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| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
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| ```{r, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| collapse = TRUE, | ||
| comment = "#>", | ||
| cache = TRUE, | ||
| out.width = "100%" | ||
| ) | ||
| ``` | ||
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| # MultiAssayExperiment <a href='https://waldronlab.io/MultiAssayExperiment'><img src='https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/MultiAssayExperiment/MultiAssayExperiment.png' align="right" height="100" /></a> | ||
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| ## Software For The Integration Of Multi-Omics Experiments In Bioconductor | ||
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| <https://doi.org/10.1158/0008-5472.CAN-17-0344> | ||
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| <!-- badges: start --> | ||
| [](https://bioconductor.org/checkResults/release/bioc-LATEST/MultiAssayExperiment) | ||
| [](https://www.bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html#archives) | ||
| [](https://codecov.io/github/waldronlab/MultiAssayExperiment?branch=devel) | ||
| [](https://bioconductor.org/packages/stats/bioc/MultiAssayExperiment) | ||
| <!-- badges: end --> | ||
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| ## Installation | ||
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| We recommend installing the stable release version of MultiAssayExperiment in | ||
| Bioconductor. This can be done using `BiocManager`: | ||
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| ```{r, eval = FALSE} | ||
| if (!require("BiocManager", quietly = TRUE)) | ||
| install.packages("BiocManager") | ||
| BiocManager::install("MultiAssayExperiment") | ||
| ``` | ||
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| ## Schematic | ||
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| Here is a visual overview of the `MultiAssayExperiment` class. | ||
| The three main components are: | ||
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| * `colData` - phenotype data | ||
| * `ExperimentList` - a list of tables from experimental results | ||
| * `sampleMap` - a graph representation of 'samples' and 'participants' | ||
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| _Note_. For simplicity, we use the terms 'samples' and 'participants' to | ||
| elucidate the relationship although `MultiAssayExperiment` can work on other | ||
| biological specimens. | ||
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| ```{r, out.height = "354px", out.width = "384px", echo = FALSE, fig.cap = "MultiAssayExperiment schematic"} | ||
| knitr::include_graphics("vignettes/MultiAssayExperiment.png") | ||
| ``` | ||
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| ## Cheatsheet | ||
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| <a href="https://github.com/waldronlab/cheatsheets/blob/main/MultiAssayExperiment_QuickRef.pdf"><img src="https://raw.githubusercontent.com/waldronlab/cheatsheets/main/pngs/MultiAssayExperiment_QuickRef.png" width="989" height="1091"/></a> | ||
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| ## Ready-to-use `MultiAssayExperiment` objects | ||
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| For easy-to-use and ready-made MultiAssayExperiment objects, use the | ||
| `curatedTCGAData` experiment data package. | ||
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| ```{r, eval = FALSE} | ||
| BiocManager::install("curatedTCGAData") | ||
| ``` | ||
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| ## Companion package for working with TCGA data | ||
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| TCGAutils is a handy package for working with `MultiAssayExperiment` data | ||
| objects from `curatedTCGAData`. It is highly recommended to use `TCGAutils` for | ||
| identifier manipulation, sample identification and more. | ||
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| ```{r, eval = FALSE} | ||
| BiocManager::install("TCGAutils") | ||
| ``` | ||
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| ## Documentation | ||
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| The `MultiAssayExperiment` API is available by browsing to the | ||
| [API wiki](https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API). | ||
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| ## The `MultiAssayExperiment` Bioconductor Special Interest Group | ||
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| This group meets remotely to discuss this project approximately every 3 weeks. | ||
| If you are interested, please join the | ||
| [MultiAssayExperiment Google Group](https://groups.google.com/forum/#!forum/biocmultiassay) | ||
| and see the | ||
| [calendar](https://www.google.com/calendar/embed?src=9ar0qc8mpkv6b9intgmdcdf0ss%40group.calendar.google.com&ctz=America/New_York) | ||
| of upcoming meetings. | ||
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| ## Contributor Code of Conduct | ||
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| 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. | ||
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| 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. | ||
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| 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. | ||
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| 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. | ||
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| Instances of abusive, harassing, or otherwise unacceptable behavior | ||
| may be reported by opening an issue or contacting one or more of the | ||
| project maintainers. | ||
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| This Code of Conduct is adapted from the [Contributor | ||
| Covenant](http://contributor-covenant.org), version 1.0.0, available | ||
| at | ||
| [http://contributor-covenant.org/version/1/0/0/](http://contributor-covenant.org/version/1/0/0/) |
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