- recipe bioconductor-genomicalignments
Representation and manipulation of short genomic alignments
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/GenomicAlignments.html
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: genomicalignments
Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
- package bioconductor-genomicalignments¶
- versions:
1.38.0-1,1.38.0-0,1.36.0-0,1.34.0-1,1.34.0-0,1.30.0-2,1.30.0-1,1.30.0-0,1.28.0-0,1.38.0-1,1.38.0-0,1.36.0-0,1.34.0-1,1.34.0-0,1.30.0-2,1.30.0-1,1.30.0-0,1.28.0-0,1.26.0-1,1.26.0-0,1.24.0-0,1.22.0-0,1.20.1-0,1.20.0-0,1.18.1-0,1.18.0-0,1.16.0-0,1.14.1-0,1.14.0-0,1.12.2-0,1.10.0-0,1.8.4-0,1.6.3-1,1.6.3-0,1.6.1-0,1.6.0-0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends r-base:
>=4.3,<4.4.0a0- 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-genomicalignments and update with:: mamba update bioconductor-genomicalignments
To create a new environment, run:
mamba create --name myenvname bioconductor-genomicalignments
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-genomicalignments:<tag> (see `bioconductor-genomicalignments/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-genomicalignments/README.html)
