Changes in version 0.1.0.9000                      

Smaller package

  - The three largest objects (filtered_txi, dds and zscore_mat) are no
    longer installed with the package. They are files of the v0.1.0
    GitHub release, and the new function download_data() downloads them
    the first time they are used and then reads the saved copy. The
    package now requires R >= 4.0.
  - Only the "Get started" guides (intro_es, intro_en) are installed as
    vignettes. The lessons, the functions guide and the data download
    page are now only on the website.
  - Smaller figures, and the unused logo and overview.png were removed.

Functions

  - New download_data() to get filtered_txi, dds and zscore_mat.
  - processGO() and Reduce_GOTerm() were renamed process_go() and
    reduce_go_terms(), so that all the functions follow the same style
    (snake_case). The old names still work, but are deprecated and show
    a warning.

Website

  - New "Shinyapp" section in the README and the home page sidebar, with
    a link to the GeneExprLupusMx Shinyapp (for now, only in Spanish).

                        Changes in version 0.1.0                        

First public release of GeneExprLupusMx, archived in Zenodo.

Lessons

  - Learning path with seven lessons that reproduce the article's
    figures, plus a getting-started guide, in Spanish (*_es) and English
    (*_en):
      - intro: getting started with the package.
      - clinical (Lesson 1): descriptive statistics, Table 1 and Figure
        S3.
      - intro_RNAseq (Lesson 2): import, normalization, heatmaps and
        PCA; Figure S2.
      - l3_DEGs (Lesson 3): differential expression SLE vs Ctrl;
        Figure 2.
      - l4_GOterms (Lesson 4): functional enrichment with g:Profiler;
        Figures 3 and S4, hypergeometric and Fisher's exact tests of ISG
        enrichment, and Spearman correlation between ISGs and SLEDAI
        (supplementary tables).
      - l5_DEGs_monocytes_diff (Lesson 5): differentiation of monocytes
        into dendritic cells; Figures 4 and 5.
      - l6_DEGs_tolDcs (Lesson 6): transcriptional signature of tolDCs;
        Figure 6, and genes concordant and divergent with the Robertson
        et al. signature.
      - l7_DEGs_between_groups (Lesson 7): interaction model
        Group:Cell_type; Figures 7A and 7B, and supplementary figure of
        expression trajectories of the interaction DEGs.
  - Guide on how to use the package functions (functions_es,
    functions_en), with real examples of get_heatmap_mat(),
    create_heatmap(), processGO() and Reduce_GOTerm().
  - Lesson 7 ends with an illustrative figure summarizing the findings
    of the learning path.
  - Data download pages in Spanish and English (download_es,
    download_en).
  - Each lesson opens with an illustrative summary image (after the
    glossary), in Spanish and English: input data, the lesson steps with
    its real figures, key findings and checkpoints.
  - Each lesson includes a glossary, lesson map, challenges with
    solutions, figure and table captions with values computed in the
    code, and per-language navigation buttons.
  - Lessons harmonized: same step format, unified glossary,
    prerequisites with full titles, and captions for every figure and
    table (including Table 1).

Data

  - New reference data: volunteer_info, biotype_summary, sle_genes,
    isg_genes, moDC_genes, dc_genes, tolDC_genes.
  - New checkpoints between lessons: dds, zscore_mat, de_results,
    go_results, de_celltype_results, go_celltype_results,
    de_interaction_results, go_interaction_results.
  - Scripts in data-raw/ to regenerate each object (archived g:Profiler,
    version e113).
  - Corrected documentation of filtered_txi and metadata_cleaned.

Functions

  - get_heatmap_mat(), create_heatmap() (rasterization off by default),
    processGO() and Reduce_GOTerm().

Website and documentation

  - New home page (index.Rmd) with the Overview image and lesson table.
  - Bilingual README (Spanish and English).
  - Changelog in Spanish (articles/news_es.html) and English (this
    file).
  - inst/CITATION file: citation("GeneExprLupusMx") returns the package
    citation; the data citations (article and Zenodo dataset) are listed
    in the citation sections of the website and README. The package
    Zenodo DOI is pending.
  - pkgdown menus: Getting started, Tutorials (Spanish and English
    lessons), Functions, data download and changelog; navigation buttons
    with white text.