Create a simple package with an R Markdown vignette

[jwokaty]

Welcome Outreachy applicants!

Note: Multiple Outreachy applicants can work on this issue.

Please choose this as your first contribution task to Bioconductor as it will familiarize you with R, R Markdown, RStudio, git, documentation, and GitHub processes we use on this project.

If you're not familiar with R and R Markdown, please learn a little about them. The following links should be sufficient to get you started:

• R Primer - Programming basics
• R Markdown

Prep Work

• Install R.
• Install RStudio
• In RStudio or through the terminal, install devtools and BiocManager:

  install.packages(c("devtools", "BiocManager"))
  # Use Bioconductor devel with BiocManager; we always Bioconductor devel with this project
  BiocManager::install(version = "devel")

Contribution Task

Create a simple package that includes a function and a vignette, the long-form documentation that explains how to use the package.

1. Clone the packageTemplate repository at https://github.com/jwokaty/packageTemplate but rename it.
2. Write a simple function that imports data from BugSigDB using bugsigdbr, takes some inputs, to filter the data in some way and return a filtered data frame. Note: This is intentionally pretty vague to give you room to explore the bioinformatics aspect of this project.
3. Create a vignette in R Markdown that explains how to use your package and includes examples using your function. Verify that you can knit your vignette with 'knitr' into HTML.
4. Update your DESCRIPTION file such that it reflects that you made it, the correct package name, its description, and add bugsigdbr as a dependency.
5. Update the README.
6. Push your changes to GitHub.
7. Make a comment in this issue with a link to your repository.

If you have any general questions about this contribution task, you're welcome to ask here so that we can learn from each other.

Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2022-internship-round/communities/bioconductor/convert-sweave-vignettes-to-r-markdown/contributions/.

[hsadia538]

Hi @jwokaty, Thank you for the detailed description. I am an outrechy applicant and aim to record this as my first contribution. I am already done with the setup. I will reach out with more questions if any. Thanks a lot.

[phayena]

Hi @jwokaty thanks for the breakdown setup my packages will let you know if I have any questions

[Torimela]

Thank you for this information, I look forward to making my contribution to this project.. I will come for answers to my questions when I am stuck.

[BeatriceTA]

Hello, @jwokaty Thank you for sharing all the necessary details regarding this project. I look forward to making a contribution and also to contacting you if and when the need arises.

[Tofiyinkay]

Hello, @jwokaty Thank you for sharing the steps to go about this project. Hope to make a contribution soon.

[hsadia538]

Hi @jwokaty, I have pushed the task to my repository that I clone from the package template. Adding the link here, please take a look. Thanks

Link to repo

[Torimela]

I figured out how to download it already, thank you, I wil have to put down the post now.

[baimamboukar]

Special thanks for adding details and guide 🎉 @jwokaty

[jwokaty]

Note: I've updated the instructions for installing R above. If you already installed the devel version and everything worked, that's fine. If you're having issues, install the release version, which are at the top of the page at https://cran.r-project.org/.

I will be reviewing contributions in the order I receive them. Thanks again for your enthusiasm!

[baimamboukar]

Hello @jwokaty !

I have completed the first task 🎉🎉🎉

• installed R devel for linux and Rstudio
• cloned and renamed the package template repository
• installed BiocManager and bugsigdbr library
• create R markdown vignette
• updated description and REAME

Here is The link to my repository 🚀

[Damian-chibuike]

Thank you for the detailed explanation @jwokaty I'm still on the contribution. I'll post updates from time to time

[phyleria]

Hello @jwokaty Here's the link to the repo aiming to solve the first issue. Thank you!

[Damian-chibuike]

Hello, good day @jwokaty

I have completed my first task.

• I installed R and R studio for windows
• I installed BiocManager and Bugsigdbr packages
• I cloned the packageTemplate repository and renamed it as Outreachy-first-task
• I wrote a simple function that imports data from BugSigDB using bugsigdbr, filtered the data and returned the filtered data frame
• I created a vignette in R Markdown that explains how to use Top_ten package, included examples and knitted it into Html
• I updated the Description and Readme files and added dependency.
• I pushed the changes to my GitHub repo

Here is the link to my repository

[jwokaty]

I wanted to add another tip since you're likely not familiar with what a Bioconductor package looks like. bugsigdbr is a Bioconductor package, so you can see what its structure looks like, in particular the functions and documentation.

I will be reviewing contributions from today, so that I can give feedback next week. Thanks for your patience.

[jwokaty]

Could I ask everyone to allow 'issues' on their repositories so that I can provide individual feedback? You can do this by going to the Settings in your repository scrolling down to Features and checking Issues. @hsadia538 @baimamboukar @phyleria @Damian-chibuike

[baimamboukar]

Could I ask everyone to allow 'issues' on their repositories so that I can provide individual feedback? You can do this by going to the Settings in your repository scrolling down to Features and checking Issues. @hsadia538 @baimamboukar @phyleria @Damian-chibuike

Alright @jwokaty sir! I'm doing it now 🦸

[hsadia538]

Could I ask everyone to allow 'issues' on their repositories so that I can provide individual feedback? You can do this by going to the Settings in your repository scrolling down to Features and checking Issues. @hsadia538 @baimamboukar @phyleria @Damian-chibuike

Done @jwokaty . Also can you assign me the Biostrings/vignettes/matchprobes.Rnw on the board and add my PR for Biobase/vignettes/BiobaseDevelopment.Rnw on the board?

[jwokaty]

@hsadia538 Thank you. I've assigned you matchprobes and added your PR to the board.

[baimamboukar]

Could I ask everyone to allow 'issues' on their repositories so that I can provide individual feedback? You can do this by going to the Settings in your repository scrolling down to Features and checking Issues. @hsadia538 @baimamboukar @phyleria @Damian-chibuike

Done @jwokaty !

[phyleria]

Could I ask everyone to allow 'issues' on their repositories so that I can provide individual feedback? You can do this by going to the Settings in your repository scrolling down to Features and checking Issues. @hsadia538 @baimamboukar @phyleria @Damian-chibuike

Done @jwokaty !

[Chisomgold]

Hi @jwokaty

I have completed the first task and pushed it to my repo. Here's the link to repo

Looking forward to your feedabck

[calvnce]

Hello @jwokaty Kindly do checkout this completed task Link to repo

[jwokaty]

@calvnce Can you allow 'issues' on your repository so that I can provide individual feedback? You can do this by going to the Settings in your repository scrolling down to Features and checking Issues.

[BerylKanali]

Hi @jwokaty Here is my repo for the first task. Can you also assign me GenomeInfoDb/vignettes/Accept-organism-for-GenomeInfoDb.Rnwon the board.

[hsadia538]

Hi @jwokaty Here is my repo for the first task. Can you also assign me GenomeInfoDb/vignettes/Accept-organism-for-GenomeInfoDb.Rnwon the board.

Hi, I am already working on the vignette. I've commented for claiming it on second contribution issue @jwokaty can you please update the board. Thanks

[BerylKanali]

Hi @jwokaty Here is my repo for the first task. Can you also assign me GenomeInfoDb/vignettes/Accept-organism-for-GenomeInfoDb.Rnwon the board.

Hi, I am already working on the vignette. I've commented for claiming it on second contribution issue @jwokaty can you please update the board. Thanks

No worries. @jwokaty can you assign me S4Vectors/vignettes/RleTricks.Rnw instead?

[jwokaty]

@BerylKanali Sure. In the future, please request these on #32, which is where we look for messages requesting work on a particular vignette.

[jwokaty]

Hi everyone! I just wanted to say thanks for your hard work and remind you to please record your contributions at https://www.outreachy.org/outreachy-december-2022-internship-round/communities/bioconductor/convert-sweave-vignettes-to-r-markdown/contributions/.

[lumenCodes]

After much difficulty, I created a package for this first task.

@jwokaty please look at it. I am sure there will be a lot of room for improvement.

The link to the repo and I have enabled issues so that you can make corrections.