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Last updated: 2021-02-09

Checks: 2 0

Knit directory: melanoma_publication_old_data/

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: dd1e815

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 dd1e815. 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:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    ._.DS_Store
    Ignored:    code/.DS_Store
    Ignored:    code/._.DS_Store
    Ignored:    code/helper_functions/._findCommunity.R
    Ignored:    data/.DS_Store
    Ignored:    data/._.DS_Store
    Ignored:    data/._density_infiltration_BlockID.csv
    Ignored:    data/._layer_1_classification_rna.csv
    Ignored:    data/._manual_infiltration_scoring.csv
    Ignored:    data/._manual_infiltration_scoring_BlockID.csv
    Ignored:    data/._manual_infiltration_scoring_RC.csv
    Ignored:    data/._manual_infiltration_scoring_TH.csv
    Ignored:    data/._survdat_for_modelling.csv
    Ignored:    data/12plex_validation/
    Ignored:    data/200323_TMA_256_Hot Cold_Clinical Data_Updated Response Data_For Collaborators_latest updated_Mar_2020_for_Coxph_modeling.csv
    Ignored:    data/colour_vector.rds
    Ignored:    data/density_infiltration_BlockID.csv
    Ignored:    data/fraction_and_infiltration_scoring.csv
    Ignored:    data/layer_1_classification_protein.csv
    Ignored:    data/layer_1_classification_protein.rds
    Ignored:    data/layer_1_classification_rna.csv
    Ignored:    data/manual_infiltration_scoring.csv
    Ignored:    data/manual_infiltration_scoring_BlockID.csv
    Ignored:    data/manual_infiltration_scoring_RC.csv
    Ignored:    data/manual_infiltration_scoring_TH.csv
    Ignored:    data/protein/
    Ignored:    data/rna/
    Ignored:    data/safety_copy_SCE/
    Ignored:    data/sce_RNA.rds
    Ignored:    data/sce_protein.rds
    Ignored:    data/survdat_for_modelling.csv
    Ignored:    output/.DS_Store
    Ignored:    output/._.DS_Store
    Ignored:    output/._protein_neutrophil.png
    Ignored:    output/._rna_neutrophil.png
    Ignored:    output/PSOCKclusterOut/
    Ignored:    output/bcell_grouping.png
    Ignored:    output/dysfunction_correlation.pdf

Untracked files:
    Untracked:  analysis/06_RNA_chemokine_patch_detection.rmd
    Untracked:  analysis/07_TCF7_PD1_gating.rmd
    Untracked:  analysis/08_color_vectors.rmd
    Untracked:  analysis/09_Tcell_Score.Rmd
    Untracked:  analysis/10_Dysfunction_Score.rmd
    Untracked:  analysis/11_Bcell_Score.Rmd

Unstaged changes:
    Modified:   .gitignore
    Deleted:    analysis/05_protein_Tcell_quantification.Rmd
    Deleted:    analysis/06_Protein_Ki67status.Rmd
    Deleted:    analysis/06_RNA_chemokine_community_definition.rmd
    Deleted:    analysis/07_RNA_chemokine_community_clustering.Rmd
    Deleted:    analysis/08_RNA_neighbourhood_analysis_chemokines.rmd
    Deleted:    analysis/09_manual_scoring.rmd
    Deleted:    analysis/10_coloring.rmd
    Deleted:    analysis/11_Bcell_TLS_identifiaction.Rmd
    Deleted:    analysis/12_dysfunction_score.rmd
    Deleted:    analysis/13_TCF7_PD1.rmd
    Modified:   analysis/Figure_4.rmd
    Modified:   analysis/_site.yml

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
html	d1c9a41	toobiwankenobi	2021-02-09	index file
html	3828d53	toobiwankenobi	2021-02-09	index file
html	c19bae4	toobiwankenobi	2021-02-09	add index file
Rmd	f075b06	toobiwankenobi	2020-07-28	Start workflowr project.