- recipe bioconductor-nanomethviz
Visualise methlation data from Oxford Nanopore sequencing
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/NanoMethViz.html
- License:
Apache License (>= 2.0)
- Recipe:
NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.
- package bioconductor-nanomethviz¶
- versions:
2.8.1-0,2.6.0-0,2.4.0-1,2.4.0-0,2.0.0-2,2.0.0-1,2.0.0-0,1.2.0-0,1.0.0-2,2.8.1-0,2.6.0-0,2.4.0-1,2.4.0-0,2.0.0-2,2.0.0-1,2.0.0-0,1.2.0-0,1.0.0-2,1.0.0-1- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-annotationdbi:
>=1.64.1,<1.65.0a0- depends bioconductor-biocsingular:
>=1.18.0,<1.19.0- depends bioconductor-biocsingular:
>=1.18.0,<1.19.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-bsseq:
>=1.38.0,<1.39.0- depends bioconductor-bsseq:
>=1.38.0,<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-limma:
>=3.58.0,<3.59.0- depends bioconductor-limma:
>=3.58.1,<3.59.0a0- 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 bioconductor-zlibbioc:
>=1.48.0,<1.49.0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-assertthat:
- depends r-base:
>=4.3,<4.4.0a0- depends r-cli:
- depends r-cpp11:
>=0.2.5- depends r-data.table:
- depends r-dbscan:
- depends r-dplyr:
- depends r-e1071:
- depends r-forcats:
- depends r-fs:
- depends r-ggplot2:
>=3.4.0- depends r-ggrastr:
- depends r-glue:
- depends r-patchwork:
- depends r-purrr:
- depends r-r.utils:
- depends r-rcpp:
- depends r-readr:
- depends r-rlang:
- depends r-scales:
>=1.2.0- depends r-scico:
- depends r-stringr:
- depends r-tibble:
- depends r-tidyr:
- depends r-withr:
- 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-nanomethviz and update with:: mamba update bioconductor-nanomethviz
To create a new environment, run:
mamba create --name myenvname bioconductor-nanomethviz
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-nanomethviz:<tag> (see `bioconductor-nanomethviz/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-nanomethviz/README.html)
