- recipe bioconductor-norce
NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
- Homepage:
- License:
MIT + file LICENSE
- Recipe:
While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint to a functional association. We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast.
- package bioconductor-norce¶
- versions:
1.14.0-0,1.12.0-0,1.10.0-0,1.6.0-0,1.4.0-0,1.2.0-1,1.2.0-0,1.0.0-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-biomart:
>=2.58.0,<2.59.0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-go.db:
>=3.18.0,<3.19.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-keggrest:
>=1.42.0,<1.43.0- depends bioconductor-reactome.db:
>=1.86.0,<1.87.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-rwikipathways:
>=1.22.0,<1.23.0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0- depends r-base:
>=4.3,<4.4.0a0- depends r-dbi:
- depends r-dbplyr:
- depends r-dplyr:
- depends r-ggplot2:
- depends r-igraph:
- depends r-png:
- depends r-rcurl:
- depends r-readr:
- depends r-reshape2:
- depends r-rsqlite:
- depends r-stringr:
- depends r-tidyr:
- 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-norce and update with:: mamba update bioconductor-norce
To create a new environment, run:
mamba create --name myenvname bioconductor-norce
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-norce:<tag> (see `bioconductor-norce/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-norce/README.html)
