Package Recipe 'bioconductor-seqsetvis'

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:

1.30.0-0, 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,

1.30.0-0, 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:

on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on r-base >=4.5,<4.6.0a0
on r-cowplot
on r-data.table
on r-eulerr
on r-ggplot2
on r-ggplotify
on r-pbapply
on r-pbmcapply
on r-png
on r-rcolorbrewer
on r-scales
on r-upsetr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-seqsetvis

to add into an existing workspace instead, run:

pixi add bioconductor-seqsetvis

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-seqsetvis

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-seqsetvis

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-seqsetvis/README.html)