recipe bioconductor-damsel

Damsel: an end to end analysis of DamID

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/Damsel.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-damsel/meta.yaml

Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R.

package bioconductor-damsel

versions:

1.2.0-0

depends bioconductor-annotationdbi:

>=1.68.0,<1.69.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0

depends bioconductor-edger:

>=4.4.0,<4.5.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicfeatures:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-ggbio:

>=1.54.0,<1.55.0

depends bioconductor-goseq:

>=1.58.0,<1.59.0

depends bioconductor-plyranges:

>=1.26.0,<1.27.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rsubread:

>=2.20.0,<2.21.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-patchwork:

depends r-reshape2:

depends r-rlang:

depends r-stringr:

depends r-tidyr:

requirements:

additional platforms:

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-damsel

and update with::

   mamba update bioconductor-damsel

To create a new environment, run:

mamba create --name myenvname bioconductor-damsel

with myenvname being 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-damsel:<tag>

(see `bioconductor-damsel/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-damsel/README.html)