Last updated: 2026-04-23

Checks: 2 0

Knit directory: cf-eti-bal-scrna/

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    ._.DS_Store
    Ignored:    code/._bal_RecM.integration_clustering.R
    Ignored:    data/._README.md
    Ignored:    data/AM.markers.csv
    Ignored:    data/DE/AM-CCL/CFB_vs_C/
    Ignored:    data/DE/AM-CCL/CFN_vs_C/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/GO_BP/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/GO_CC/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/GO_MF/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/Reactome/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/WikiPathway/
    Ignored:    data/DE/Prolif M/CFB_vs_C/GO_BP/
    Ignored:    data/DE/Prolif M/CFB_vs_C/GO_CC/
    Ignored:    data/DE/Prolif M/CFB_vs_C/GO_MF/
    Ignored:    data/DE/Prolif M/CFB_vs_C/Reactome/
    Ignored:    data/DE/Prolif M/CFB_vs_C/WikiPathway/
    Ignored:    data/DE/Prolif M/CFN_vs_C/
    Ignored:    data/DE/ruv/
    Ignored:    data/Fig3A.stat.csv
    Ignored:    data/Li.stat.csv
    Ignored:    data/Liao.stat.csv
    Ignored:    data/Major.markers.csv
    Ignored:    data/Morrell.stat.csv
    Ignored:    data/Present.stat.csv
    Ignored:    data/RecM.markers.csv
    Ignored:    data/SCEs
    Ignored:    data/Wendisch.stat.csv
    Ignored:    data/cellbender
    Ignored:    data/cytokine
    Ignored:    data/plots
    Ignored:    data/sample_sheets
    Ignored:    data/vireo
    Ignored:    output/plots/combined/

Unstaged changes:
    Modified:   analysis/about.Rmd
    Modified:   data/README.md

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 c689c0a tcwong1994 2026-04-23 Update index.Rmd
html 9a73276 tcwong1994 2026-04-23 Build site.
Rmd 69aa89b tcwong1994 2026-04-23 Commit index Rmd
Rmd e9cb32b tcwong1994 2026-04-23 Commit all analysis Rmd sources
html 8ac1a7b tcwong1994 2026-04-22 Build site.
Rmd 8ca4b8f tcwong1994 2026-04-22 workflowr::wflow_publish("analysis/index.Rmd", verbose = TRUE)
html 7b2fd64 tcwong1994 2026-04-22 Publish pre-rendered workflowr HTML pages
html e13f610 tcwong1994 2026-04-22 Initialize workflowr scaffold
Rmd 8496b1d tcwong1994 2026-04-22 Start workflowr project.

Overview

This site presents the code and results of demultiplexing and QC of BAL single-cell RNA-seq data used for Chapter 2 of Wong ATC’s PhD thesis [1].

Developers: Anson Wong, Hieu T Nim
Affiliation: Transcriptomics & Bioinformatics Group, Stem Cell Medicine Theme, Murdoch Children’s Research Institute

Data Processing

Demultiplexing

Quality control

References

[1] Wong ATC. Integrated airway and blood immune profiling in early life cystic fibrosis [PhD thesis]. Melbourne: University of Melbourne; 2026.