- recipe bioconductor-gdnax
Diagnostics for assessing genomic DNA contamination in RNA-seq data
- Homepage:
- License:
Artistic-2.0
- Recipe:
Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.
- package bioconductor-gdnax¶
- versions:
1.0.0-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-annotationhub:
>=3.10.0,<3.11.0- 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-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicfiles:
>=1.38.0,<1.39.0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends r-base:
>=4.3,<4.4.0a0- depends r-bitops:
- depends r-plotrix:
- 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-gdnax and update with:: mamba update bioconductor-gdnax
To create a new environment, run:
mamba create --name myenvname bioconductor-gdnax
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-gdnax:<tag> (see `bioconductor-gdnax/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-gdnax/README.html)
