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
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# Session info (for reproducibility / future reference)
devtools::session_info()─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.5.0 (2025-04-11)
os Ubuntu 22.04.5 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate C.UTF-8
ctype C.UTF-8
tz America/Detroit
date 2025-06-19
rstudio 2024.12.1+563 Kousa Dogwood (server)
pandoc 3.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/x86_64/ (via rmarkdown)
quarto 1.5.57 @ /usr/lib/rstudio-server/bin/quarto/bin/quarto
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-8 2024-09-12 [2] CRAN (R 4.5.0)
assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.5.0)
bit 4.6.0 2025-03-06 [2] CRAN (R 4.5.0)
bit64 4.6.0-1 2025-01-16 [2] CRAN (R 4.5.0)
bslib 0.9.0 2025-01-30 [2] CRAN (R 4.5.0)
cachem 1.1.0 2024-05-16 [2] CRAN (R 4.5.0)
cli 3.6.5 2025-04-23 [2] CRAN (R 4.5.0)
cluster 2.1.8.1 2025-03-12 [2] CRAN (R 4.5.0)
codetools 0.2-20 2024-03-31 [2] CRAN (R 4.5.0)
cowplot 1.1.3 2024-01-22 [2] CRAN (R 4.5.0)
crayon 1.5.3 2024-06-20 [2] CRAN (R 4.5.0)
data.table 1.17.4 2025-05-26 [2] CRAN (R 4.5.0)
deldir 2.0-4 2024-02-28 [2] CRAN (R 4.5.0)
devtools 2.4.5 2022-10-11 [2] CRAN (R 4.5.0)
digest 0.6.37 2024-08-19 [2] CRAN (R 4.5.0)
dotCall64 1.2 2024-10-04 [2] CRAN (R 4.5.0)
dplyr * 1.1.4 2023-11-17 [2] CRAN (R 4.5.0)
ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.5.0)
evaluate 1.0.3 2025-01-10 [2] CRAN (R 4.5.0)
farver 2.1.2 2024-05-13 [2] CRAN (R 4.5.0)
fastDummies 1.7.5 2025-01-20 [2] CRAN (R 4.5.0)
fastmap 1.2.0 2024-05-15 [2] CRAN (R 4.5.0)
fitdistrplus 1.2-2 2025-01-07 [2] CRAN (R 4.5.0)
forcats * 1.0.0 2023-01-29 [2] CRAN (R 4.5.0)
fs 1.6.6 2025-04-12 [2] CRAN (R 4.5.0)
future * 1.58.0 2025-06-05 [2] CRAN (R 4.5.0)
future.apply 1.20.0 2025-06-06 [2] CRAN (R 4.5.0)
generics 0.1.4 2025-05-09 [2] CRAN (R 4.5.0)
ggplot2 * 3.5.2 2025-04-09 [2] CRAN (R 4.5.0)
ggrepel 0.9.6 2024-09-07 [2] CRAN (R 4.5.0)
ggridges 0.5.6 2024-01-23 [2] CRAN (R 4.5.0)
globals 0.18.0 2025-05-08 [2] CRAN (R 4.5.0)
glue 1.8.0 2024-09-30 [2] CRAN (R 4.5.0)
goftest 1.2-3 2021-10-07 [2] CRAN (R 4.5.0)
gridExtra 2.3 2017-09-09 [2] CRAN (R 4.5.0)
gtable 0.3.6 2024-10-25 [2] CRAN (R 4.5.0)
hms 1.1.3 2023-03-21 [2] CRAN (R 4.5.0)
htmltools 0.5.8.1 2024-04-04 [2] CRAN (R 4.5.0)
htmlwidgets 1.6.4 2023-12-06 [2] CRAN (R 4.5.0)
httpuv 1.6.16 2025-04-16 [2] CRAN (R 4.5.0)
httr 1.4.7 2023-08-15 [2] CRAN (R 4.5.0)
ica 1.0-3 2022-07-08 [2] CRAN (R 4.5.0)
igraph 2.1.4 2025-01-23 [2] CRAN (R 4.5.0)
irlba 2.3.5.1 2022-10-03 [2] CRAN (R 4.5.0)
jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.5.0)
jsonlite 2.0.0 2025-03-27 [2] CRAN (R 4.5.0)
kableExtra * 1.4.0.15 2025-06-12 [3] Github (haozhu233/kableExtra@2f58f89)
KernSmooth 2.23-26 2025-01-01 [2] CRAN (R 4.5.0)
klippy * 0.0.0.9500 2025-06-12 [3] Github (umich-brcf-bioinf/workshop-klippy@a1be090)
knitr * 1.50 2025-03-16 [2] CRAN (R 4.5.0)
labeling 0.4.3 2023-08-29 [2] CRAN (R 4.5.0)
later 1.4.2 2025-04-08 [2] CRAN (R 4.5.0)
lattice 0.22-7 2025-04-02 [2] CRAN (R 4.5.0)
lazyeval 0.2.2 2019-03-15 [2] CRAN (R 4.5.0)
lifecycle 1.0.4 2023-11-07 [2] CRAN (R 4.5.0)
listenv 0.9.1 2024-01-29 [2] CRAN (R 4.5.0)
lmtest 0.9-40 2022-03-21 [2] CRAN (R 4.5.0)
lubridate * 1.9.4 2024-12-08 [2] CRAN (R 4.5.0)
magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.5.0)
MASS 7.3-65 2025-02-28 [2] CRAN (R 4.5.0)
Matrix 1.7-3 2025-03-11 [2] CRAN (R 4.5.0)
matrixStats 1.5.0 2025-01-07 [2] CRAN (R 4.5.0)
memoise 2.0.1 2021-11-26 [2] CRAN (R 4.5.0)
mime 0.13 2025-03-17 [2] CRAN (R 4.5.0)
miniUI 0.1.2 2025-04-17 [2] CRAN (R 4.5.0)
nlme 3.1-168 2025-03-31 [2] CRAN (R 4.5.0)
parallelly 1.45.0 2025-06-02 [2] CRAN (R 4.5.0)
patchwork 1.3.0 2024-09-16 [2] CRAN (R 4.5.0)
pbapply 1.7-2 2023-06-27 [2] CRAN (R 4.5.0)
pillar 1.10.2 2025-04-05 [2] CRAN (R 4.5.0)
pkgbuild 1.4.8 2025-05-26 [2] CRAN (R 4.5.0)
pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.5.0)
pkgload 1.4.0 2024-06-28 [2] CRAN (R 4.5.0)
plotly 4.10.4 2024-01-13 [2] CRAN (R 4.5.0)
plyr 1.8.9 2023-10-02 [2] CRAN (R 4.5.0)
png 0.1-8 2022-11-29 [2] CRAN (R 4.5.0)
polyclip 1.10-7 2024-07-23 [2] CRAN (R 4.5.0)
profvis 0.4.0 2024-09-20 [2] CRAN (R 4.5.0)
progressr 0.15.1 2024-11-22 [2] CRAN (R 4.5.0)
promises 1.3.3 2025-05-29 [2] CRAN (R 4.5.0)
purrr * 1.0.4 2025-02-05 [2] CRAN (R 4.5.0)
R6 2.6.1 2025-02-15 [2] CRAN (R 4.5.0)
ragg 1.4.0 2025-04-10 [2] CRAN (R 4.5.0)
RANN 2.6.2 2024-08-25 [2] CRAN (R 4.5.0)
RColorBrewer 1.1-3 2022-04-03 [2] CRAN (R 4.5.0)
Rcpp 1.0.14 2025-01-12 [2] CRAN (R 4.5.0)
RcppAnnoy 0.0.22 2024-01-23 [2] CRAN (R 4.5.0)
RcppHNSW 0.6.0 2024-02-04 [2] CRAN (R 4.5.0)
readr * 2.1.5 2024-01-10 [2] CRAN (R 4.5.0)
remotes 2.5.0 2024-03-17 [2] CRAN (R 4.5.0)
reshape2 1.4.4 2020-04-09 [2] CRAN (R 4.5.0)
reticulate 1.42.0 2025-03-25 [2] CRAN (R 4.5.0)
rlang 1.1.6 2025-04-11 [2] CRAN (R 4.5.0)
rmarkdown * 2.29 2024-11-04 [2] CRAN (R 4.5.0)
ROCR 1.0-11 2020-05-02 [2] CRAN (R 4.5.0)
RSpectra 0.16-2 2024-07-18 [2] CRAN (R 4.5.0)
rstudioapi 0.17.1 2024-10-22 [2] CRAN (R 4.5.0)
Rtsne 0.17 2023-12-07 [2] CRAN (R 4.5.0)
sass 0.4.10 2025-04-11 [2] CRAN (R 4.5.0)
scales 1.4.0 2025-04-24 [2] CRAN (R 4.5.0)
scattermore 1.2 2023-06-12 [2] CRAN (R 4.5.0)
sctransform 0.4.2 2025-04-30 [2] CRAN (R 4.5.0)
sessioninfo 1.2.3 2025-02-05 [2] CRAN (R 4.5.0)
Seurat * 5.3.0 2025-04-23 [2] CRAN (R 4.5.0)
SeuratObject * 5.1.0 2025-04-22 [2] CRAN (R 4.5.0)
shiny 1.10.0 2024-12-14 [2] CRAN (R 4.5.0)
sp * 2.2-0 2025-02-01 [2] CRAN (R 4.5.0)
spam 2.11-1 2025-01-20 [2] CRAN (R 4.5.0)
spatstat.data 3.1-6 2025-03-17 [2] CRAN (R 4.5.0)
spatstat.explore 3.4-3 2025-05-21 [2] CRAN (R 4.5.0)
spatstat.geom 3.4-1 2025-05-20 [2] CRAN (R 4.5.0)
spatstat.random 3.4-1 2025-05-20 [2] CRAN (R 4.5.0)
spatstat.sparse 3.1-0 2024-06-21 [2] CRAN (R 4.5.0)
spatstat.univar 3.1-3 2025-05-08 [2] CRAN (R 4.5.0)
spatstat.utils 3.1-4 2025-05-15 [2] CRAN (R 4.5.0)
stringi 1.8.7 2025-03-27 [2] CRAN (R 4.5.0)
stringr * 1.5.1 2023-11-14 [2] CRAN (R 4.5.0)
survival 3.8-3 2024-12-17 [2] CRAN (R 4.5.0)
svglite 2.2.1 2025-05-12 [3] CRAN (R 4.5.0)
systemfonts 1.2.3 2025-04-30 [2] CRAN (R 4.5.0)
tensor 1.5 2012-05-05 [2] CRAN (R 4.5.0)
textshaping 1.0.1 2025-05-01 [2] CRAN (R 4.5.0)
tibble * 3.3.0 2025-06-08 [2] CRAN (R 4.5.0)
tidyr * 1.3.1 2024-01-24 [2] CRAN (R 4.5.0)
tidyselect 1.2.1 2024-03-11 [2] CRAN (R 4.5.0)
tidyverse * 2.0.0 2023-02-22 [2] CRAN (R 4.5.0)
timechange 0.3.0 2024-01-18 [2] CRAN (R 4.5.0)
tzdb 0.5.0 2025-03-15 [2] CRAN (R 4.5.0)
urlchecker 1.0.1 2021-11-30 [2] CRAN (R 4.5.0)
usethis 3.1.0 2024-11-26 [2] CRAN (R 4.5.0)
utf8 1.2.6 2025-06-08 [2] CRAN (R 4.5.0)
uwot 0.2.3 2025-02-24 [2] CRAN (R 4.5.0)
vctrs 0.6.5 2023-12-01 [2] CRAN (R 4.5.0)
viridisLite 0.4.2 2023-05-02 [2] CRAN (R 4.5.0)
vroom 1.6.5 2023-12-05 [2] CRAN (R 4.5.0)
withr 3.0.2 2024-10-28 [2] CRAN (R 4.5.0)
xfun 0.52 2025-04-02 [2] CRAN (R 4.5.0)
xml2 1.3.8 2025-03-14 [2] CRAN (R 4.5.0)
xtable 1.8-4 2019-04-21 [2] CRAN (R 4.5.0)
yaml 2.3.10 2024-07-26 [2] CRAN (R 4.5.0)
zoo 1.8-14 2025-04-10 [2] CRAN (R 4.5.0)
[1] /home/workshop/cgates/R/x86_64-pc-linux-gnu-library/4.5
[2] /efs/workshop/R/library
[3] /efs/workshop/R/workshop-dev-libs
[4] /usr/local/lib/R/site-library
[5] /usr/lib/R/site-library
[6] /usr/lib/R/library
* ── Packages attached to the search path.
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────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.
Can I continue to use the RStudio environments we used in the workshop?
The RStudio workshop compute environment will be available through 4/11/2025.
- Please save all your R scripts now so that we can “right-size” the compute environment immediately following today’s workshop session.
You can download files from the workshop environment from your terminal/command line window as below. (You will need to substitute your actual workshop username and type workshop password when prompted.)
mkdir workshop-intro-r-rstudio scp -r YOUR_USERNAME@bfx-workshop01.med.umich.edu:"IRR*" workshop-intro-r-rstudioHow could I install this software on my workstation/laptop?
- See Advanced setup instructions for details on how to install programs on your own computer.
Where can I learn more about RStudio packages and functions?
- A nifty collection of cheatsheets for R and links to download some our favorites:
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.
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)
Thank you
Thanks to/from the workshop team
 |
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 |
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|---|---|---|---|
| Chris | Marci | Travis | Bill |
 |
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|
| Dana | Clair | 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