├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── check-bioc.yml │ └── pkgdown.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── download.R ├── hpa_histology_data.R ├── one.R ├── sysdata.rda ├── utils.R ├── vis.R └── xml.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── data └── hpa_histology_data.rda ├── data_raw ├── download_list.csv ├── example_data.R ├── gene_ensembl_lookup_table.R └── make_download_list.R ├── docs ├── 404.html ├── LICENSE-text.html ├── _config.yml ├── articles │ ├── a_HPAanalyze_quick_start.html │ ├── a_HPAanalyze_quick_start_files │ │ ├── elevate-section-attrs-2.0 │ │ │ └── elevate-section-attrs.js │ │ ├── figure-html │ │ │ ├── hpaVisPatho_eg-1.png │ │ │ ├── hpaVis_eg-1.png │ │ │ └── hpaVis_eg3-1.png │ │ └── jquery-1.11.3 │ │ │ └── jquery.min.js │ ├── b_HPAanalyze_indepth.html │ ├── b_HPAanalyze_indepth_files │ │ ├── elevate-section-attrs-2.0 │ │ │ └── elevate-section-attrs.js │ │ ├── figure-html │ │ │ ├── hpaVis_eg-1.png │ │ │ ├── visPatho-1.png │ │ │ ├── visSubcell-1.png │ │ │ └── visTissue-1.png │ │ └── jquery-1.11.3 │ │ │ └── jquery.min.js │ ├── c_HPAanalyze_case_query.html │ ├── c_HPAanalyze_case_query_files │ │ ├── elevate-section-attrs-2.0 │ │ │ └── elevate-section-attrs.js │ │ └── jquery-1.11.3 │ │ │ └── jquery.min.js │ ├── d_HPAanalyze_case_offline_xml.html │ ├── d_HPAanalyze_case_offline_xml_files │ │ ├── elevate-section-attrs-2.0 │ │ │ └── elevate-section-attrs.js │ │ └── jquery-1.11.3 │ │ │ └── jquery.min.js │ ├── e_HPAanalyze_case_json.html │ ├── e_HPAanalyze_case_json_files │ │ ├── elevate-section-attrs-2.0 │ │ │ └── elevate-section-attrs.js │ │ └── jquery-1.11.3 │ │ │ └── jquery.min.js │ ├── f_HPAanalyze_case_images.html │ ├── f_HPAanalyze_case_images_files │ │ ├── elevate-section-attrs-2.0 │ │ │ └── elevate-section-attrs.js │ │ └── jquery-1.11.3 │ │ │ └── jquery.min.js │ ├── figures │ │ ├── hex.png │ │ ├── query_dropdown.png │ │ ├── query_fields.png │ │ ├── query_search.png │ │ ├── query_tsvlink.png │ │ ├── query_vis.png │ │ └── workflow.png │ ├── index.html │ ├── z_HPAanalyze_paper_figures.html │ └── z_HPAanalyze_paper_figures_files │ │ ├── elevate-section-attrs-2.0 │ │ └── elevate-section-attrs.js │ │ └── jquery-1.11.3 │ │ └── jquery.min.js ├── authors.html ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── TP53_EGFR_in_tissue_cancer.xlsx.xlsx │ ├── hpaDownload.html │ ├── hpaExport.html │ ├── hpaListParam.html │ ├── hpaVis-1.png │ ├── hpaVis.html │ ├── hpaVisPatho-1.png │ ├── hpaVisPatho.html │ ├── hpaVisSubcell-1.png │ ├── hpaVisSubcell.html │ ├── hpaVisTissue-1.png │ ├── hpaVisTissue.html │ ├── hpaXml.html │ ├── hpaXmlAntibody.html │ ├── hpaXmlGet.html │ ├── hpaXmlProtClass.html │ ├── hpaXmlTissueExpr.html │ ├── hpaXmlTissueExprSum.html │ ├── hpa_downloaded_histology_v18.html │ ├── hpa_histology_data.html │ └── index.html ├── inst └── CITATION ├── man ├── hpaDownload.Rd ├── hpaExport.Rd ├── hpaListParam.Rd ├── hpaVis.Rd ├── hpaVisPatho.Rd ├── hpaVisSubcell.Rd ├── hpaVisTissue.Rd ├── hpaXml.Rd ├── hpaXmlAntibody.Rd ├── hpaXmlGet.Rd ├── hpaXmlProtClass.Rd ├── hpaXmlTissueExpr.Rd ├── hpaXmlTissueExprSum.Rd └── hpa_histology_data.Rd └── vignettes ├── a_HPAanalyze_quick_start.Rmd ├── b_HPAanalyze_indepth.Rmd ├── c_HPAanalyze_case_query.Rmd ├── d_HPAanalyze_case_offline_xml.Rmd ├── data ├── ENSG00000134057.xml └── copyright ├── e_HPAanalyze_case_json.Rmd ├── f_HPAanalyze_case_images.Rmd ├── figures ├── hex.png ├── query_dropdown.png ├── query_fields.png ├── query_search.png ├── query_tsvlink.png ├── query_vis.png └── workflow.png └── z_HPAanalyze_paper_figures.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/anhtr/HPAanalyze/HEAD/.Rbuildignore 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