recipe bioconductor-psichomics

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/psichomics.html

License

MIT + file LICENSE

Recipe

/bioconductor-psichomics/meta.yaml

package bioconductor-psichomics

(downloads) docker_bioconductor-psichomics

Versions

1.8.1-0

Depends bioconductor-annotationhub

>=2.14.0,<2.15.0

Depends bioconductor-edger

>=3.24.0,<3.25.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-recount

>=1.8.0,<1.9.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends libgcc-ng

>=7.3.0

Depends libstdcxx-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-cluster

Depends r-colourpicker

Depends r-data.table

Depends r-digest

Depends r-dplyr

Depends r-dt

>=0.2

Depends r-fastica

Depends r-fastmatch

Depends r-ggplot2

Depends r-ggrepel

Depends r-highcharter

>=0.5.0

Depends r-htmltools

Depends r-httr

Depends r-jsonlite

Depends r-misctools

Depends r-pairsd3

Depends r-plyr

Depends r-r.utils

Depends r-rcpp

>=0.12.14

Depends r-shiny

>=1.0.3

Depends r-shinybs

Depends r-shinyjs

Depends r-stringr

Depends r-survival

Depends r-xml

Depends r-xtable

Requirements

Installation

With an activated Bioconda channel (see 2. 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>)