- recipe bioconductor-psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/psichomics.html
- License:
MIT + file LICENSE
- Recipe:
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:
1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.20.2-0,1.20.1-0,1.20.0-0,1.18.1-0,1.16.0-1,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.20.2-0,1.20.1-0,1.20.0-0,1.18.1-0,1.16.0-1,1.16.0-0,1.13.1-0,1.12.0-0,1.10.0-1,1.8.1-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-annotationdbi:
>=1.64.1,<1.65.0a0- depends bioconductor-annotationhub:
>=3.10.0,<3.11.0- depends bioconductor-annotationhub:
>=3.10.0,<3.11.0a0- depends bioconductor-biocfilecache:
>=2.10.0,<2.11.0- depends bioconductor-biocfilecache:
>=2.10.1,<2.11.0a0- depends bioconductor-edger:
>=4.0.0,<4.1.0- depends bioconductor-edger:
>=4.0.2,<4.1.0a0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-limma:
>=3.58.1,<3.59.0a0- depends bioconductor-recount:
>=1.28.0,<1.29.0- depends bioconductor-recount:
>=1.28.0,<1.29.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- 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-pairsd3:
- depends r-plyr:
- depends r-purrr:
- depends r-r.utils:
- depends r-rcpp:
>=0.12.14- depends r-reshape2:
- depends r-rfast:
- depends r-shiny:
>=1.7.0- depends r-shinybs:
- depends r-shinyjs:
- depends r-stringr:
- depends r-survival:
- depends r-xml:
- depends r-xtable:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-psichomics and update with:: mamba update bioconductor-psichomics
To create a new environment, run:
mamba create --name myenvname bioconductor-psichomics
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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:
[](http://bioconda.github.io/recipes/bioconductor-psichomics/README.html)
