.0- depends bioconductor-biostrings:
>=2.68.0,<2.69.0- depends bioconductor-edger:
>=3.42.0,<3.43.0- depends bioconductor-genomeinfodb:
>=1.36.0,<1.37.0- depends bioconductor-genomeintervals:
>=1.56.0,<1.57.0- depends bioconductor-genomicalignments:
>=1.36.0,<1.37.0- depends bioconductor-genomicranges:
>=1.52.0,<1.53.0- depends bioconductor-iranges:
>=2.34.0,<2.35.0- depends bioconductor-rsamtools:
>=2.16.0,<2.17.0- depends bioconductor-s4vectors:
>=0.38.0,<0.39.0- depends bioconductor-shortread:
>=1.58.0,<1.59.0- depends bioconductor-summarizedexperiment:
>=1.30.0,<1.31.0- depends r-base:
>=4.3,<4.4.0a0- depends r-locfit:
- depends r-lsd:
>=4.1-0- depends r-rappdirs:
>=0.3.1- 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-easyrnaseq and update with:: mamba update bioconductor-easyrnaseq
To create a new environment, run:
mamba create --name myenvname bioconductor-easyrnaseq
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-easyrnaseq:<tag> (see `bioconductor-easyrnaseq/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-easyrnaseq/README.html)
