Last updated: 2024-06-21

Checks: 1 1

Knit directory: diff_expression_spatial_linear_models/

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.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Repository version: 40a1708

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 40a1708. 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:    analysis/.DS_Store
    Ignored:    analysis/.Rhistory
    Ignored:    code/.DS_Store
    Ignored:    code/diff_expr_hpcrun_spamm/.DS_Store
    Ignored:    code/diff_expr_hpcrun_spamm/code/.DS_Store
    Ignored:    code/diff_expr_hpcrun_spamm/code/.Rhistory
    Ignored:    code/diff_expr_hpcrun_spamm/code/logs/
    Ignored:    code/diff_expr_hpcrun_spamm/data/.DS_Store
    Ignored:    code/diff_expr_hpcrun_spamm/data/geomx_stlist_w_clusters_soabrain.RDS
    Ignored:    code/diff_expr_hpcrun_spamm/data/geomx_stlist_w_clusters_soaliver.RDS
    Ignored:    code/diff_expr_hpcrun_spamm/data/smi_stlist_w_clusters_liver.RDS
    Ignored:    code/diff_expr_hpcrun_spamm/data/smi_stlist_w_clusters_lungcancer.RDS
    Ignored:    code/diff_expr_hpcrun_spamm/data/visium_stlist_w_clusters_maynardbrain.RDS
    Ignored:    code/diff_expr_hpcrun_spamm/data/visium_stlist_w_clusters_raviglioblastoma.RDS
    Ignored:    code/diff_expr_hpcrun_spamm/results/
    Ignored:    code/stdiff_hpcrun_spamm_pairwise_tests/.DS_Store
    Ignored:    code/stdiff_hpcrun_spamm_pairwise_tests/results/
    Ignored:    data/.DS_Store
    Ignored:    data/cosmx_smi_liver_nanostring/
    Ignored:    data/cosmx_smi_lung_nsclc_nanostring/
    Ignored:    data/geomx_spatial_organ_atlas_data/
    Ignored:    data/maynard_2021_prefrontal_cortex/
    Ignored:    data/ravi_2022_glioblastoma/
    Ignored:    data/ravi_gbm_spata_objects/

Unstaged changes:
    Modified:   README.md
    Modified:   analysis/about.Rmd
    Modified:   analysis/diff_expr_example_stdiff.Rmd
    Modified:   analysis/diff_expr_spatial_linear_models.Rmd
    Modified:   analysis/index.Rmd

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.

There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

This repository contains code to reproduce the figures in the manuscript entitled “Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models” (Ospina et al. 2024). The contents of the repository are briefly detailed here: