initial commit

Author: menoldmt

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: git setup
+        # Set up git and export env vars to be used in later steps.
+        #   Note the unconventional mechanism for exporting envs by appending to
+        #   $GITHUB_ENV.
+        id: git-setup
+        run: |
+          git config --global user.email "action@github.com"
+          git config --global user.name "GitHub Action"
+          echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV
+          echo "WORKDIR=$(pwd)" >> $GITHUB_ENV
+
+      - name: Set up Miniforge and create environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Miniforge3
+          miniforge-version: latest
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          channel-priority: strict
+          environment-file: environment/env.yaml
+          activate-environment: env
+
+      - name: Generate test data with R
+        shell: bash -l {0}
+        run: |
+          cd $WORKDIR
+          Rscript data/test_data.R
+
+      - name: Run R tests
+        shell: bash -l {0}
+        run: |
+          cd $WORKDIR
+          Rscript -e "devtools::document('AnalyzeOlink'); devtools::test('AnalyzeOlink')"
+
+      - name: Run Snakemake
+        shell: bash -l {0}
+        run: |
+          cd $WORKDIR/snakemake
+          snakemake -j 2

.gitignore

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+# Conda environemnt
+environment/env
+# Hidden snakemake directories
+snakemake/.snakemake
+# Data
+data/ELISA/
+data/PEA/
+# Output HTML reports
+*.html
+# Output directories
+output/
+# Rmarkdown files
+*_cache/
+*_files/
+# Intermediate files
+*.Rds
+# R project files
+.Rhistory
+.RData
+.Ruserdata
+.Rproj.user/
+# RStudio files
+*.Rproj
+# Package check directory
+AnalyzeOlink.Rcheck/
+# Devtools build artifacts
+*.tar.gz
+# Knitr intermediate files
+*.utf8.md
+*.knit.md

AnalyzeOlink/DESCRIPTION

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+Package: AnalyzeOlink
+Title: Apply Various Statistical Frameworks to Analyze Olink PEA Data
+Version: 0.1.0
+Authors@R:
+    c(
+      person("Matthew", "Menold", email = "Matthew.Menold@gmail.com", role = c("aut", "cre")),
+      person("Ryan", "Dale", role = c("aut", "ctb"))
+    )
+Description: AnalyzeOlink provides a configurable framework for analyzing
+ Olink Proximity Extension Assay (PEA) data, including differential abundance
+ testing and downstream validation. Supported statistical methods include Type
+ III ANCOVA and linear mixed-effects models (via the 'afex' package), t-tests
+ and Wilcoxon tests (paired and unpaired), as well as Kruskal–Wallis and
+ Friedman tests. The package includes nine R Markdown analysis reports that
+ cover key workflow components such as assumption checks for ANOVA and LMER
+ models, leave-one-out sensitivity analyses for model terms and sample-level
+ robustness, ELISA validation, and non-parametric covariate effect and NPX
+ correlations testing. An annotations module integrates Human Protein Atlas
+ (HPA) metadata, including tissue- and cell-type–specific expression profiles
+ and Tau specificity scores, enabling annotation of downstream visualizations
+ such as volcano plots and estimate-vs-estimate comparisons.
+License: use_mit_license()
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Imports:
+    dplyr,
+    purrr,
+    org.Hs.eg.db
+Suggests:
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

AnalyzeOlink/NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(add_PatientID)
+export(add_centered_baseline)
+export(add_extra_hpa_data)
+export(add_pes)
+export(add_pes_rob)
+export(add_raw_npx)
+export(afex_test)
+export(annotations_estimate_plot)
+export(annotations_heatmap)
+export(annotations_make_volcano)
+export(annotations_volcano)
+export(append_brain_annotations_tbl)
+export(append_cols)
+export(append_geneid)
+export(assess_sample_fit)
+export(boxplot)
+export(bridgeability)
+export(brms_contrast)
+export(build_brms_contrasts)
+export(build_outlier_removed_se)
+export(center_numerics)
+export(check_se_object)
+export(choose_frameworks)
+export(compute_delta_sd)
+export(compute_spearman)
+export(cov_adjust)
+export(dotplot)
+export(dotplot_corr)
+export(dotplot_corr_list)
+export(enrich)
+export(enrich_correlations)
+export(enrich_gsea_corr)
+export(enrich_ora_corr)
+export(estimate_nu_from_kurtosis)
+export(estimate_plot)
+export(export_annotations)
+export(export_data)
+export(export_enrichment_corr)
+export(export_enrichment_results)
+export(export_hpa_ihc_data)
+export(export_lost_proteins)
+export(export_removed_rows)
+export(export_spearman)
+export(export_stats_results)
+export(filter_elisa_outliers)
+export(find_treatment_1_overlap)
+export(format_annotations_results)
+export(format_correlations_results)
+export(format_cov_results)
+export(format_enrich_results)
+export(format_results)
+export(from_list_with_names)
+export(get_assay_labels)
+export(get_num_sig)
+export(get_num_sig_corr)
+export(get_num_sig_lost)
+export(get_params)
+export(get_sig)
+export(get_test_name)
+export(import_data)
+export(interaction_emm)
+export(interaction_plot)
+export(keep_primary_effects)
+export(kruskal_test)
+export(label_plot)
+export(linear_mixed_model)
+export(make_dirs)
+export(make_dotplot_gsea_corr)
+export(make_dotplot_ora_corr)
+export(make_priors)
+export(make_therapeutic_reversal_results)
+export(make_volcano)
+export(mdcat)
+export(more_levels)
+export(norm_hist)
+export(npx_hist)
+export(olink_boxplot_2)
+export(one_car)
+export(one_mixed)
+export(one_robustbase)
+export(one_robustlmm)
+export(ordinal_regression)
+export(parallel_assess_sample_fit_with_cooks)
+export(parallel_assess_sample_fit_with_residuals)
+export(parallel_enrich)
+export(parallel_export_annotations)
+export(parallel_test_runner)
+export(pathway_heatmap)
+export(pathway_visualization)
+export(pca)
+export(plot_covariate_dist)
+export(plot_elisa_outliers)
+export(plot_qq)
+export(plot_qq_npx)
+export(plot_qq_protein)
+export(plot_spearman_violins)
+export(positive_pair_summary)
+export(prep_data)
+export(prepare_covariate_coldata)
+export(prepare_data_for_se_list)
+export(print_covariate_analysis)
+export(print_data)
+export(print_enrichment_corr)
+export(print_enrichment_results)
+export(print_enrichment_results_corr)
+export(print_lost_proteins)
+export(print_spearman_tables)
+export(print_stats_results)
+export(print_summary_table)
+export(print_top10_abs)
+export(print_top_corr_plots)
+export(protein_heatmap)
+export(qc)
+export(record_standard_assumption_violations)
+export(report_num_sig_corr)
+export(report_num_significant)
+export(robust_test)
+export(run_covariate_test)
+export(run_tests)
+export(save_covariates)
+export(sensitivity)
+export(sort_all_results)
+export(sort_results)
+export(subchunkify)
+export(subset_se)
+export(summarize_shared_significant)
+export(sync_se_to_metadata)
+export(t_test)
+export(test_for_covariates)
+export(tests)
+export(top_sig)
+export(tukey_outliers_list)
+export(two_levels)
+export(umap)
+export(upset)
+export(validate_parameters)
+export(volcano)
+export(wald_anova_rlmer)
+export(wilcox_test)
+export(write_normality)
+export(write_outlier_frequency_table)
+importFrom(stats,pchisq)
+importFrom(tibble,tibble)