Package Recipe 'bioconductor-psichomics'

recipe bioconductor-psichomics

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

package bioconductor-psichomics¶

Versions:

1.36.1-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.20.2-0, 1.20.1-0, 1.20.0-0,

1.36.1-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.20.2-0, 1.20.1-0, 1.20.0-0, 1.18.1-0, 1.16.0-1, 1.16.0-0, 1.13.1-0, 1.12.0-0, 1.10.0-1, 1.8.1-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-annotationdbi >=1.72.0,<1.73.0a0
on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-annotationhub >=4.0.0,<4.1.0a0
on bioconductor-biocfilecache >=3.0.0,<3.1.0
on bioconductor-biocfilecache >=3.0.0,<3.1.0a0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-edger >=4.8.2,<4.9.0a0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-limma >=3.66.0,<3.67.0a0
on bioconductor-recount >=1.36.0,<1.37.0
on bioconductor-recount >=1.36.0,<1.37.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-cluster
on r-colourpicker
on r-data.table
on r-digest
on r-dplyr
on r-dt >=0.2
on r-fastica
on r-fastmatch
on r-ggplot2
on r-ggrepel
on r-highcharter >=0.5.0
on r-htmltools
on r-httr
on r-jsonlite
on r-pairsd3
on r-plyr
on r-purrr
on r-r.utils
on r-rcpp >=0.12.14
on r-reshape2
on r-rfast
on r-shiny >=1.7.0
on r-shinybs
on r-shinyjs
on r-stringr
on r-survival
on r-xml
on r-xtable

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-psichomics

to add into an existing workspace instead, run:

pixi add bioconductor-psichomics

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-psichomics

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-psichomics

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-psichomics:<tag>

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