Last updated: 2026-02-11
Checks: 7 0
Knit directory: Digital Research Skills Network -
DigitalResearchSkillsNetwork/
This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(1337) was run prior to running the
code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 38b66d0. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .RData
Ignored: .Rhistory
Ignored: analysis/.RData
Ignored: analysis/.Rhistory
Ignored: plots/
Ignored: raw/
Ignored: todo.R
Untracked files:
Untracked: .849C9593-D756-4E56-8D6E-42412F2A707B
Untracked: analysis/0_schedule copy.Rmd
Untracked: analysis/adit/template.Rmd
Untracked: analysis/archive/x202504.Rmd
Untracked: analysis/archive/x202504_InFocus.Rmd
Untracked: analysis/archive/x202504_Seminar.Rmd
Untracked: analysis/archive/x202504_Workshop.Rmd
Untracked: analysis/archive/x202505.Rmd
Untracked: analysis/archive/x202505_InFocus.Rmd
Untracked: analysis/archive/x202505_Seminar.Rmd
Untracked: analysis/archive/x202505_Workshop (2).Rmd
Untracked: analysis/archive/x202505_Workshop.Rmd
Untracked: analysis/archive/x202506.Rmd
Untracked: analysis/archive/x202506_stats.Rmd
Untracked: analysis/archive/x202506_tidyverse.Rmd
Untracked: analysis/archive/x202507.Rmd
Untracked: analysis/archive/x202508.Rmd
Unstaged changes:
Modified: analysis/0_resources.Rmd
Deleted: analysis/202504.Rmd
Deleted: analysis/202505.Rmd
Deleted: analysis/202505_Workshop.Rmd
Deleted: analysis/202506.Rmd
Deleted: analysis/202506_stats.Rmd
Deleted: analysis/202506_tidyverse.Rmd
Deleted: analysis/202507.Rmd
Deleted: analysis/202508.Rmd
Modified: analysis/202509.Rmd
Modified: analysis/202510.Rmd
Modified: analysis/202511.Rmd
Modified: analysis/_site.yml
Deleted: analysis/adit/custom.css
Deleted: analysis/flowcytometry/0_test.Rmd
Deleted: analysis/x202504_InFocus.Rmd
Deleted: analysis/x202504_Seminar.Rmd
Deleted: analysis/x202504_Workshop.Rmd
Deleted: analysis/x202505_InFocus.Rmd
Deleted: analysis/x202505_Seminar.Rmd
Deleted: analysis/x202505_Workshop.Rmd
Modified: workflow.R
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown (analysis/0_schedule.Rmd) and HTML
(docs/0_schedule.html) files. If you’ve configured a remote
Git repository (see ?wflow_git_remote), click on the
hyperlinks in the table below to view the files as they were in that
past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 38b66d0 | YuchenLi | 2026-02-11 | wflow_publish(c("analysis/0_schedule.Rmd", "analysis/index.Rmd")) |
| html | 85bd64d | DrThomasOneil | 2026-02-02 | Build site. |
| html | 66d99ab | DrThomasOneil | 2025-12-03 | Build site. |
| Rmd | 9b96327 | DrThomasOneil | 2025-12-03 | wflow_publish(c("analysis/0_schedule.Rmd", "analysis/index.Rmd")) |
| html | 19fca60 | DrThomasOneil | 2025-11-12 | Build site. |
| html | 12264e4 | DrThomasOneil | 2025-11-12 | Build site. |
| Rmd | 42546e8 | DrThomasOneil | 2025-11-12 | wflow_publish(c("analysis/0_schedule.Rmd", "analysis/202511.Rmd", |
| html | 2047fe7 | DrThomasOneil | 2025-11-03 | Build site. |
| Rmd | 0c45a2e | DrThomasOneil | 2025-11-03 | wflow_publish(c("analysis/0_schedule.Rmd")) |
| html | 8ea7ae2 | DrThomasOneil | 2025-09-29 | Build site. |
| html | e870dd9 | DrThomasOneil | 2025-09-29 | Build site. |
| html | 9826ba5 | DrThomasOneil | 2025-09-10 | Build site. |
| Rmd | d773fea | DrThomasOneil | 2025-09-10 | wflow_publish("analysis/0_schedule.Rmd") |
| html | f8b8ad5 | DrThomasOneil | 2025-09-10 | Build site. |
| Rmd | e850d21 | DrThomasOneil | 2025-09-10 | wflow_publish(c("analysis/index.Rmd", "analysis/0_schedule.Rmd", |
| html | 377b249 | DrThomasOneil | 2025-09-05 | Build site. |
| html | 6f8a683 | DrThomasOneil | 2025-09-04 | Build site. |
| Rmd | c73a3b6 | DrThomasOneil | 2025-09-04 | wflow_publish(files) |
| html | 55aa009 | DrThomasOneil | 2025-08-13 | Build site. |
| Rmd | 25745f1 | DrThomasOneil | 2025-08-13 | wflow_publish("analysis/0_schedule.Rmd") |
| html | 0dd27e2 | DrThomasOneil | 2025-08-13 | Build site. |
| Rmd | cee8dd2 | DrThomasOneil | 2025-08-13 | wflow_publish(files) |
| html | 05dd2b2 | DrThomasOneil | 2025-08-12 | Build site. |
| Rmd | f7d60d2 | DrThomasOneil | 2025-08-12 | wflow_publish(files) |
| html | eccc357 | DrThomasOneil | 2025-07-31 | Build site. |
| Rmd | 35c6977 | DrThomasOneil | 2025-07-31 | wflow_publish("analysis/0_schedule.Rmd") |
| html | 5336148 | DrThomasOneil | 2025-06-30 | Build site. |
| Rmd | f271226 | DrThomasOneil | 2025-06-30 | wflow_publish(files) |
| html | 80762c1 | DrThomasOneil | 2025-05-23 | Build site. |
| html | e794405 | DrThomasOneil | 2025-05-15 | Build site. |
| html | fb553e5 | DrThomasOneil | 2025-05-14 | Build site. |
| html | cff7923 | DrThomasOneil | 2025-05-07 | Build site. |
| Rmd | ff95f8f | DrThomasOneil | 2025-05-07 | wflow_publish(files) |
| html | 16a9613 | DrThomasOneil | 2025-04-30 | Build site. |
| html | 862d6b6 | DrThomasOneil | 2025-04-29 | Build site. |
| Rmd | b68287f | DrThomasOneil | 2025-04-29 | wflow_publish(files) |
| html | 938818e | DrThomasOneil | 2025-04-14 | Build site. |
| html | ed690e6 | DrThomasOneil | 2025-04-14 | Build site. |
| html | cb886ef | DrThomasOneil | 2025-04-10 | Build site. |
| html | f6c0433 | YuchenLi | 2025-04-09 | Build site. |
| html | 8d78b0f | YuchenLi | 2025-04-09 | Build site. |
| html | 7421f69 | DrThomasOneil | 2025-04-08 | Build site. |
| Rmd | 155c73a | DrThomasOneil | 2025-04-08 | wflow_publish("analysis/*.Rmd") |
Upcoming Events
Using Qupath: A multiplex imaging toolkit workshop
Using Qupath: A multiplex imaging toolkit workshop
By Elizabeth Dunn
Time: 1-3p., Wednesday, 25th of February.
Location: WIMR L2 seminar room
QuPath is a user-friendly companion to ImageJ, with greater flexibility for high-parameter and complex imaging workflows. In this hands-on workshop, Elizabeth will walk you through the QuPath interface, introduce a cell-segmentation plugin, and demonstrate spot counting for applications such as RNAscope.
By the end of the session, you’ll be able to:
Import and organise images
Perform cell segmentation
Run spot counting
Export results to CSV for downstream analysis in R or GraphPad Prism
Vote on upcoming content
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8
[2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
time zone: Australia/Sydney
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reactable_0.4.4 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] jsonlite_2.0.0 compiler_4.4.1 promises_1.3.2 Rcpp_1.0.14
[5] stringr_1.5.2 git2r_0.35.0 callr_3.7.6 later_1.4.1
[9] jquerylib_0.1.4 yaml_2.3.10 fastmap_1.2.0 R6_2.6.1
[13] knitr_1.49 htmlwidgets_1.6.4 tibble_3.2.1 rprojroot_2.0.4
[17] bslib_0.9.0 pillar_1.11.1 rlang_1.1.5 cachem_1.1.0
[21] stringi_1.8.7 reactR_0.6.1 httpuv_1.6.15 xfun_0.50
[25] getPass_0.2-4 fs_1.6.5 sass_0.4.9 cli_3.6.3
[29] magrittr_2.0.3 crosstalk_1.2.1 ps_1.8.1 digest_0.6.37
[33] processx_3.8.5 rstudioapi_0.17.1 lifecycle_1.0.4 vctrs_0.6.5
[37] evaluate_1.0.3 glue_1.8.0 whisker_0.4.1 rmarkdown_2.29
[41] httr_1.4.7 tools_4.4.1 pkgconfig_2.0.3 htmltools_0.5.8.1
