Last updated: 2026-04-01

Checks: 7 0

Knit directory: paediatric-cf-inflammation-citeseq/

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.

R Markdown file: up-to-date

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.

Environment: empty

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.

Seed: set.seed(20240216)

The command set.seed(20240216) 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.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: ff8cd64

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 ff8cd64. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/obsolete/
    Ignored:    code/obsolete/
    Ignored:    data/.DS_Store
    Ignored:    data/C133_Neeland_batch0/
    Ignored:    data/C133_Neeland_batch1/
    Ignored:    data/C133_Neeland_batch2/
    Ignored:    data/C133_Neeland_batch3/
    Ignored:    data/C133_Neeland_batch4/
    Ignored:    data/C133_Neeland_batch5/
    Ignored:    data/C133_Neeland_batch6/
    Ignored:    data/C133_Neeland_merged/
    Ignored:    data/Neeland_processed_data_1.h5ad
    Ignored:    data/Neeland_processed_data_2.h5ad
    Ignored:    data/Neeland_processed_data_3.h5ad
    Ignored:    data/intermediate_objects/.DS_Store
    Ignored:    data/updated_h5ad_files/
    Ignored:    output/.DS_Store
    Ignored:    renv/library/
    Ignored:    renv/staging/

Untracked files:
    Untracked:  analysis/cellxgene_submission.Rmd
    Untracked:  data/GOBP_CYTOKINE_MEDIATED_SIGNALING_PATHWAY.v2025.1.Hs.tsv
    Untracked:  data/cellxgene_cell_ontologies_ann_level_3.xlsx
    Untracked:  data/gencode.v44.primary_assembly.annotation.gtf

Unstaged changes:
    Modified:   .DS_Store
    Modified:   .gitignore
    Modified:   analysis/13.0_DGE_analysis_macrophages.Rmd
    Modified:   analysis/13.1_DGE_analysis_macro-alveolar.Rmd
    Modified:   analysis/13.2_DGE_analysis_macro-APOC2+.Rmd
    Modified:   analysis/13.3_DGE_analysis_macro-CCL.Rmd
    Modified:   analysis/13.4_DGE_analysis_macro-IFI27.Rmd
    Modified:   analysis/13.5_DGE_analysis_macro-lipid.Rmd
    Modified:   analysis/13.6_DGE_analysis_macro-monocyte-derived.Rmd
    Modified:   analysis/13.7_DGE_analysis_macro-proliferating.Rmd
    Modified:   analysis/14.0_DGE_analysis_CD4-T-cells.Rmd
    Modified:   analysis/14.1_DGE_analysis_CD8-T-cells.Rmd
    Modified:   analysis/14.2_DGE_analysis_DC-cells.Rmd
    Modified:   analysis/15.0_proportions_analysis_ann_level_1.Rmd
    Modified:   analysis/15.1_proportions_analysis_ann_level_3_non-macrophages.Rmd
    Modified:   analysis/15.2_proportions_analysis_ann_level_3_macrophages.Rmd
    Modified:   analysis/16.0_Figure_1.Rmd
    Modified:   analysis/16.1_Figure_2.Rmd
    Modified:   analysis/16.2_Figure_3.Rmd
    Modified:   analysis/16.3_Figure_4.Rmd
    Modified:   analysis/16.4_Figure_5.Rmd
    Modified:   analysis/16.5_Figure_6.Rmd
    Modified:   analysis/getting_started.Rmd
    Deleted:    output/Figure1A.jpeg
    Modified:   output/Figure1A.png
    Modified:   output/dge_analysis/macrophages/CAM.FIBROSIS.CF.IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.FIBROSIS.CF.IVAvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.FIBROSIS.CF.LUMA_IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.FIBROSIS.CF.NO_MOD.SvCF.NO_MOD.M.csv
    Modified:   output/dge_analysis/macrophages/CAM.FIBROSIS.CF.NO_MODvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.GO.CF.IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.GO.CF.IVAvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.GO.CF.LUMA_IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.GO.CF.NO_MOD.SvCF.NO_MOD.M.csv
    Modified:   output/dge_analysis/macrophages/CAM.GO.CF.NO_MODvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.HALLMARK.CF.IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.HALLMARK.CF.IVAvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.HALLMARK.CF.LUMA_IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.HALLMARK.CF.NO_MOD.SvCF.NO_MOD.M.csv
    Modified:   output/dge_analysis/macrophages/CAM.HALLMARK.CF.NO_MODvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.REACTOME.CF.IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.REACTOME.CF.IVAvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.REACTOME.CF.LUMA_IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.REACTOME.CF.NO_MOD.SvCF.NO_MOD.M.csv
    Modified:   output/dge_analysis/macrophages/CAM.REACTOME.CF.NO_MODvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.WP.CF.IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.WP.CF.IVAvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CAM.WP.CF.LUMA_IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CAM.WP.CF.NO_MOD.SvCF.NO_MOD.M.csv
    Modified:   output/dge_analysis/macrophages/CAM.WP.CF.NO_MODvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CF.IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CF.IVAvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/CF.LUMA_IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/CF.NO_MOD.SvCF.NO_MOD.M.csv
    Modified:   output/dge_analysis/macrophages/CF.NO_MODvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/ORA.GO.CF.IVAvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/ORA.GO.CF.NO_MOD.SvCF.NO_MOD.M.csv
    Modified:   output/dge_analysis/macrophages/ORA.GO.CF.NO_MODvNON_CF.CTRL.csv
    Modified:   output/dge_analysis/macrophages/ORA.HALLMARK.CF.IVAvCF.NO_MOD.csv
    Modified:   output/dge_analysis/macrophages/ORA.REACTOME.CF.NO_MODvNON_CF.CTRL.csv
    Modified:   output/pdf_figures/Figure_1.pdf
    Modified:   output/pdf_figures/Figure_4.pdf
    Modified:   output/pdf_figures/Figure_5.pdf
    Modified:   output/pdf_figures/Figure_6.pdf

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/index.Rmd) and HTML (docs/index.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	ff8cd64	Jovana Maksimovic	2026-04-01	wflow_publish(c("analysis/16.6_Supplementary_Figure_2.Rmd", "analysis/16.7_Supplementary_Figures.Rmd",
html	d5115ae	Jovana Maksimovic	2026-04-01	Build site.
Rmd	48b6fc4	Jovana Maksimovic	2026-04-01	wflow_publish(c("analysis/14.3_epithelial_cell_analysis.Rmd",
html	bcc86bf	Jovana Maksimovic	2025-02-20	Build site.
Rmd	7654aa3	Jovana Maksimovic	2025-02-20	wflow_publish("analysis/index.Rmd")
html	4da7e60	Jovana Maksimovic	2025-02-17	Build site.
Rmd	8570b01	Jovana Maksimovic	2025-02-17	wflow_publish("analysis/index.Rmd")
html	4c945a5	Jovana Maksimovic	2025-02-17	Build site.
Rmd	06eea5f	Jovana Maksimovic	2025-02-17	wflow_publish("analysis/index.Rmd")
html	46deec5	Jovana Maksimovic	2025-02-17	Build site.
Rmd	fe39889	Jovana Maksimovic	2025-02-17	wflow_publish("analysis/index.Rmd")
html	313a19b	Jovana Maksimovic	2025-02-17	Build site.
Rmd	feb99f9	Jovana Maksimovic	2025-02-17	wflow_publish("analysis/index.Rmd")
html	578fe51	Jovana Maksimovic	2025-02-17	Build site.
Rmd	3349c27	Jovana Maksimovic	2025-02-17	wflow_publish("analysis/index.Rmd")
html	eee49c7	Jovana Maksimovic	2025-02-17	Build site.
Rmd	f658337	Jovana Maksimovic	2025-02-17	wflow_publish("analysis/index.Rmd")
html	38ed75b	Jovana Maksimovic	2025-01-08	Build site.
Rmd	d981df6	Jovana Maksimovic	2025-01-08	wflow_publish("analysis/index.Rmd")
html	8fda8e1	Jovana Maksimovic	2025-01-07	Build site.
Rmd	f997c86	Jovana Maksimovic	2025-01-07	wflow_publish("analysis/index.Rmd")
html	46af878	Jovana Maksimovic	2025-01-06	Build site.
Rmd	e9817e4	Jovana Maksimovic	2025-01-06	wflow_publish("analysis/index.Rmd")
html	ad7e033	Jovana Maksimovic	2024-12-24	Build site.
Rmd	0d7ad6c	Jovana Maksimovic	2024-12-24	wflow_publish("analysis/index.Rmd")
html	e879c15	Jovana Maksimovic	2024-12-05	Build site.
html	8224316	Jovana Maksimovic	2024-12-05	Build site.
Rmd	e41ab7d	Jovana Maksimovic	2024-12-05	wflow_publish("analysis/index.Rmd")
html	e7e3228	Jovana Maksimovic	2024-12-05	Build site.
Rmd	208daae	Jovana Maksimovic	2024-12-05	wflow_publish("analysis/index.Rmd")
html	8f1bb39	Jovana Maksimovic	2024-12-05	Build site.
Rmd	9826fd9	Jovana Maksimovic	2024-12-05	wflow_publish("analysis/index.Rmd")
html	6496315	Jovana Maksimovic	2024-12-05	Build site.
Rmd	2de0391	Jovana Maksimovic	2024-12-05	wflow_publish("analysis/index.Rmd")
html	66a77b8	Jovana Maksimovic	2024-12-05	Build site.
Rmd	b827cd3	Jovana Maksimovic	2024-12-05	wflow_publish("analysis/index.Rmd")
html	58e67bc	Jovana Maksimovic	2024-12-05	Build site.
Rmd	36374d2	Jovana Maksimovic	2024-12-05	wflow_publish("analysis/index.Rmd")
html	c52df9b	Jovana Maksimovic	2024-12-05	Build site.
Rmd	ccdf2fe	Jovana Maksimovic	2024-12-05	wflow_publish("analysis/index.Rmd")
html	551d1cd	Jovana Maksimovic	2024-10-08	Build site.
Rmd	2f6af9a	Jovana Maksimovic	2024-10-08	wflow_publish("analysis/index.Rmd")
html	cc35a23	Jovana Maksimovic	2024-10-07	Build site.
Rmd	5d26d19	Jovana Maksimovic	2024-10-07	wflow_publish("analysis/index.Rmd")
html	08a6cad	Jovana Maksimovic	2024-09-20	Build site.
Rmd	d984571	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	940146e	Jovana Maksimovic	2024-09-20	Build site.
Rmd	a6a40cf	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	a424d2c	Jovana Maksimovic	2024-09-20	Build site.
Rmd	ec7a1e7	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	3ae6d3a	Jovana Maksimovic	2024-09-20	Build site.
Rmd	ef32d0e	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	b4b0451	Jovana Maksimovic	2024-09-20	Build site.
Rmd	96ba6ad	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	cdc811c	Jovana Maksimovic	2024-09-20	Build site.
Rmd	ebde854	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	409ab83	Jovana Maksimovic	2024-09-20	Build site.
Rmd	e8a0431	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	965bc3a	Jovana Maksimovic	2024-09-20	Build site.
Rmd	ad95c63	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	b0e1d6a	Jovana Maksimovic	2024-09-20	Build site.
Rmd	485c7da	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	eb4219f	Jovana Maksimovic	2024-09-20	Build site.
Rmd	073c6c8	Jovana Maksimovic	2024-09-20	wflow_publish("analysis/index.Rmd")
html	d3d3208	Jovana Maksimovic	2024-09-10	Build site.
Rmd	d6becda	Jovana Maksimovic	2024-09-10	wflow_publish("analysis/index.Rmd")
html	a2bdb1a	Jovana Maksimovic	2024-09-09	Build site.
Rmd	1220c10	Jovana Maksimovic	2024-09-09	wflow_publish("analysis/index.Rmd")
html	b8aa02b	Jovana Maksimovic	2024-09-09	Build site.
Rmd	20d5234	Jovana Maksimovic	2024-09-09	wflow_publish("analysis/index.Rmd")
html	9f3cc9c	Jovana Maksimovic	2024-09-05	Build site.
Rmd	89fab0f	Jovana Maksimovic	2024-09-05	wflow_publish("analysis/index.Rmd")
html	e8f4078	Jovana Maksimovic	2024-08-09	Build site.
Rmd	67d23a6	Jovana Maksimovic	2024-08-09	wflow_publish("analysis/index.Rmd")
html	0a984c7	Jovana Maksimovic	2024-08-09	Build site.
Rmd	409ecff	Jovana Maksimovic	2024-08-09	wflow_publish("analysis/index.Rmd")
html	0588973	Jovana Maksimovic	2024-08-06	Build site.
Rmd	4ed52fb	Jovana Maksimovic	2024-08-06	wflow_publish("analysis/index.Rmd")
html	839ebca	Jovana Maksimovic	2024-08-06	Build site.
Rmd	61a99c6	Jovana Maksimovic	2024-08-06	wflow_publish("analysis/index.Rmd")
html	fa2ea71	Jovana Maksimovic	2024-07-05	Build site.
Rmd	ee9d775	Jovana Maksimovic	2024-07-05	wflow_publish(c("analysis/index.Rmd", "analysis/11.0_manual_annotations_t_cells_decontx.Rmd"))
html	0b24220	Jovana Maksimovic	2024-07-05	Build site.
Rmd	256e8cf	Jovana Maksimovic	2024-07-05	wflow_publish(c("analysis/index.Rmd", "analysis/12.0_manual_annotations_other_cells.Rmd"))
html	4d7d217	Jovana Maksimovic	2024-07-04	Build site.
Rmd	13a1d06	Jovana Maksimovic	2024-07-04	wflow_publish(c("analysis/13.0_DGE_analysis_macro-alveolar_cells_CF-only-samples.Rmd",
html	b1c0edc	Jovana Maksimovic	2024-06-28	Build site.
Rmd	14a581d	Jovana Maksimovic	2024-06-28	wflow_publish("analysis/index.Rmd")
html	c51f4fb	Jovana Maksimovic	2024-06-24	Build site.
Rmd	351975f	Jovana Maksimovic	2024-06-24	wflow_publish("analysis/index.Rmd")
html	d1785d7	Jovana Maksimovic	2024-05-20	Build site.
Rmd	d178efc	Jovana Maksimovic	2024-05-20	wflow_publish("analysis/index.Rmd")
html	facb05f	Jovana Maksimovic	2024-04-27	Build site.
Rmd	2c5e5ac	Jovana Maksimovic	2024-04-27	wflow_publish(c("analysis/index.Rmd", "analysis/09.1_integrate_cluster_macro_cells_decontx.Rmd"))
html	048f0f3	Jovana Maksimovic	2024-03-20	Build site.
Rmd	6f4600b	Jovana Maksimovic	2024-03-20	wflow_publish(c("analysis/index.Rmd", "analysis/integrate_cluster"))
html	fb50017	Jovana Maksimovic	2024-03-19	Build site.
Rmd	3e9ce40	Jovana Maksimovic	2024-03-19	wflow_publish(c("analysis/index.Rmd", "analysis/integrate"))
html	7701592	Jovana Maksimovic	2024-02-26	Build site.
Rmd	e6e53e9	Jovana Maksimovic	2024-02-26	wflow_publish(c("analysis/index.Rmd"))
html	ecfde3d	Jovana Maksimovic	2024-02-26	Build site.
Rmd	025ceae	Jovana Maksimovic	2024-02-26	wflow_publish(c("analysis/index.Rmd", "analysis/01*"))
html	e719a2c	Jovana Maksimovic	2024-02-21	Build site.
Rmd	20cce23	Jovana Maksimovic	2024-02-21	wflow_publish("analysis/index.Rmd")
html	7b431a0	Jovana Maksimovic	2024-02-21	Build site.
Rmd	9f3012a	Jovana Maksimovic	2024-02-21	wflow_publish("analysis/index.Rmd")
Rmd	c1716bb	Jovana Maksimovic	2024-02-16	Start workflowr project.

This site presents the code and results of the analyses described in the manuscript: “Single-cell profiling of BAL in preschool cystic fibrosis reveals macrophage dysregulation and ivacaftor-modified inflammatory programs in the early life lung”.

All the code and results of this analysis are available from GitHub at https://github.com/Oshlack/paediatric-cf-inflammation-citeseq. To reproduce the complete analysis follow the instructions on the getting started page.

Abstract

Aberrant inflammation and structural lung damage occurs early in life for people with cystic fibrosis (CF). Even in the era of CFTR modulators, anti-inflammatory therapy may still be needed to prevent establishment and lifelong consequences of bronchiectasis. In this study, we integrated transcriptome-wide single-cell RNA sequencing data and highly multiplexed surface protein expression to create the largest comprehensive paediatric lower airway atlas of >190,000 cells from 45 bronchoalveolar lavage (BAL) samples resulting in 43 immune and epithelial cell populations, all available for exploration on CELLxGENE. We then investigated inflammatory cell responses in children with CF to show widespread gene expression dysregulation of macrophage populations in the preschool CF lung. This included alterations in pathways associated with TNF and IFN signalling, cholesterol homeostasis, as well as pulmonary fibrosis, that were further altered by the early development of bronchiectasis. We showed that the CFTR modulator ivacaftor restores some of these macrophage-related functional deficits and reduces expression of pathways associated with neutrophil infiltration, however the modulator lumacaftor/ivacaftor did not result in any detectable changes in transcriptional response. This work represents a comprehensive, multi-omic single-cell analysis of BAL from preschool children and the results may inform the future development of anti-inflammatory therapy for children with CF.

Authors

Jovana Maksimovic^1,2,9*, Shivanthan Shanthikumar ^2,3,4*, George Howitt^1,9, Gunjan Dixit^1,9, Peter F Hickey^5,6, William Ho⁵, Casey J.A. Anttila⁵, Daniel V. Brown⁵, Anne Senabouth^7,8, Dominik Kaczorowski^7,8, Daniela Amann-Zalcenstein^5,6, Joseph E. Powell^7,8, Sarath C. Ranganathan^2,3,4, Alicia Oshlack^1,9, Melanie R. Neeland^2,3#.

¹ Computational Biology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia

² Respiratory Diseases, Murdoch Children’s Research Institute, Parkville, VIC, Australia

³ Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia

⁴ Respiratory and Sleep Medicine, Royal Children’s Hospital, Parkville, VIC, Australia

⁵ Advanced Genomics Facility, Advanced Technology and Biology Division, WEHI, Parkville, VIC, Australia

⁶ Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia

⁷ Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia

⁸ UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia

⁹ Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia

^*Contributed equally

Analysis Overview

Follow the links below to view the different parts of the analysis.

Quality Control and Filtering

Remove empty droplets and demultiplex
1. Batch 0
2. Batch 1
3. Batch 2
4. Batch 3
5. Batch 4
6. Batch 5
7. Batch 6

Cell Clustering and Annotation

Annotate using Human Lung Cell Atlas v2.0
1. Without ambient removal
2. With ambient removal

Differential Expression Analysis between Conditions

Differential expression analysis of macrophages

Differential expression analysis of T/NK and rare cells

Analyse cell types proportions

Manuscript Figures

Manuscript figures

Licenses

The code in this analysis is covered by the MIT license and the written content on this website is covered by a Creative Commons CC-BY license.

Version Information

R version: R version 4.3.3 (2024-02-29)

Bioconductor version: 3.18

sessionInfo()

R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Australia/Melbourne
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.8      compiler_4.3.3      BiocManager_1.30.22
 [4] renv_1.1.4          promises_1.2.1      Rcpp_1.0.12        
 [7] stringr_1.5.1       git2r_0.33.0        callr_3.7.3        
[10] later_1.3.2         jquerylib_0.1.4     yaml_2.3.8         
[13] fastmap_1.1.1       R6_2.5.1            knitr_1.50         
[16] tibble_3.2.1        rprojroot_2.0.4     bslib_0.6.1        
[19] pillar_1.9.0        rlang_1.1.6         utf8_1.2.4         
[22] cachem_1.0.8        stringi_1.8.3       httpuv_1.6.14      
[25] xfun_0.52           getPass_0.2-4       fs_1.6.6           
[28] sass_0.4.10         cli_3.6.5           magrittr_2.0.3     
[31] ps_1.7.6            digest_0.6.34       processx_3.8.3     
[34] rstudioapi_0.15.0   lifecycle_1.0.4     vctrs_0.6.5        
[37] evaluate_0.23       glue_1.8.0          whisker_0.4.1      
[40] fansi_1.0.6         rmarkdown_2.29      httr_1.4.7         
[43] tools_4.3.3         pkgconfig_2.0.3     htmltools_0.5.8.1