Overview

MultiAssayExperiment provides an integrative representation of multi-’omics data on a set of samples. You can choose to represent your data using this infrastructure or use pre-processed datasets from curatedTCGAData.

Introduction

We recommend installing the stable release version of MultiAssayExperiment in Bioconductor. This can be done using BiocManager:

if (!require("BiocManager"))
    install.packages("BiocManager")

library(BiocManager)

install("MultiAssayExperiment")

Documentation website

The MultiAssayExperiment quick reference, vignettes, and function help pages are available by browsing to the package website.

Cheatsheet

We provide a reference cheat sheet for a summary of available functionality in MultiAssayExperiment.

Ready-to-use datasets from The Cancer Genome Atlas (TCGA)

For easy-to-use and analysis-ready MultiAssayExperiment objects, use the curatedTCGAData experiment data package:

install("curatedTCGAData")

How to make working with TCGA data easier

TCGAutils is a handy package for working with TCGA data represented as MultiAssayExperiment objects. It is highly recommended to use TCGAutils for TCGA identifier manipulation, sample identification and separation, and much more.

To install TCGAutils, run the following:

install("TCGAutils")

Getting help

If you find a bug or error within MultiAssayExperiment, curatedTCGAData, or TCGAutils, please provide a reproducible example in the respective GitHub issues pages: ‘http://github.com/waldronlab//issues’.

If you have a question about using any of the packages listed above, create a post on https://support.bioconductor.org/.

The MultiAssayExperiment Bioconductor Special Interest Group

This group meets remotely to discuss this project approximately every 3 weeks. If you are interested, please join the MultiAssayExperiment Google Group and see the calendar of upcoming meetings.

The Fine Print

Contributor Code of Conduct

As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.

We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, age, or religion.

Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other disrespectful conduct.

Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.

This Code of Conduct is adapted from the Contributor Covenant, version 1.0.0, available at http://contributor-covenant.org/version/1/0/0/