diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000..8ff32a8 --- /dev/null +++ b/README.Rmd @@ -0,0 +1,126 @@ +--- +output: github_document +--- + + + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + cache = TRUE, + out.width = "100%" +) +``` + +# MultiAssayExperiment + +## Software For The Integration Of Multi-Omics Experiments In Bioconductor + + + + +[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/MultiAssayExperiment.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/MultiAssayExperiment) +[![Platforms](http://www.bioconductor.org/shields/availability/release/MultiAssayExperiment.svg)](https://www.bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html#archives) +[![Coverage Status](https://codecov.io/github/waldronlab/MultiAssayExperiment/coverage.svg?branch=devel)](https://codecov.io/github/waldronlab/MultiAssayExperiment?branch=devel) +[![Downloads](http://www.bioconductor.org/shields/downloads/release/MultiAssayExperiment.svg)](https://bioconductor.org/packages/stats/bioc/MultiAssayExperiment) + + +## Installation + +We recommend installing the stable release version of MultiAssayExperiment in +Bioconductor. This can be done using `BiocManager`: + +```{r, eval = FALSE} +if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +BiocManager::install("MultiAssayExperiment") +``` + +## Schematic + +Here is a visual overview of the `MultiAssayExperiment` class. +The three main components are: + +* `colData` - phenotype data +* `ExperimentList` - a list of tables from experimental results +* `sampleMap` - a graph representation of 'samples' and 'participants' + +_Note_. For simplicity, we use the terms 'samples' and 'participants' to +elucidate the relationship although `MultiAssayExperiment` can work on other +biological specimens. + +```{r, out.height = "354px", out.width = "384px", echo = FALSE, fig.cap = "MultiAssayExperiment schematic"} +knitr::include_graphics("vignettes/MultiAssayExperiment.png") +``` + +## Cheatsheet + + + +## Ready-to-use `MultiAssayExperiment` objects + +For easy-to-use and ready-made MultiAssayExperiment objects, use the +`curatedTCGAData` experiment data package. + +```{r, eval = FALSE} +BiocManager::install("curatedTCGAData") +``` + +## Companion package for working with TCGA data + +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. + +```{r, eval = FALSE} +BiocManager::install("TCGAutils") +``` + +## Documentation + +The `MultiAssayExperiment` API is available by browsing to the +[API wiki](https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API). + +## 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](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. + +## 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](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/) diff --git a/README.md b/README.md index bcfa143..32d1b82 100644 --- a/README.md +++ b/README.md @@ -1,42 +1,56 @@ + + + # MultiAssayExperiment ## Software For The Integration Of Multi-Omics Experiments In Bioconductor -https://doi.org/10.1158/0008-5472.CAN-17-0344 + + + -[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/MultiAssayExperiment.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/MultiAssayExperiment) +[![BioC +status](http://www.bioconductor.org/shields/build/release/bioc/MultiAssayExperiment.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/MultiAssayExperiment) [![Platforms](http://www.bioconductor.org/shields/availability/release/MultiAssayExperiment.svg)](https://www.bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html#archives) -[![Coverage Status](https://codecov.io/github/waldronlab/MultiAssayExperiment/coverage.svg?branch=devel)](https://codecov.io/github/waldronlab/MultiAssayExperiment?branch=devel) +[![Coverage +Status](https://codecov.io/github/waldronlab/MultiAssayExperiment/coverage.svg?branch=devel)](https://codecov.io/github/waldronlab/MultiAssayExperiment?branch=devel) [![Downloads](http://www.bioconductor.org/shields/downloads/release/MultiAssayExperiment.svg)](https://bioconductor.org/packages/stats/bioc/MultiAssayExperiment) + ## Installation -We recommend installing the stable release version of MultiAssayExperiment in -Bioconductor. This can be done using `BiocManager`: +We recommend installing the stable release version of +MultiAssayExperiment in Bioconductor. This can be done using +`BiocManager`: -``` -if (!require("BiocManager")) +``` r +if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") -library(BiocManager) - -install("MultiAssayExperiment") +BiocManager::install("MultiAssayExperiment") ``` ## Schematic -Here is a visual overview of the `MultiAssayExperiment` class. -The three main components are: +Here is a visual overview of the `MultiAssayExperiment` class. The three +main components are: -* `colData` - phenotype data -* `ExperimentList` - a list of tables from experimental results -* `sampleMap` - a graph representation of 'samples' and 'participants' +- `colData` - phenotype data +- `ExperimentList` - a list of tables from experimental results +- `sampleMap` - a graph representation of ‘samples’ and ‘participants’ -_Note_. For simplicity, we use the terms 'samples' and 'participants' to -elucidate the relationship although `MultiAssayExperiment` can work on other -biological specimens. +*Note*. For simplicity, we use the terms ‘samples’ and ‘participants’ to +elucidate the relationship although `MultiAssayExperiment` can work on +other biological specimens. -MultiAssayExperiment schematic +
+ +MultiAssayExperiment schematic +

+MultiAssayExperiment schematic +

+ +
## Cheatsheet @@ -47,30 +61,30 @@ biological specimens. For easy-to-use and ready-made MultiAssayExperiment objects, use the `curatedTCGAData` experiment data package. -``` -install("curatedTCGAData") +``` r +BiocManager::install("curatedTCGAData") ``` ## Companion package for working with TCGA data -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. +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. -``` -install("TCGAutils") +``` r +BiocManager::install("TCGAutils") ``` ## Documentation -The `MultiAssayExperiment` API is available by browsing to the -[API wiki](https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API). +The `MultiAssayExperiment` API is available by browsing to the [API +wiki](https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API). ## 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](https://groups.google.com/forum/#!forum/biocmultiassay) +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. @@ -84,14 +98,13 @@ 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. +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. +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 @@ -99,11 +112,10 @@ 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. +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](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/) +Covenant](http://contributor-covenant.org), version 1.0.0, available at +