Package Recipe 'bioconductor-phantasus'

recipe bioconductor-phantasus

Visual and interactive gene expression analysis

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/phantasus.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-phantasus/meta.yaml

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

package bioconductor-phantasus¶

Versions:

1.30.0-0, 1.26.0-0, 1.22.2-0, 1.20.2-0, 1.18.2-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0,

1.30.0-0, 1.26.0-0, 1.22.2-0, 1.20.2-0, 1.18.2-0, 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, 1.2.1-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-apeglm >=1.32.0,<1.33.0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-fgsea >=1.36.0,<1.37.0
on bioconductor-geoquery >=2.78.0,<2.79.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-phantasuslite >=1.8.0,<1.9.0
on bioconductor-rhdf5 >=2.54.0,<2.55.0
on bioconductor-rhdf5client >=1.32.0,<1.33.0
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-ccapp
on r-config >=0.3.2
on r-curl
on r-data.table
on r-fs
on r-ggplot2
on r-gtable
on r-htmltools
on r-httpuv
on r-httr
on r-jsonlite
on r-matrix
on r-opencpu
on r-pheatmap
on r-protolite
on r-rook
on r-scales
on r-stringr
on r-svglite
on r-tidyr
on r-xml
on r-yaml

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-phantasus

to add into an existing workspace instead, run:

pixi add bioconductor-phantasus

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-phantasus

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-phantasus

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-phantasus:<tag>

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