recipe bioconductor-psichomics

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Homepage:

https://bioconductor.org/packages/3.16/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:

1.24.0-0,  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, 

1.24.0-0,  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:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-annotationhub >=3.6.0,<3.7.0

• bioconductor-biocfilecache >=2.6.0,<2.7.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-recount >=1.24.0,<1.25.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-cluster

• r-colourpicker

• r-data.table

• r-digest

• r-dplyr

• r-dt >=0.2

• r-fastica

• r-fastmatch

• r-ggplot2

• r-ggrepel

• r-highcharter >=0.5.0

• r-htmltools

• r-httr

• r-jsonlite

• r-pairsd3

• r-plyr

• r-purrr

• r-r.utils

• r-rcpp >=0.12.14

• r-reshape2

• r-rfast

• r-shiny >=1.7.0

• r-shinybs

• r-shinyjs

• r-stringr

• r-survival

• r-xml

• r-xtable

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-psichomics

and update with:

conda update bioconductor-psichomics

or use the docker container:

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

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

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)