first commit

.Rbuildignore

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+^renv$
+^renv\.lock$
+^LICENSE\.md$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^data-raw$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^README\.Rmd$
+^\.github$
+^vignettes/articles$
+^dev$
+^codecov\.yml$
+^R/monocle\.R$
+^R/monocle2\.R$
+^\.here$
+^\.dockerignore$
+^convert_function_to_method\.R$
+^euler$
+^figures$
+^convert_cyclone_pairs_to_symbol\.R$
+^README_cache$
+^README_docs$
+^Dockerfile$
+^cache$
+^rsconnect$
+^doc$
+^Meta$

.github/.gitignore

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+*.html

.github/CODE_OF_CONDUCT.md

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+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

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+# Contributing to chevreul
+
+This outlines how to propose a change to chevreul.
+For a detailed discussion on contributing to this and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
+
+## 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).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### 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("whtns/chevreul", 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 chevreul 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/feature_request_template.md

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+---
+name: Feature Request
+about: Suggest an idea for this package
+title: "[Feature Request] A short description of the feature"
+labels: ''
+assignees: ''
+---
+
+Please ask questions about how to use `chevreul` on the Bioconductor
+Support Site at <https://support.bioconductor.org> using the appropriate tag(s)
+including the one for this package.
+
+**Note**. Update the issue title to summarize the feature request.
+
+## Is the feature request related to a problem?
+
+Please provide a clear and concise description of what the problem
+is. Ex. I'm always frustrated when [...]
+
+## Describe the solution
+
+A clear and concise description of what you want to happen.
+
+## Describe any alternatives considered
+
+A clear and concise description of any alternative solutions or
+features you've considered.
+
+## Additional context
+
+Add any other context about the feature request here. You may include web links
+(e.g., from GitHub) to:
+
+* raw code
+* a commit
+* code inside a commit
+* code from an R package

.github/ISSUE_TEMPLATE/issue_template.md

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+---
+name: Bug Report
+about: Describe the bug in detail
+title: "[BUG] A short description of the bug"
+labels: ''
+assignees: ''
+---
+
+Please ask questions about how to use `chevreul` on the
+[Bioconductor Support Site](https://support.bioconductor.org) using the
+appropriate tag(s) including the one for this package.
+
+**Note**. Update the issue title to concisely describe the bug.
+
+## Describe the bug
+
+Please provide a clear and concise description of what the bug is.
+
+### Provide a minimally reproducible example (reprex)
+
+Provide a clear and concise description of the bug. It can be easily (but not
+necessarily) illustrated with a minimally reproducible example using the
+[`reprex` package](https://reprex.tidyverse.org/articles/learn-reprex.html).
+
+For tips on creating a reprex, see this
+[StackOverflow link](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example).
+
+## Expected behavior
+
+A clear and concise description of what you expected to happen.
+
+## R Session Information
+
+Please report the output of either `sessionInfo()` or
+`sessioninfo::session_info()` here.
+
+<details>
+
+```R
+options(width = 120)
+## insert session info here
+# sessioninfo::session_info() ## provides GitHub, pandoc, and other details
+# sessionInfo() ## base R function in case you don't want to install sessioninfo
+```
+
+</details>
+
+Indicate whether `BiocManager::valid()` returns `TRUE`. 
+
+- [ ] `BiocManager::valid()` is `TRUE`
+
+**Note**. To avoid potential issues with version mixing and reproducibility, do
+not install packages from `GitHub`.
+
+## Additional Context
+
+Provide some additional context for the bug report. You may include web links
+(e.g., from GitHub) to:
+
+* raw code
+* a commit
+* code inside a commit
+* code from an R package
+
+## Is the package installed via bioconda? 
+
+We find that [bioconda](https://bioconda.github.io/) installations can often be
+problematic due to the nature of the setup environment and potential for version
+mixing.
+
+The preferred method for installing Bioconductor software through `BiocManager`
+and we do not support issues related to `bioconda` installations at this time.
+

.github/SUPPORT.md

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+# Getting help with `chevreul`
+
+Thank you for using `chevreul`!
+Before filing an issue, there are few things you should know to make the process
+as smooth as possible for both parties.
+
+## Make a reprex
+
+Start by making a minimally **repr**oducible **ex**ample, also known as a
+'reprex'. You may use the [`reprex`](https://reprex.tidyverse.org/) R package to
+create one, though it is not necessary but it does help. It will make all of
+your R-question-asking endeavors easier. Learning
+[how to use it](https://reprex.tidyverse.org/articles/learn-reprex.html) takes
+about 5 to 10 minutes.
+
+For more tips on how to make a minimally **repr**oducible **ex**ample, see this
+[StackOverflow link](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example).
+
+## Where to post it?
+
+The [Bioconductor help](http://bioconductor.org/help/) web page gives an
+overview of places that may help answer your question.
+
+* Bioconductor software related questions, such as bug reports and feature
+  requests, should be addressed in the appropriate `Bioconductor/chevreul`
+  GitHub repository. Follow our bug report and feature request templates on
+  GitHub. If the package does not have a GitHub repository, see the next bullet
+  point.
+
+* Bioconductor software usage questions should be addressed in the
+  [Bioconductor Support Website](https://support.bioconductor.org/). Make sure
+  to use the
+  [appropriate package tag](https://support.bioconductor.org/tag/chevreul),
+  otherwise the package authors will not get a notification.
+
+* General R questions can be posed at StackOverflow or at the
+  [RStudio Community](https://community.rstudio.com/) website especially if they
+  pertain to the `tidyverse` or the RStudio GUI or related products.
+
+## Issues or Feature Requests
+
+Before opening a new issue or feature request, be sure to
+[search issues and pull requests](https://github.com/whtns/chevreul/issues)
+to ensure that one does not already exist or has been implemented in the
+development version.
+
+**Note**. You can remove the `is:open` search term in the issues page to search
+through open and closed issues. See
+[this link to learn more](https://help.github.com/articles/searching-issues-and-pull-requests/)
+about modifying the search.
+
+## What happens next?
+
+Our Bioconductor maintainers are limited in resources but they do strive to be
+as responsive as possible.
+
+Please do not forget to tag the appropriate maintainer in the issue with their
+GitHub username (e.g., @username).
+
+In order to make it easy as possible for Bioconductor core developers to
+remediate the issue. Provide an accurate, brief, and reproducible report
+as outlined in the issue templates.
+
+Thank you for trusting Bioconductor.

.github/workflows/pkgdown.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+inst/doc
+*.rds
+*.svg
+velocity_embedding.png
+velocity_expression.png
+*.Rproj
+dev/
+euler/
+figures/
+convert_function_to_method.R
+Rprof.out
+convert_cyclone_pairs_to_symbol.R
+chevreul_0.5.0.tar.gz
+.Rprofile
+.DS_Store
+.Renviron
+.dockerignore
+.here
+.travis.yml
+Dockerfile
+README_cache
+codecov.yml
+rsconnect
+/doc/
+/Meta/
+docs