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.
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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.
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The results in this page were generated with repository version 8a408d9. 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:
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Ignored: .Rproj.user/
Ignored: analysis/.DS_Store
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Untracked files:
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Untracked: data/cellxgene_cell_ontologies_ann_level_3.xlsx
Untracked: data/gencode.v44.primary_assembly.annotation.gtf
Unstaged changes:
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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/getting_started.Rmd) and
HTML (docs/getting_started.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 | 8a408d9 | Jovana Maksimovic | 2026-04-01 | wflow_publish("analysis/getting_started.Rmd") |
| html | eb4eb01 | Jovana Maksimovic | 2025-02-20 | Build site. |
| Rmd | 98fe953 | Jovana Maksimovic | 2025-02-20 | wflow_publish("analysis/getting_started.Rmd") |
This page describes how to download the data and code used in this
analysis, set up the project directory and reproduce the analysis. We
have used the workflowr and renv packages to organise this project and
ensure reproducibility.
All the code and outputs of this analysis are available from GitHub at https://github.com/Oshlack/paediatric-cf-inflammation-citeseq. If you want to replicate the analysis you can either clone the repository or download it as a zipped directory.
Once you have a local copy of the repository you should see the following directory structure:
analysis/ - Contains the RMarkdown documents with the
various stages of analysis. These are numbered according to the order
they should be run.code/ - R scripts with custom functions used in some
analysis stages.data/ - This directory contains the data files used in
the analysis with sub-directories for different data types (see Getting the data for details). Processed intermediate
data files will also be placed here.docs/ - This directory contains the analysis website
html files hosted at https://oshlacklab.com/paediatric-cf-inflammation-citeseq/,
as well as the image files.output/ - Directory for output files produced by the
analysis.renv/README.md - README describing the project..Rprofile - Custom R profile for the project including
set up for workflowr..gitattributes.gitignore - Details of files and directories that are
excluded from the repository._workflowr.yml - workflowr configuration
file.paediatric-cf-inflammation-citeseq.Rproj - RStudio
project file.renv.lock - renv lock file, used to
restore and install correct versions of R packages required for this
project.This analysis was completed using R version 4.3.3 (2024-02-29). To
ensure reproducibility the renv package was used to track
package sources and versions. Ensure you have the correct version of R
and renv installed prior to beginning. To install the
necessary package versions you can use:
renv::restore()For more information on using renv see the
renv website.
Note on data availability: The data provided represents the earliest stage of processing that can be shared openly. Upstream steps (01.0–01.6) required genetic information from participants for sample demultiplexing; interested parties requiring access to the raw FASTQ files may contact the authors, and access may be arranged subject to appropriate institutional ethics and governance approvals. The preprocessed count data provided here has been generated after demultiplexing and does not contain genetic information.
The preprocessed single-cell RNA-seq and CITE-seq count data generated for this study can be downloaded from Zenodo. To unpack the data into the correct directory structure, place the archive in the root of the cloned repository and run:
tar -xzf C133_Neeland_preprocessed_SCEs.tar.gz -C data
on the command line.
The cell and gene quality filtered, raw and normalised RNA data can also be explored and downloaded from CELLxGENE.
The analysis directory contains the following analysis
files:
[1] "01.0_preprocess_batch0.Rmd"
[2] "01.1_preprocess_batch1.Rmd"
[3] "01.2_preprocess_batch2.Rmd"
[4] "01.3_preprocess_batch3.Rmd"
[5] "01.4_preprocess_batch4.Rmd"
[6] "01.5_preprocess_batch5.Rmd"
[7] "01.6_preprocess_batch6.Rmd"
[8] "02.0_quality_control.Rmd"
[9] "03.0_identify_doublets.Rmd"
[10] "04.0_filter_doublets.Rmd"
[11] "05.0_remove_ambient.Rmd"
[12] "06.0_azimuth_annotation.Rmd"
[13] "06.1_azimuth_annotation_decontx.Rmd"
[14] "07.1_integrate_cluster_t_cells_decontx.Rmd"
[15] "08.1_integrate_cluster_other_cells_decontx.Rmd"
[16] "09.0_integrate_cluster_macro_cells.Rmd"
[17] "10.0_manual_annotations_macro_cells.Rmd"
[18] "11.0_manual_annotations_t_cells_decontx.Rmd"
[19] "12.0_manual_annotations_other_cells.Rmd"
[20] "13.0_DGE_analysis_macrophages.Rmd"
[21] "13.1_DGE_analysis_macro-alveolar.Rmd"
[22] "13.2_DGE_analysis_macro-APOC2+.Rmd"
[23] "13.3_DGE_analysis_macro-CCL.Rmd"
[24] "13.4_DGE_analysis_macro-IFI27.Rmd"
[25] "13.5_DGE_analysis_macro-lipid.Rmd"
[26] "13.6_DGE_analysis_macro-monocyte-derived.Rmd"
[27] "13.7_DGE_analysis_macro-proliferating.Rmd"
[28] "14.0_DGE_analysis_CD4-T-cells.Rmd"
[29] "14.1_DGE_analysis_CD8-T-cells.Rmd"
[30] "14.2_DGE_analysis_DC-cells.Rmd"
[31] "14.3_epithelial_cell_analysis.Rmd"
[32] "15.0_proportions_analysis_ann_level_1.Rmd"
[33] "15.1_proportions_analysis_ann_level_3_non-macrophages.Rmd"
[34] "15.2_proportions_analysis_ann_level_3_macrophages.Rmd"
[35] "16.0_Figure_1.Rmd"
[36] "16.1_Figure_2.Rmd"
[37] "16.2_Figure_3.Rmd"
[38] "16.3_Figure_4.Rmd"
[39] "16.4_Figure_5.Rmd"
[40] "16.5_Figure_6.Rmd"
[41] "16.6_Supplementary_Figure_2.Rmd"
[42] "16.7_Supplementary_Figures.Rmd" As indicated by the numbering they should be run in this order. The
analysis can be reproduced starting from the data in the Getting the data section by running individual stages
of the analysis starting from step 02.0, either by providing the names
of the file you want to run to workflowr::wflow_build() or
by manually knitting the document (for example using the ‘Knit’ button
in RStudio). Note, most parts of the analysis require outputs generated
by a previous step and so will not run unless the preceding steps have
already been executed.
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 here_1.0.1 R6_2.5.1
[16] knitr_1.50 tibble_3.2.1 rprojroot_2.0.4
[19] bslib_0.6.1 pillar_1.9.0 rlang_1.1.6
[22] utf8_1.2.4 cachem_1.0.8 stringi_1.8.3
[25] httpuv_1.6.14 xfun_0.52 getPass_0.2-4
[28] fs_1.6.6 sass_0.4.10 cli_3.6.5
[31] magrittr_2.0.3 ps_1.7.6 digest_0.6.34
[34] processx_3.8.3 rstudioapi_0.15.0 lifecycle_1.0.4
[37] vctrs_0.6.5 evaluate_0.23 glue_1.8.0
[40] whisker_0.4.1 fansi_1.0.6 rmarkdown_2.29
[43] httr_1.4.7 tools_4.3.3 pkgconfig_2.0.3
[46] htmltools_0.5.8.1