add .github directory and rbuildignore

.Rbuildignore

@@ -1,3 +1,5 @@
 ^DeDHeD\.Rproj$
 ^\.Rproj\.user$
 ^dev$
+^README\.Rmd$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,17 @@
+The Bioconductor community values
+
+* an open approach to science that promotes the sharing of ideas, code, and expertise
+* collaboration
+* diversity and inclusivity
+* a kind and welcoming environment
+* community contributions
+
+In line with these values, Bioconductor is dedicated to providing a welcoming, supportive, collegial, experience free of harassment, intimidation, and bullying regardless of:
+
+* identity: gender, gender identity and expression, sexual orientation, disability, physical appearance, ethnicity, body size, race, age, religion, etc.
+* intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.
+* stage of career
+
+In order to uphold these values, members of the Bioconductor community are required to follow the Code of Conduct.The latest version of Bioconductor project Code of Conduct is available at http://bioconductor.org/about/code-of-conduct/. Please read the Code of Conduct before contributing to this project.
+
+Thank you!

.github/CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# Contributing to DeDHeD
+
+This outlines how to propose a change to DeDHeD. 
+For more detailed info about contributing to this, and other tidyverse packages, please see the
+[**development contributing guide**](https://rstd.io/tidy-contrib). 
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. 
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. 
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("LieberInstitute/DeDHed", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that the DeDHeD project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/ISSUE_TEMPLATE/issue_template.md

@@ -0,0 +1,56 @@
+---
+name: Bug report or feature request
+about: Describe a bug you've seen or make a case for a new feature
+title: "[BUG] Your bug or feature request"
+labels: ''
+assignees: ''
+---
+
+Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://support.bioconductor.org/> using the appropriate tag(s) including one for this package.
+
+## Context
+
+Provide some context for your bug report or feature request. This could be the:
+
+* link to raw code, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/blob/master/00-template.Rmd#L24-L28
+* link to a commit, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/commit/6aa30b22eda614d932c12997ba611ba582c435d7
+* link to a line of code inside a commit, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/commit/6aa30b22eda614d932c12997ba611ba582c435d7#diff-e265269fe4f17929940e81341b92b116R17
+* link to code from an R package, example: https://github.com/LieberInstitute/spatialLIBD/blob/master/R/run_app.R#L51-L55
+
+## Code
+
+Include the code you ran and comments
+
+```R
+## prompt an error
+stop('hola')
+
+## check the error trace
+traceback()
+```
+
+## Small reproducible example
+
+If you copy the lines of code that lead to your error, you can then run [`reprex::reprex()`](https://reprex.tidyverse.org/reference/reprex.html) which will create a small website with code you can then easily copy-paste here in a way that will be easy to work with later on.
+
+```R
+## prompt an error
+stop('hola')
+#> Error in eval(expr, envir, enclos): hola
+
+## check the error trace
+traceback()
+#> No traceback available
+```
+
+
+## R session information
+
+Remember to include your full R session information.
+
+```R
+options(width = 120)
+sessioninfo::session_info()
+```
+
+The output of `sessioninfo::session_info()` includes relevant GitHub installation information and other details that are missed by `sessionInfo()`.

.github/SUPPORT.md

@@ -0,0 +1,35 @@
+# Getting help with `DeDHeD`
+
+Thanks for using `DeDHeD`!
+Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
+
+## Make a reprex
+
+Start by making a minimal **repr**oducible **ex**ample using the  [reprex](https://reprex.tidyverse.org/) package.
+If you haven't heard of or used reprex before, you're in for a treat!
+Seriously, reprex will make all of your R-question-asking endeavors easier (which is a pretty insane ROI for the five to ten minutes it'll take you to learn what it's all about).
+For additional reprex pointers, check out the [Get help!](https://www.tidyverse.org/help/) section of the tidyverse site.
+
+## Where to ask?
+
+Armed with your reprex, the next step is to figure out [where to ask](https://www.tidyverse.org/help/#where-to-ask). See also the [Bioconductor help](http://bioconductor.org/help/) website.
+
+*   If it's a question: start with [community.rstudio.com](https://community.rstudio.com/), and/or StackOverflow. If this a Bioconductor-related question, please ask it at the [Bioconductor Support Website](https://support.bioconductor.org/) using the [appropriate package tag](https://support.bioconductor.org/t/DeDHeD) (the website will send an automatic email to the package authors). There are more people there to answer questions.
+
+*   If it's a bug: you're in the right place, [file an issue](https://github.com/LieberInstitute/DeDHed/issues/new).
+
+*   If you're not sure: let the community help you figure it out!
+    If your problem _is_ a bug or a feature request, you can easily return here and report it.
+
+Before opening a new issue, be sure to [search issues and pull requests](https://github.com/LieberInstitute/DeDHed/issues) to make sure the bug hasn't been reported and/or already fixed in the development version.
+By default, the search will be pre-populated with `is:issue is:open`.
+You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/)  (e.g. `is:pr`, `is:closed`) as needed.
+For example, you'd simply remove `is:open` to search _all_ issues in the repo, open or closed.
+
+## What happens next?
+
+To be as efficient as possible, development of tidyverse packages tends to be very bursty, so you shouldn't worry if you don't get an immediate response.
+Typically we don't look at a repo until a sufficient quantity of issues accumulates, then there’s a burst of intense activity as we focus our efforts.
+That makes development more efficient because it avoids expensive context switching between problems, at the cost of taking longer to get back to you.
+This process makes a good reprex particularly important because it might be multiple months between your initial report and when we start working on it.
+If we can’t reproduce the bug, we can’t fix it!