Last updated: 2025-02-20
Checks: 7 0
Knit directory: paed-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.
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(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.
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 98fe953. 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/obsolete/
Ignored: data/.DS_Store
Ignored: data/C133_Neeland_batch1/
Ignored: data/C133_Neeland_merged/
Ignored: output/dge_analysis/obsolete/
Ignored: renv/library/
Ignored: renv/staging/
Untracked files:
Untracked: analysis/16.2_Figure_3.Rmd
Untracked: analysis/16.3_Figure_4.Rmd
Untracked: analysis/16.4_Figure_5.Rmd
Untracked: analysis/16.5_Supplementary_Figure_ADTs.Rmd
Untracked: analysis/cellxgene_submission.Rmd
Untracked: analysis/cellxgene_submission.nb.html
Untracked: analysis/figure/
Untracked: analysis/site_libs/
Untracked: broad_markers_seurat.csv
Untracked: code/background_job.R
Untracked: code/reverse_modifier_severity_comparisons.sh
Untracked: data/.Rprofile
Untracked: data/.gitattributes
Untracked: data/.gitignore
Untracked: data/.renvignore
Untracked: data/Homo_sapiens.gene_info.gz
Untracked: data/analysis/
Untracked: data/cellxgene_cell_ontologies_ann_level_1.xlsx
Untracked: data/cellxgene_cell_ontologies_ann_level_3 (1).xlsx
Untracked: data/cellxgene_cell_ontologies_ann_level_3.xlsx
Untracked: data/code/
Untracked: data/data/
Untracked: data/homologs.rds
Untracked: data/intermediate_objects/CD4 T cells.CF_samples.fit.rds
Untracked: data/intermediate_objects/CD4 T cells.all_samples.fit.rds
Untracked: data/intermediate_objects/CD8 T cells.CF_samples.fit.rds
Untracked: data/intermediate_objects/CD8 T cells.all_samples.fit.rds
Untracked: data/intermediate_objects/DC cells.CF_samples.fit.rds
Untracked: data/intermediate_objects/DC cells.all_samples.fit.rds
Unstaged changes:
Modified: .gitignore
Modified: analysis/06.0_azimuth_annotation.Rmd
Modified: analysis/09.0_integrate_cluster_macro_cells.Rmd
Modified: analysis/13.1_DGE_analysis_macro-alveolar.Rmd
Modified: analysis/13.7_DGE_analysis_macro-proliferating.Rmd
Modified: analysis/15.0_proportions_analysis_ann_level_1.Rmd
Deleted: analysis/99.0_Figure_1.Rmd
Deleted: analysis/99.0_Figure_2.Rmd
Deleted: analysis/99.0_Figure_3.Rmd
Deleted: analysis/99.0_Figure_4.Rmd
Deleted: analysis/99.0_Figure_5.Rmd
Deleted: analysis/99.0_Supplementary_Figure_3-5.Rmd
Deleted: analysis/99.0_Supplementary_Figure_ADTs.Rmd
Modified: analysis/index.Rmd
Modified: code/utility.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/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 | 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.gitmodules.gitignore - Details of files and directories that are
excluded from the repository..renvignore - renv ignore file_workflowr.yml - workflowr configuration
file.paed-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.
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] "15.0_proportions_analysis_ann_level_1.Rmd"
[32] "15.1_proportions_analysis_ann_level_3_non-macrophages.Rmd"
[33] "15.2_proportions_analysis_ann_level_3_macrophages.Rmd"
[34] "16.0_Figure_1.Rmd"
[35] "16.1_Figure_2.Rmd"
[36] "16.2_Figure_3.Rmd"
[37] "16.3_Figure_4.Rmd"
[38] "16.4_Figure_5.Rmd"
[39] "16.5_Supplementary_Figure_ADTs.Rmd"
[40] "16.6_Supplementary_Figures.Rmd" As indicated by the numbering they should be run in this order. If
you want to reproduce the entire analysis this can be easily done using
workflowr.
workflowr::wflow_build(republish = TRUE)It is also possible to run individual stages of the analysis, 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: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
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_1.0.3 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_1.45 tibble_3.2.1 rprojroot_2.0.4
[19] bslib_0.6.1 pillar_1.9.0 rlang_1.1.4
[22] utf8_1.2.4 cachem_1.0.8 stringi_1.8.3
[25] httpuv_1.6.14 xfun_0.42 getPass_0.2-4
[28] fs_1.6.5 sass_0.4.9 cli_3.6.3
[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_2.25
[43] httr_1.4.7 tools_4.3.3 pkgconfig_2.0.3
[46] htmltools_0.5.8.1