BCB410H: Applied Bioinformatics
Initial submission of R package + Presentation
Anjali Silva, PhD
Fall, 2021
Due: 16 November 2021
Introduction
In this year’s course you will define a useful tool for the analysis of biological data, write an R package to
support it, review and critique other packages, and improve and document your work. As a first step, in
Journal Entry 4 Assessment, you proposed your tool. By now you must have shared a description and
GitHub URL in âA˘IJJournal Entry 4 - R packages" Discussion Board of BCB410. It is your responsibility
to check the Discussion Board to ensure that no other student is developing an R package similar to yours.
For more details, see Journal Entry 4 Assessment.
Now, we are at the second step of developing your package. You will develop your tool as an R package
following principles outlined in ‘R packages’ book: https://r-pkgs.org/index.html. Your package must
be available publicly via GitHub. It must be completed (i.e., it must pass without errors or warnings)
before 11.59 pm (23:59) on 16 November 2021. IMPORTANT: No late submissions are accepted for this
assessment. Also, you must NOT make updates to the GitHub repository until 25 November 2021,
when the review sessions are done. You will be penalized for -10% of total weight for each day of
change. Read ALL instructions carefully. There are 4 pages.
• You must adhere to “Plagiarism" guidelines. This is very important: http://steipe.biochemistry.
utoronto.ca/abc/index.php/ABC-Plagiarism.
• Your package, , must be accessible to your peers and the instructor via following
commands:
> require("devtools")
> devtools::install_github("/", build_vignettes = TRUE)
> library("")
E.g., if the GitHub URL you shared on Discussion Board is https://github.com/anjalisilva/
mixGaussian, anyone should be able to use this information with following commands to download
the package:
> require("devtools")
> devtools::install_github("anjalisilva/mixGaussian", build_vignettes = TRUE)
> library("mixGaussian")
1
BCB410H1F - 2021
1 Package/project requirements
Your project/package must be posted on GitHub. It must result in a new, working project in RStudio
when checked from GitHub. When building the package within the project locally, it must pass build
checks without errors and warnings (or notes). It must be installable from GitHub. There should be NO
Shiny implementation at this point.
• You must have a README.md file with the following elements, in order, and it should be visible
when user visits package GitHub URL. For an example, see https://github.com/anjalisilva/
TestingPackage.
– Description: A paragraph that describes the purpose of the package. Explain how your pack-
age add to or improve a current work flow in bioinformatics or computational biology (i.e., how
is it unique?, what issue does it address?).
Finally, include the R version (not RStudio version) and platform (Mac, Windows, Linux (De-
bian, Fedora/Redhat, Ubuntu)), used to develop the package.
– Installation:
To download the package:
require("devtools")
devtools::install_github("/", build_vignettes = TRUE)
library("")
To run the shinyApp:
Under construction
– Overview:
ls("package:")
data(package = "") # optional
After these commands, provide an overview that briefly describes the main components of the
package. Point the user to vignettes for more details. Include an image illustrating the overview
of the package. For an example, see https://github.com/anjalisilva/TestingPackage. Ad-
ditionally, you may use a package tree structure.
browseVignettes("")
– Contributions:
Provide a note clearly indicating contributions from you and contributions from other pack-
ages/sources for each function. Remember your individual contributions to the package are
important. For an example, see https://github.com/anjalisilva/TestingPackage.
– References:
Provide full references for all sources used in one specific format. For an example, see https:
//github.com/anjalisilva/TestingPackage.
– Acknowledgements: Use the following sentence.
This package was developed as part of an assessment for 2021 BCB410H: Applied Bioinfor-
matics, University of Toronto, Toronto, CANADA.
2/4
BCB410H1F - 2021
• Additionally need:
– Ensure the .Rproj file is available on GitHub. Do NOT add it to .gitignore
– DESCRIPTION
– NAMESPACE
– LICENSE
– Man subdirectory
– R subdirectory
∗ Evidence of some graphical output
∗ Functions should have clear examples with data (own dataset or dataset from another
package)
– vignettes subdirectory
– tests subdirectory
– (data subdirectory with data OR clear examples with data from another package)
• There should be a record of the changes made to the package via Git commit messages. This can be
checked by going to ‘History’ of each file/subdirectory in GitHub. Only you should be listed as a
contributor. If you have multiple GitHub accounts, use only one account for everything.
• Important: In your GitHub account, you must use your full name as provided in the course. This
can be checked/changed by going to Settings→ Public profile→ Name. E.g., Kevin Smith should
not use “Kev S" as the GitHub name. “Kevin Smith" must be used, if that is the name provided in
the course.
2 Code requirements
• Must adhere to R coding style rules for this course. The coding style rules are defined here: http:
//steipe.biochemistry.utoronto.ca/abc/index.php/RPR-Coding_style.
• Code must be covered with unit and integration tests, as appropriate and test must run via the
testthat functions.
3 Presentation requirements
• Prepare a one-minute pitch about your R package tool. Be sure to point out its objective, audience of
the package, how it is unique, etc. You will be timed and a hard cutoff of 60 seconds applies. Upload
a clear audio file with minimal background noise to https://mymedia.library.utoronto.ca/ using
LASTNAME_FirstInitial_P1.mp3 (.mp3 or any acceptable format).
• Share the following on ‘Initial Submission of R Package: Presentation About R package’ Discus-
sion Board: GitHub URL and mymedia URL. One user must only have ONE Discussion Board entry.
Use the format shown in the example below.
E.g., GitHub: https://github.com/anjalisilva/mixGaussian.
MymediaURL: https://play.library.utoronto.ca/4165ce83cdabcff535128d81d568db6.
You must share this information on Discussion Board, otherwise, you will receive a mark of zero for
this assessment. Note, these presentations will be available for the entire class to listen. You must use
the same information from Journal Entry 4. Ensure both URLs are working. A zero will be assigned if the
instructor/peers cannot reach your GitHub repository or presentation using the URLs provided.
3/4
BCB410H1F - 2021
4 Grading Scheme
Refer to syllabus for weight.
5 Alumni Examples
Examples from BCB410 Alumni are listed under ‘Student Packages’ at https://github.com/anjalisilva/
TestingPackage. Note, these are final packages submitted by previous BCB410 students and may
have extra/less features that are not required from your submission. For your requirements, read
ALL above instructions carefully. There should be NO Shiny implementation at this point.
4/4




















, must be accessible to your peers and the instructor via following
commands:
> require("devtools")
> devtools::install_github("/", build_vignettes = TRUE)
> library("")
E.g., if the GitHub URL you shared on Discussion Board is https://github.com/anjalisilva/
mixGaussian, anyone should be able to use this information with following commands to download
the package:
> require("devtools")
> devtools::install_github("anjalisilva/mixGaussian", build_vignettes = TRUE)
> library("mixGaussian")
1
BCB410H1F - 2021
1 Package/project requirements
Your project/package must be posted on GitHub. It must result in a new, working project in RStudio
when checked from GitHub. When building the package within the project locally, it must pass build
checks without errors and warnings (or notes). It must be installable from GitHub. There should be NO
Shiny implementation at this point.
• You must have a README.md file with the following elements, in order, and it should be visible
when user visits package GitHub URL. For an example, see https://github.com/anjalisilva/
TestingPackage.
– Description: A paragraph that describes the purpose of the package. Explain how your pack-
age add to or improve a current work flow in bioinformatics or computational biology (i.e., how
is it unique?, what issue does it address?).
Finally, include the R version (not RStudio version) and platform (Mac, Windows, Linux (De-
bian, Fedora/Redhat, Ubuntu)), used to develop the package.
– Installation:
To download the package:
require("devtools")
devtools::install_github("/", build_vignettes = TRUE)
library("")
To run the shinyApp:
Under construction
– Overview:
ls("package:")
data(package = "") # optional
After these commands, provide an overview that briefly describes the main components of the
package. Point the user to vignettes for more details. Include an image illustrating the overview
of the package. For an example, see https://github.com/anjalisilva/TestingPackage. Ad-
ditionally, you may use a package tree structure.
browseVignettes("")
– Contributions:
Provide a note clearly indicating contributions from you and contributions from other pack-
ages/sources for each function. Remember your individual contributions to the package are
important. For an example, see https://github.com/anjalisilva/TestingPackage.
– References:
Provide full references for all sources used in one specific format. For an example, see https:
//github.com/anjalisilva/TestingPackage.
– Acknowledgements: Use the following sentence.
This package was developed as part of an assessment for 2021 BCB410H: Applied Bioinfor-
matics, University of Toronto, Toronto, CANADA.
2/4
BCB410H1F - 2021
• Additionally need:
– Ensure the .Rproj file is available on GitHub. Do NOT add it to .gitignore
– DESCRIPTION
– NAMESPACE
– LICENSE
– Man subdirectory
– R subdirectory
∗ Evidence of some graphical output
∗ Functions should have clear examples with data (own dataset or dataset from another
package)
– vignettes subdirectory
– tests subdirectory
– (data subdirectory with data OR clear examples with data from another package)
• There should be a record of the changes made to the package via Git commit messages. This can be
checked by going to ‘History’ of each file/subdirectory in GitHub. Only you should be listed as a
contributor. If you have multiple GitHub accounts, use only one account for everything.
• Important: In your GitHub account, you must use your full name as provided in the course. This
can be checked/changed by going to Settings→ Public profile→ Name. E.g., Kevin Smith should
not use “Kev S" as the GitHub name. “Kevin Smith" must be used, if that is the name provided in
the course.
2 Code requirements
• Must adhere to R coding style rules for this course. The coding style rules are defined here: http:
//steipe.biochemistry.utoronto.ca/abc/index.php/RPR-Coding_style.
• Code must be covered with unit and integration tests, as appropriate and test must run via the
testthat functions.
3 Presentation requirements
• Prepare a one-minute pitch about your R package tool. Be sure to point out its objective, audience of
the package, how it is unique, etc. You will be timed and a hard cutoff of 60 seconds applies. Upload
a clear audio file with minimal background noise to https://mymedia.library.utoronto.ca/ using
LASTNAME_FirstInitial_P1.mp3 (.mp3 or any acceptable format).
• Share the following on ‘Initial Submission of R Package: Presentation About R package’ Discus-
sion Board: GitHub URL and mymedia URL. One user must only have ONE Discussion Board entry.
Use the format shown in the example below.
E.g., GitHub: https://github.com/anjalisilva/mixGaussian.
MymediaURL: https://play.library.utoronto.ca/4165ce83cdabcff535128d81d568db6.
You must share this information on Discussion Board, otherwise, you will receive a mark of zero for
this assessment. Note, these presentations will be available for the entire class to listen. You must use
the same information from Journal Entry 4. Ensure both URLs are working. A zero will be assigned if the
instructor/peers cannot reach your GitHub repository or presentation using the URLs provided.
3/4
BCB410H1F - 2021
4 Grading Scheme
Refer to syllabus for weight.
5 Alumni Examples
Examples from BCB410 Alumni are listed under ‘Student Packages’ at https://github.com/anjalisilva/
TestingPackage. Note, these are final packages submitted by previous BCB410 students and may
have extra/less features that are not required from your submission. For your requirements, read
ALL above instructions carefully. There should be NO Shiny implementation at this point.
4/4

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