isoformUniverse

isoformUniverse is an umbrella R package for isoform-level analysis — inspired by how tidyverse manages its ecosystem.

The vision behind isoformUniverse is to provide a coordinated “universe” of R packages for a comprehensive, integrated multi-faceted analysis of isoforms across data modalities, biological contexts, and disease settings. The package currently brings together two IsoformUniverse packages, with several additional tools under active development by the Isoform Analysis Group and collaborators.

A single call to library(IsoformUniverse) loads and keeps in sync a curated set of isoform-analysis packages hosted on Bioconductor and GitHub.

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Packages included

Package	Source	Description
pairedGSEA	Bioconductor	Paired gene-set enrichment analysis for gene and isoform expression
IsoformSwitchAnalyzeR	GitHub	Identify, annotate, and visualise isoform switches with functional consequences

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Installation

Install isoformUniverse

# Install from GitHub
remotes::install_github("IsoformAnalysisGroup/isoformUniverse")

Install all member packages

library(isoformUniverse)

# Install any missing member packages
isoformUniverse_install()

# Attach member packages that are not already loaded
isoformUniverse_attach()

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Usage

library(isoformUniverse)
#> ── isoformUniverse ─────────────────────────────────────────────────────────
#> ✔ pairedGSEA 1.4.0
#> ✔ IsoformSwitchAnalyzeR 2.4.0

Update all member packages

isoformUniverse_update()

Inspect the package registry

isoformUniverse_packages()
#>                  package        source                                repo
#> 1             pairedGSEA  Bioconductor                                <NA>
#> 2  IsoformSwitchAnalyzeR        GitHub  kvittingseerup/IsoformSwitchAnalyzeR
#> deps: <list-column; each element is a dependency data.frame>

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Functions

Function	Description
library(IsoformUniverse)	Loads all member packages (calls isoformUniverse_attach() automatically)
isoformUniverse_packages()	Returns a data frame of all member packages, sources, repositories, and explicit pre-dependencies
isoformUniverse_install()	Installs any missing member packages (with optional explicit pre-dependencies (Bioconductor or GitHub))
isoformUniverse_update()	Updates all member packages to their latest versions
isoformUniverse_attach()	Attaches all member packages and prints a startup message

Contributing new packages

Please reach out to Kristoffer Vitting-Seerup if you are interested in contributing a package to the isoformUniverse