recipe bioconductor-sitadela

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

Homepage

https://bioconductor.org/packages/3.13/bioc/html/sitadela.html

License

Artistic-2.0

Recipe

/bioconductor-sitadela/meta.yaml

Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported.

package bioconductor-sitadela

Versions

1.0.0-0

Depends

• bioconductor-biobase >=2.52.0,<2.53.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biomart >=2.48.0,<2.49.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• r-base >=4.1,<4.2.0a0

• r-rsqlite

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-sitadela

and update with:

conda update bioconductor-sitadela

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-sitadela:<tag>

(see bioconductor-sitadela/tags for valid values for <tag>)

Download stats

Link to this page

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