recipe bioconductor-seqsetvis

Set Based Visualizations for Next-Gen Sequencing Data

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-seqsetvis/meta.yaml

seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.

package bioconductor-seqsetvis

versions:

1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0, 

1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends r-base:

>=4.4,<4.5.0a0

depends r-cowplot:

depends r-data.table:

depends r-eulerr:

depends r-ggplot2:

depends r-ggplotify:

depends r-pbapply:

depends r-pbmcapply:

depends r-png:

depends r-rcolorbrewer:

depends r-scales:

depends r-upsetr:

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-seqsetvis

and update with::

   mamba update bioconductor-seqsetvis

To create a new environment, run:

mamba create --name myenvname bioconductor-seqsetvis

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-seqsetvis:<tag>

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

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