Package Recipe 'bioconductor-profileplyr'

recipe bioconductor-profileplyr

Visualization and annotation of read signal over genomic ranges with profileplyr

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/profileplyr.html
License:: GPL (>= 3)
Recipe:: /bioconductor-profileplyr/meta.yaml

Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.

package bioconductor-profileplyr¶

Versions:

1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0, 1.4.3-0,

1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0, 1.4.3-0, 1.2.0-0, 1.0.1-0

Depends:

on bioconductor-biocgenerics >=0.52.0,<0.53.0
on bioconductor-biocparallel >=1.40.0,<1.41.0
on bioconductor-chipseeker >=1.42.0,<1.43.0
on bioconductor-complexheatmap >=2.22.0,<2.23.0
on bioconductor-enrichedheatmap >=1.36.0,<1.37.0
on bioconductor-genomeinfodb >=1.42.0,<1.43.0
on bioconductor-genomicfeatures >=1.58.0,<1.59.0
on bioconductor-genomicranges >=1.58.0,<1.59.0
on bioconductor-iranges >=2.40.0,<2.41.0
on bioconductor-org.hs.eg.db >=3.20.0,<3.21.0
on bioconductor-org.mm.eg.db >=3.20.0,<3.21.0
on bioconductor-rgreat >=2.8.0,<2.9.0
on bioconductor-rsamtools >=2.22.0,<2.23.0
on bioconductor-rtracklayer >=1.66.0,<1.67.0
on bioconductor-s4vectors >=0.44.0,<0.45.0
on bioconductor-soggi >=1.38.0,<1.39.0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0
on bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0
on bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0
on bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0
on bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0
on r-base >=4.4,<4.5.0a0
on r-circlize
on r-dplyr
on r-ggplot2
on r-magrittr
on r-pheatmap
on r-r.utils
on r-rjson
on r-rlang
on r-tidyr
on r-tiff

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-profileplyr

to add into an existing workspace instead, run:

pixi add bioconductor-profileplyr

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-profileplyr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-profileplyr

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-profileplyr:<tag>

(see bioconductor-profileplyr/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-profileplyr/README.html)