Last updated: 2022-10-05

Checks: 2 0

Knit directory: Multimodal-Plasmacell_manuscript/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). 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.

Repository version: 4bb059d

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 4bb059d. 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/figure/

Untracked files:
    Untracked:  analysis/cellstate_sidetest.Rmd
    Untracked:  analysis/hallmarks.Rmd
    Untracked:  analysis/supplements.Rmd
    Untracked:  code/Import_and_create_seuratobject.R
    Untracked:  data/Seq2Science/
    Untracked:  data/azimuth_PBMCs/
    Untracked:  data/azimuth_bonemarrow/
    Untracked:  data/citeseqcount_htseqcount.zip
    Untracked:  data/genelist.plots.diffmarkers.txt
    Untracked:  data/genelist.plots.diffmarkers2.txt
    Untracked:  data/raw/
    Untracked:  data/supplementary/
    Untracked:  output/MOFA_analysis_Donorgroup.hdf5
    Untracked:  output/MOFA_analysis_Donorgroup.rds
    Untracked:  output/MOFA_analysis_Donorgroup_clustered.rds
    Untracked:  output/extra plots.docx
    Untracked:  output/paper_figures/
    Untracked:  output/seu.PROT_fix.rds
    Untracked:  output/seu.PROT_live.rds
    Untracked:  output/seu.RNA.rds
    Untracked:  output/seu.fix_norm.rds
    Untracked:  output/seu.fix_norm_cellstate.rds
    Untracked:  output/seu.fix_norm_plasmacells.rds
    Untracked:  output/seu.live_norm.rds
    Untracked:  output/seu.live_norm_cellstate.rds
    Untracked:  output/seu.live_norm_plasmacells.rds
    Untracked:  output/seu.live_norm_plasmacells_RNA.rds
    Untracked:  output/top-PROT-loadings_IgA.tsv
    Untracked:  output/top-PROT-loadings_IgG.tsv
    Untracked:  output/top-PROT-loadings_IgM.tsv
    Untracked:  output/top-gene-loadings_IgA.tsv
    Untracked:  output/top-gene-loadings_IgG.tsv
    Untracked:  output/top-gene-loadings_IgM.csv
    Untracked:  output/top-gene-loadings_IgM.tsv

Unstaged changes:
    Modified:   analysis/QC.Rmd
    Modified:   analysis/cellstate.Rmd
    Modified:   code/load_packages.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/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 4bb059d Jessie van Buggenum 2022-10-05 small update text
html b33343c jessievb 2021-12-04 Build site.
Rmd ba1ceb0 jessievb 2021-12-04 update citation
html 11ef483 jessievb 2021-12-04 Build site.
Rmd 6cadc7b jessievb 2021-12-04 edit typo
html d07b5eb jessievb 2021-12-04 Build site.
Rmd ff5bdfc jessievb 2021-12-04 edit home-page. Abstract, links and GEO
html 4680ae2 jessievb 2021-10-07 Build site.
html a5a4eeb jessievb 2021-10-07 Build site.
html 0d76cee jessievb 2021-10-07 Build site.
Rmd a3282f4 jessievb 2021-10-07 publish initital project files
Rmd 06f88ae jessievb 2021-10-05 Start workflowr project.

Abstract

Antibody secreting cells are key components of humoral immunity by secreting antibodies and providing protection against pathogens. These cells can be of IgM, IgA, or IgG subclass and migrate to class-specific niches. Localization and rareness of these cells make it challenge to define subclass-specific molecular hallmarks. Here, we describe how in-vitro differentiation of peripheral B-cells results in antibody-secreting cells. Using a single-cell multi-modal sequencing approach we find subclass-specific hallmark transcriptional profiles, surface protein expression and signaling pathway activation.

In this repository

The pages contain code to process, analyze and create figures presented in the full manuscript:

Attribution

We are very thankful for the efforts made by developers of Seurat, MOFA+ and workflowr. These (well documented) R-packages enable respectively extensive multi-modal data-analysis and reproducible code documentation.

The content in this repository is available under the CC BY 4.0 license.

For proper attribution, please cite our publication (##)) containing description and analysis of all presented data and results.