Files in SydneyBioX/scFeatures
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/data.R R/helper_CCI.R R/helper_bulk_expression.R R/helper_celltype_expression.R R/helper_pathway.R R/helper_proportion.R R/helper_spatial_metrics.R R/run_scfeatures.R R/utils.R R/wrapper_run_scfeatures.R README.md
_pkgdown.yml
data/example_scrnaseq.RData
data/scfeatures_result.RData
docs/404.html
docs/articles/index.html
docs/articles/scFeatures_associationstudy.html
docs/articles/scFeatures_associationstudy_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/scFeatures_detail.html
docs/articles/scFeatures_detail_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/scFeatures_detail_files/figure-html/unnamed-chunk-12-1.png
docs/articles/scFeatures_detail_files/figure-html/unnamed-chunk-13-1.png
docs/articles/scFeatures_detail_files/figure-html/unnamed-chunk-19-1.png
docs/articles/scFeatures_detail_files/figure-html/unnamed-chunk-20-1.png
docs/articles/scFeatures_overview.html
docs/articles/scFeatures_overview_files/figure-html/unnamed-chunk-5-1.png
docs/articles/scFeatures_overview_files/figure-html/unnamed-chunk-6-1.png
docs/articles/scFeatures_summary.html
docs/articles/scFeatures_summary_files/accessible-code-block-0.0.1/empty-anchor.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.3/bootstrap.min.css
docs/deps/bootstrap-5.1.3/font.css
docs/deps/bootstrap-5.1.3/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff
docs/deps/bootstrap-5.1.3/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff
docs/deps/bootstrap-5.1.3/fonts/4iCs6KVjbNBYlgo6ew.woff
docs/deps/bootstrap-5.1.3/fonts/4iCs6KVjbNBYlgoKfw7w.woff
docs/deps/bootstrap-5.1.3/fonts/4iCv6KVjbNBYlgoCxCvTtA.woff
docs/deps/bootstrap-5.1.3/fonts/4iCv6KVjbNBYlgoCxCvjsGyL.woff
docs/deps/bootstrap-5.1.3/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff
docs/deps/bootstrap-5.1.3/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff
docs/deps/bootstrap-5.1.3/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff
docs/deps/bootstrap-5.1.3/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff
docs/deps/bootstrap-5.1.3/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff
docs/deps/bootstrap-5.1.3/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff
docs/deps/bootstrap-5.1.3/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff
docs/deps/bootstrap-5.1.3/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff
docs/deps/bootstrap-5.1.3/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff
docs/deps/bootstrap-5.1.3/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff
docs/deps/bootstrap-5.1.3/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff
docs/deps/bootstrap-5.1.3/fonts/CSR64z1Qlv-GDxkbKVQ_TOQ.woff
docs/deps/bootstrap-5.1.3/fonts/CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff
docs/deps/bootstrap-5.1.3/fonts/JTURjIg1_i6t8kCHKm45_ZpC7g0.woff
docs/deps/bootstrap-5.1.3/fonts/JTURjIg1_i6t8kCHKm45_dJE7g0.woff
docs/deps/bootstrap-5.1.3/fonts/JTUSjIg1_i6t8kCHKm45xW0.woff
docs/deps/bootstrap-5.1.3/fonts/KFOlCnqEu92Fr1MmEU9fBBc-.woff
docs/deps/bootstrap-5.1.3/fonts/KFOlCnqEu92Fr1MmEU9vAA.woff
docs/deps/bootstrap-5.1.3/fonts/KFOlCnqEu92Fr1MmSU5fBBc-.woff
docs/deps/bootstrap-5.1.3/fonts/KFOlCnqEu92Fr1MmSU5vAA.woff
docs/deps/bootstrap-5.1.3/fonts/KFOlCnqEu92Fr1MmWUlfBBc-.woff
docs/deps/bootstrap-5.1.3/fonts/KFOlCnqEu92Fr1MmWUlvAA.woff
docs/deps/bootstrap-5.1.3/fonts/KFOmCnqEu92Fr1Me5g.woff
docs/deps/bootstrap-5.1.3/fonts/KFOmCnqEu92Fr1Mu4mxM.woff
docs/deps/bootstrap-5.1.3/fonts/QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff
docs/deps/bootstrap-5.1.3/fonts/S6u8w4BMUTPHjxsAXC-s.woff
docs/deps/bootstrap-5.1.3/fonts/S6u8w4BMUTPHjxswWA.woff
docs/deps/bootstrap-5.1.3/fonts/S6u9w4BMUTPHh6UVSwiPHw.woff
docs/deps/bootstrap-5.1.3/fonts/S6u9w4BMUTPHh6UVeww.woff
docs/deps/bootstrap-5.1.3/fonts/S6u9w4BMUTPHh7USSwiPHw.woff
docs/deps/bootstrap-5.1.3/fonts/S6u9w4BMUTPHh7USeww.woff
docs/deps/bootstrap-5.1.3/fonts/S6uyw4BMUTPHjx4wWA.woff
docs/deps/bootstrap-5.1.3/fonts/S6uyw4BMUTPHvxo.woff
docs/deps/bootstrap-5.1.3/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff
docs/deps/bootstrap-5.1.3/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff
docs/deps/bootstrap-5.1.3/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff
docs/deps/bootstrap-5.1.3/fonts/XRXV3I6Li01BKof4MQ.woff
docs/deps/bootstrap-5.1.3/fonts/XRXW3I6Li01BKofA6sKkZQ.woff
docs/deps/bootstrap-5.1.3/fonts/XRXW3I6Li01BKofAjsOkZQ.woff
docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
docs/deps/bootstrap-5.1.3/fonts/pe03MImSLYBIv1o4X1M8cc9iB_5p.woff
docs/deps/bootstrap-5.1.3/fonts/pe0qMImSLYBIv1o4X1M8cfe5.woff
docs/deps/bootstrap-5.1.3/fonts/q5uGsou0JOdh94bfvQlr.woff
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/bootstrap-5.2.2/font.css
docs/deps/bootstrap-5.2.2/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff
docs/deps/bootstrap-5.2.2/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff
docs/deps/bootstrap-5.2.2/fonts/1adeadb2fe618c5ed46221f15e12b9c8.woff
docs/deps/bootstrap-5.2.2/fonts/4iCs6KVjbNBYlgo6ew.woff
docs/deps/bootstrap-5.2.2/fonts/4iCs6KVjbNBYlgoKfw7w.woff
docs/deps/bootstrap-5.2.2/fonts/4iCv6KVjbNBYlgoCxCvTtA.woff
docs/deps/bootstrap-5.2.2/fonts/4iCv6KVjbNBYlgoCxCvjsGyL.woff
docs/deps/bootstrap-5.2.2/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff
docs/deps/bootstrap-5.2.2/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff
docs/deps/bootstrap-5.2.2/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff
docs/deps/bootstrap-5.2.2/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff
docs/deps/bootstrap-5.2.2/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff
docs/deps/bootstrap-5.2.2/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff
docs/deps/bootstrap-5.2.2/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff
docs/deps/bootstrap-5.2.2/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff
docs/deps/bootstrap-5.2.2/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff
docs/deps/bootstrap-5.2.2/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff
docs/deps/bootstrap-5.2.2/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff
docs/deps/bootstrap-5.2.2/fonts/CSR64z1Qlv-GDxkbKVQ_TOQ.woff
docs/deps/bootstrap-5.2.2/fonts/CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff
docs/deps/bootstrap-5.2.2/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff
docs/deps/bootstrap-5.2.2/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQhM0.woff
docs/deps/bootstrap-5.2.2/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTbI1rSg.woff
docs/deps/bootstrap-5.2.2/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTsoprSg.woff
docs/deps/bootstrap-5.2.2/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff
docs/deps/bootstrap-5.2.2/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff
docs/deps/bootstrap-5.2.2/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff
docs/deps/bootstrap-5.2.2/fonts/KFOlCnqEu92Fr1MmEU9fBBc-.woff
docs/deps/bootstrap-5.2.2/fonts/KFOlCnqEu92Fr1MmEU9vAA.woff
docs/deps/bootstrap-5.2.2/fonts/KFOlCnqEu92Fr1MmSU5fBBc-.woff
docs/deps/bootstrap-5.2.2/fonts/KFOlCnqEu92Fr1MmSU5vAA.woff
docs/deps/bootstrap-5.2.2/fonts/KFOlCnqEu92Fr1MmWUlfBBc-.woff
docs/deps/bootstrap-5.2.2/fonts/KFOlCnqEu92Fr1MmWUlvAA.woff
docs/deps/bootstrap-5.2.2/fonts/KFOmCnqEu92Fr1Me5g.woff
docs/deps/bootstrap-5.2.2/fonts/KFOmCnqEu92Fr1Mu4mxM.woff
docs/deps/bootstrap-5.2.2/fonts/QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff
docs/deps/bootstrap-5.2.2/fonts/S6u8w4BMUTPHjxsAXC-s.woff
docs/deps/bootstrap-5.2.2/fonts/S6u8w4BMUTPHjxswWA.woff
docs/deps/bootstrap-5.2.2/fonts/S6u9w4BMUTPHh6UVSwiPHw.woff
docs/deps/bootstrap-5.2.2/fonts/S6u9w4BMUTPHh6UVeww.woff
docs/deps/bootstrap-5.2.2/fonts/S6u9w4BMUTPHh7USSwiPHw.woff
docs/deps/bootstrap-5.2.2/fonts/S6u9w4BMUTPHh7USeww.woff
docs/deps/bootstrap-5.2.2/fonts/S6uyw4BMUTPHjx4wWA.woff
docs/deps/bootstrap-5.2.2/fonts/S6uyw4BMUTPHvxo.woff
docs/deps/bootstrap-5.2.2/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff
docs/deps/bootstrap-5.2.2/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff
docs/deps/bootstrap-5.2.2/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff
docs/deps/bootstrap-5.2.2/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDFwmRTA.woff
docs/deps/bootstrap-5.2.2/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDGUmRTA.woff
docs/deps/bootstrap-5.2.2/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDLshRTA.woff
docs/deps/bootstrap-5.2.2/fonts/a98f7a7574819ba83bec6279a2cecd95.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff
docs/deps/bootstrap-5.2.2/fonts/q5uGsou0JOdh94bfvQlr.woff
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/L_stats.html
docs/reference/Rplot001.png
docs/reference/bulk_sample.html
docs/reference/bulk_sample_celltype.html
docs/reference/check_data.html
docs/reference/example_scrnaseq.html
docs/reference/generateBPParam.html
docs/reference/get_num_cell_per_celltype.html
docs/reference/get_num_cell_per_spot.html
docs/reference/index.html
docs/reference/individual_geneset_proportion_celltype.html
docs/reference/makeSeurat.html
docs/reference/process_data.html
docs/reference/rearrange_string.html
docs/reference/remove_mito.html
docs/reference/remove_mito_ribo.html
docs/reference/run_CCI.html
docs/reference/run_L_function.html
docs/reference/run_Morans_I.html
docs/reference/run_association_study_report.html
docs/reference/run_celltype_interaction.html
docs/reference/run_gene_cor.html
docs/reference/run_gene_cor_celltype.html
docs/reference/run_gene_mean.html
docs/reference/run_gene_mean_celltype.html
docs/reference/run_gene_prop.html
docs/reference/run_gene_prop_celltype.html
docs/reference/run_nn_correlation.html
docs/reference/run_pathway_gsva.html
docs/reference/run_pathway_mean.html
docs/reference/run_pathway_prop.html
docs/reference/run_proportion_logit.html
docs/reference/run_proportion_ratio.html
docs/reference/run_proportion_raw.html
docs/reference/scFeatures.html
docs/reference/scfeatures_result.html
docs/search.json
docs/sitemap.xml
inst/CITATION
inst/extdata/figure/CCI_example_figures.png
inst/extdata/figure/aggregatedgene_example_figures.png
inst/extdata/figure/celltypegene_example_figures.png
inst/extdata/figure/celltypeproportion_example_figures.png
inst/extdata/figure/pathway_example_figures.png
inst/extdata/figure/spatial_example_figures.png
inst/extdata/output_report.Rmd
inst/overview.png
inst/script/example_scrnaseq
inst/sticker.png
man/example_scrnaseq.Rd man/get_num_cell_per_spot.Rd man/remove_mito_ribo.Rd man/run_CCI.Rd man/run_L_function.Rd man/run_Morans_I.Rd man/run_association_study_report.Rd man/run_celltype_interaction.Rd man/run_gene_cor.Rd man/run_gene_cor_celltype.Rd man/run_gene_mean.Rd man/run_gene_mean_celltype.Rd man/run_gene_prop.Rd man/run_gene_prop_celltype.Rd man/run_nn_correlation.Rd man/run_pathway_gsva.Rd man/run_pathway_mean.Rd man/run_pathway_prop.Rd man/run_proportion_logit.Rd man/run_proportion_ratio.Rd man/run_proportion_raw.Rd man/scFeatures.Rd man/scfeatures_result.Rd
vignettes/.gitignore
vignettes/scFeatures_overview.Rmd
SydneyBioX/scFeatures documentation built on March 13, 2024, 12:36 a.m.