Wrapping up

We hope you now have more familiarity with key concepts, tools, and techniques that will enable more efficient, reproducible, and impactful computational research.

Session Info

################################################################################
# Session info (for reproducibility / future reference)
session_info::session_info()

─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.3 (2025-02-28)
 os       Ubuntu 20.04.6 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  C.UTF-8
 ctype    C.UTF-8
 tz       UTC
 date     2026-02-04
 rstudio  2025.05.1+513.pro3 Mariposa Orchid (server)
 pandoc   NA
 quarto   1.8.27 @ /usr/bin/quarto

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package      * version date (UTC) lib source
 cli            3.6.4   2025-02-13 [1] RSPM (R 4.4.0)
 colorspace     2.1-1   2024-07-26 [1] RSPM (R 4.4.0)
 dplyr        * 1.1.4   2023-11-17 [1] RSPM (R 4.4.0)
 forcats      * 1.0.0   2023-01-29 [1] RSPM (R 4.4.0)
 generics       0.1.3   2022-07-05 [1] RSPM (R 4.4.0)
 ggplot2      * 3.5.1   2024-04-23 [1] RSPM (R 4.4.0)
 ggrepel      * 0.9.6   2024-09-07 [1] RSPM (R 4.4.3)
 glue           1.8.0   2024-09-30 [1] RSPM (R 4.4.0)
 gtable         0.3.6   2024-10-25 [1] RSPM (R 4.4.0)
 hms            1.1.3   2023-03-21 [1] RSPM (R 4.4.0)
 lifecycle      1.0.4   2023-11-07 [1] RSPM (R 4.4.0)
 lubridate    * 1.9.4   2024-12-08 [1] RSPM (R 4.4.0)
 magrittr       2.0.3   2022-03-30 [1] RSPM (R 4.4.0)
 munsell        0.5.1   2024-04-01 [1] RSPM (R 4.4.0)
 pillar         1.10.2  2025-04-05 [1] RSPM (R 4.4.0)
 pkgconfig      2.0.3   2019-09-22 [1] RSPM (R 4.4.0)
 purrr        * 1.0.4   2025-02-05 [1] RSPM (R 4.4.0)
 R6             2.6.1   2025-02-15 [1] RSPM (R 4.4.0)
 RColorBrewer * 1.1-3   2022-04-03 [1] RSPM (R 4.4.0)
 Rcpp           1.1.0   2025-07-02 [1] RSPM (R 4.4.3)
 readr        * 2.1.5   2024-01-10 [1] RSPM (R 4.4.0)
 rlang          1.1.5   2025-01-17 [1] RSPM (R 4.4.0)
 rstudioapi     0.17.1  2024-10-22 [1] RSPM (R 4.4.0)
 scales         1.3.0   2023-11-28 [1] RSPM (R 4.4.0)
 sessioninfo    1.2.3   2025-02-05 [1] RSPM (R 4.4.0)
 stringi        1.8.7   2025-03-27 [1] RSPM (R 4.4.0)
 stringr      * 1.5.1   2023-11-14 [1] RSPM (R 4.4.0)
 tibble       * 3.2.1   2023-03-20 [1] RSPM (R 4.4.0)
 tidyr        * 1.3.1   2024-01-24 [1] RSPM (R 4.4.0)
 tidyselect     1.2.1   2024-03-11 [1] RSPM (R 4.4.0)
 tidyverse    * 2.0.0   2023-02-22 [1] RSPM (R 4.4.0)
 timechange     0.3.0   2024-01-18 [1] RSPM (R 4.4.0)
 tzdb           0.5.0   2025-03-15 [1] RSPM (R 4.4.0)
 vctrs          0.6.5   2023-12-01 [1] RSPM (R 4.4.0)
 withr          3.0.2   2024-10-28 [1] RSPM (R 4.4.0)

 [1] /cloud/lib/x86_64-pc-linux-gnu-library/4.4
 [2] /opt/R/4.4.3/lib/R/library
 * ── Packages attached to the search path.
 
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

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Housekeeping

• We will email you a link to the final session recordings next week.

• This workshop website (aka “show notes”) will be available.

• The UM Bioinformatics Core Workshop Slack channel will be available for 90 days.

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Can I continue to use the RStudio environments we used in the workshop?

• The PositCloud environment used in this workshop does not expire.
• If you have a version of RStuio installed on your laptop/workstation, you can download the workshop files to your own computer by viewing your workspace and clicking ⬇ Export; Posit-cloud will zip up a downloadable file.

Where else could I use RStudio?

• See Advanced setup instructions for details on how to install RStudio and required packages on your own computer.
• PositCloud allows you to run R-Studio over the web for free. Click here to login to PositCloud and launch an R session pre-configured for this workshop. (UM users can login using their umich.edu Google account.)
• UMich users can run RStudio on the UM Great Lakes HPC.

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Where can I learn more about RStudio packages and functions?

• A nifty collection of cheatsheets for R and links to download some our favorites:
  • Base R
    
  • Data transformation with dplyr
  • Data visualization with ggplot2

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Can you recommend other relevant workshops or tutorials?

• The University of Michigan Bioinformatics Core regularly hosts workshops.
• Intro lessons and workshops in Bash / Git / R / Python :
  • Software Carpentry
  • The Carpentries at the University of Michigan host several introductory workshops each year following curricula that are developed collaboratively and using the latest research into best practices for teaching computer science content. All workshops are offered for free to learners.

Can you recommend other relevant workshops or tutorials?

• The University of Michigan Bioinformatics Core regularly hosts workshops.
• Intro lessons and workshops in Bash / Git / R / Python :
  • Software Carpentry
• Some great “practice” datasets
  • tidytuesday : a site for sharing sample datasets
  • Kaggle : a site for learning AI/ML, but you can jump right to the sample datasets 😉

Are there other tools like RStudio that can help me work with R?

• In addition to RStudio, Posit recently developed a new tool called
  Positron. Positron has many of the same features as RStudio but with better support for Python. Like Rstudio, Positron is free.

How can I learn more about computational research at University of Michigan?

• UM CoderSpaces “office hours” and UM CoderSpaces Slack workspace. (See “Useful Resources” section in CoderSpaces page for instructions on how to join and access the CoderSpaces Slack workspace.)
• Advanced Research Computing
  • Research Computing Package
  • Upcoming UM Advanced Research Computing workshops
  • Videos on getting started with Great Lakes (Requires UM login)

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Thank you

Thanks to/from the workshop team

Chris	Marci	Travis	Clair
Nick	Dana	Raymond

Thank you for participating in our workshop. We welcome your questions and feedback now and in the future.

Bioinformatics Workshop Team

bioinformatics-workshops@umich.edu
UM BRCF Bioinformatics Core

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