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.






package bioconductor-psichomics

(downloads) docker_bioconductor-psichomics



Depends bioconductor-annotationhub


Depends bioconductor-edger


Depends bioconductor-limma


Depends bioconductor-recount


Depends bioconductor-summarizedexperiment


Depends libgcc-ng


Depends libstdcxx-ng


Depends r-base


Depends r-cluster

Depends r-colourpicker

Depends r-data.table

Depends r-digest

Depends r-dplyr

Depends r-dt


Depends r-fastica

Depends r-fastmatch

Depends r-ggplot2

Depends r-ggrepel

Depends r-highcharter


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


Depends r-shiny


Depends r-shinybs

Depends r-shinyjs

Depends r-stringr

Depends r-survival

Depends r-xml

Depends r-xtable



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<tag>

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