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Changelog

Source: NEWS.md

GeneExprLupusMx (development version)

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

Website

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

GeneExprLupusMx 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

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.