├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── pkgdown.yaml ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── aggregateNonCountSignal.R ├── aggregateToPseudoBulk.R ├── aggregateVar.R ├── buildClusterTreeFromPB.R ├── cellCounts.R ├── cellTypeSpecificity.R ├── colsum2.R ├── colsum_fast.R ├── compositePosteriorTest.R ├── computeLogCPM.R ├── da_to_sparseMatrix.R ├── diffVar.R ├── dreamlet.R ├── dreamletCompareClusters.R ├── dreamletProcessedData.R ├── dropRedundantTerms.R ├── fitVarPart.R ├── mash.R ├── meta_analysis.R ├── misc.R ├── outlier.R ├── plotBeeswarm.R ├── plotCellComposition.R ├── plotForest.R ├── plotGeneHeatmap.R ├── plotHeatmap.R ├── plotPCA.R ├── plotPercentBars.R ├── plotProjection.R ├── plotVarPart.R ├── plotViolin.R ├── plotVolcano.R ├── plotVoom.R ├── processAssays.R ├── removeConstantTerms.R ├── stackAssays.R ├── vpDF.R └── zenith_gsa.R ├── README.md ├── TODO ├── _pkgdown.yml ├── docs ├── 404.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── cell_covs.html │ ├── cell_covs_files │ │ └── figure-html │ │ │ └── processAssays-1.png │ ├── dreamlet.html │ ├── dreamlet_files │ │ └── figure-html │ │ │ ├── boxplot-1.png │ │ │ ├── cellTypeSpecificity-1.png │ │ │ ├── dreamlet.contrasts-1.png │ │ │ ├── forrest-1.png │ │ │ ├── heatmap-1.png │ │ │ ├── heatmap2-1.png │ │ │ ├── plotGeneHeatmap-1.png │ │ │ ├── plotPercentBars-1.png │ │ │ ├── plotPercentBars-2.png │ │ │ ├── plotVolcano-1.png │ │ │ ├── voom.plots-1.png │ │ │ ├── vp.barplt-1.png │ │ │ └── vp.violin-1.png │ ├── errors.html │ ├── figure │ │ ├── forest-1.png │ │ ├── volcano-1.png │ │ └── zenith-1.png │ ├── h5ad_on_disk.html │ ├── index.html │ ├── mashr.html │ └── non_lin_eff.html ├── authors.html ├── deps │ ├── bootstrap-5.2.2 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ ├── bootstrap.min.css │ │ ├── font.css │ │ └── fonts │ │ │ ├── 1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff │ │ │ ├── 1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff │ │ │ ├── 4iCs6KVjbNBYlgo6ew.woff │ │ │ ├── 4iCs6KVjbNBYlgoKfw7w.woff │ │ │ ├── 4iCv6KVjbNBYlgoCxCvTtA.woff │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjsGyL.woff │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_TOQ.woff │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff │ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff │ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff │ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff │ │ │ ├── KFOlCnqEu92Fr1MmEU9fBBc-.woff │ │ │ ├── KFOlCnqEu92Fr1MmEU9vAA.woff │ │ │ ├── KFOlCnqEu92Fr1MmSU5fBBc-.woff │ │ │ ├── KFOlCnqEu92Fr1MmSU5vAA.woff │ │ │ ├── KFOlCnqEu92Fr1MmWUlfBBc-.woff │ │ │ ├── KFOlCnqEu92Fr1MmWUlvAA.woff │ │ │ ├── KFOmCnqEu92Fr1Me5g.woff │ │ │ ├── KFOmCnqEu92Fr1Mu4mxM.woff │ │ │ ├── QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff │ │ │ ├── S6u8w4BMUTPHjxsAXC-s.woff │ │ │ ├── S6u8w4BMUTPHjxswWA.woff │ │ │ ├── S6u9w4BMUTPHh6UVSwiPHw.woff │ │ │ ├── S6u9w4BMUTPHh6UVeww.woff │ │ │ ├── S6u9w4BMUTPHh7USSwiPHw.woff │ │ │ ├── S6u9w4BMUTPHh7USeww.woff │ │ │ ├── S6uyw4BMUTPHjx4wWA.woff │ │ │ ├── S6uyw4BMUTPHvxo.woff │ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff │ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff │ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff │ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDFwmRTA.woff │ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDGUmRTA.woff │ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDLshRTA.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff │ │ │ ├── pe03MImSLYBIv1o4X1M8cc9iB_5p.woff │ │ │ ├── pe0qMImSLYBIv1o4X1M8cfe5.woff │ │ │ └── q5uGsou0JOdh94bfvQlr.woff │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ ├── bootstrap.min.css │ │ ├── font.css │ │ └── fonts │ │ │ ├── 07d40e985ad7c747025dabb9f22142c4.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyC0ITw.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCAIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCIIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCMIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCkIT5lu.woff2 │ │ │ ├── 1f5e011d6aae0d98fc0518e1a303e99a.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcQ72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcg72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcw72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKew72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKfA72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKfw72.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjs2yNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjsGyN.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjtGyNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvGyNL4U.woff2 │ │ │ ├── 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6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwlxdu.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwkxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdu.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwkxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdu.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmxduz8A.woff2 │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNReuQ.woff2 │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNpeudwk.woff2 │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fO4KTet_.woff2 │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fOAKTQ.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvQlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvUlMI.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvXlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvYlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvZlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvalMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvblMIXxw.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlM-vWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMOvWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMevWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMuvWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlOevWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlPevW.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlPuvWjMY.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459W1hyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459WRhyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459WZhyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459Wdhyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459Wlhyw.woff2 │ │ │ ├── QGYpz_kZZAGCONcK2A4bGOj8mNhN.woff2 │ │ │ ├── S6u8w4BMUTPHjxsAUi-qJCY.woff2 │ │ │ ├── S6u8w4BMUTPHjxsAXC-q.woff2 │ │ │ ├── S6u9w4BMUTPHh6UVSwaPGR_p.woff2 │ │ │ ├── S6u9w4BMUTPHh6UVSwiPGQ.woff2 │ │ │ ├── S6u9w4BMUTPHh7USSwaPGR_p.woff2 │ │ │ ├── S6u9w4BMUTPHh7USSwiPGQ.woff2 │ │ │ ├── S6uyw4BMUTPHjx4wXg.woff2 │ │ │ ├── S6uyw4BMUTPHjxAwXjeu.woff2 │ │ │ ├── XRXV3I6Li01BKofIMeaBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofINeaB.woff2 │ │ │ ├── XRXV3I6Li01BKofIO-aBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofIOOaBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofIOuaBXso.woff2 │ │ │ ├── c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2 │ │ │ ├── ee91700cdbf7ce16c054c2bb8946c736.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2 │ │ │ ├── q5uGsou0JOdh94bfuQltOxU.woff2 │ │ │ └── q5uGsou0JOdh94bfvQlt.woff2 │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.4.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── favicon-16x16.png ├── favicon-32x32.png ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── logo.svg ├── news │ └── index.html ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── [,dreamletProcessedData,ANY,ANY,ANY-method.html │ ├── [,dreamletProcessedData,dreamletProcessedData-method.html │ ├── [,dreamletResult,dreamletResult-method.html │ ├── aggregateNonCountSignal.html │ ├── aggregateToPseudoBulk.html │ ├── aggregateVar.html │ ├── as.dreamletResult.html │ ├── assay,dreamletProcessedData,ANY-method.html │ ├── assay,dreamletProcessedData,dreamletProcessedData-method.html │ ├── assay,dreamletResult,dreamletResult-method.html │ ├── assay,vpDF,ANY-method.html │ ├── assay,vpDF,vpDF-method.html │ ├── assay-methods.html │ ├── assayNames,dreamletProcessedData,dreamletProcessedData-method.html │ ├── assayNames,dreamletProcessedData-method.html │ ├── assayNames,dreamletResult,dreamletResult-method.html │ ├── assayNames,vpDF,vpDF-method.html │ ├── assayNames,vpDF-method.html │ ├── assayNames-methods.html │ ├── buildClusterTreeFromPB-1.png │ ├── buildClusterTreeFromPB.html │ ├── cellCounts.html │ ├── cellSpecificityValues-class.html │ ├── cellTypeSpecificity-1.png │ ├── cellTypeSpecificity-2.png │ ├── cellTypeSpecificity-3.png │ ├── cellTypeSpecificity.html │ ├── checkFormula.html │ ├── coefNames,dreamletResult-method.html │ ├── coefNames-methods.html │ ├── colData-dreamletProcessedData-method.html │ ├── colData-set-dreamletProcessedData-ANY-method.html │ ├── compositePosteriorTest.html │ ├── computeCellCounts.html │ ├── computeLogCPM.html │ ├── computeNormCounts.html │ ├── details,dreamletProcessedData-method.html │ ├── details,dreamletResult-method.html │ ├── details,vpDF-method.html │ ├── details-methods.html │ ├── diffVar,dreamletResult,dreamletResult-method.html │ ├── diffVar-method-1.png │ ├── diffVar-method.html │ ├── diffVar-methods-1.png │ ├── diffVar-methods.html │ ├── dreamlet,dreamletProcessedData-method.html │ ├── dreamlet.html │ ├── dreamletCompareClusters-1.png │ ├── dreamletCompareClusters-2.png │ ├── dreamletCompareClusters-3.png │ ├── dreamletCompareClusters.html │ ├── dreamletProcessedData-class.html │ ├── dreamletResult-class.html │ ├── dreamlet_mash_result-class.html │ ├── dropRedundantTerms.html │ ├── equalFormulas.html │ ├── extract-methods.html │ ├── extractData,dreamletProcessedData,character-method.html │ ├── extractData,dreamletProcessedData-method.html │ ├── extractData-methods-1.png │ ├── extractData-methods.html │ ├── figures │ │ ├── diagram.png │ │ ├── logo.png │ │ └── logo.svg │ ├── fitVarPart,dreamletProcessedData-method.html │ ├── fitVarPart-1.png │ ├── fitVarPart-2.png │ ├── fitVarPart.html │ ├── getExprGeneNames.html │ ├── getTreat,dreamletResult,dreamletResult-method.html │ ├── getTreat-methods.html │ ├── index.html │ ├── meta_analysis.html │ ├── metadata,dreamletProcessedData,dreamletProcessedData-method.html │ ├── metadata-dreamletProcessedData-method.html │ ├── outlier.html │ ├── outlierByAssay.html │ ├── pbWeights.html │ ├── plotBeeswarm-1.png │ ├── plotBeeswarm.html │ ├── plotCellComposition,SingleCellExperiment-method.html │ ├── plotCellComposition,data.frame-method.html │ ├── plotCellComposition,matrix-method.html │ ├── plotCellComposition-1.png │ ├── plotCellComposition-2.png │ ├── plotCellComposition.html │ ├── plotForest,dreamletResult-method.html │ ├── plotForest,dreamlet_mash_result-method.html │ ├── plotForest-methods-1.png │ ├── plotForest-methods.html │ ├── plotGeneHeatmap,dreamletResult,dreamletResult-method.html │ ├── plotGeneHeatmap,dreamletResult-method.html │ ├── plotGeneHeatmap-methods-1.png │ ├── plotGeneHeatmap-methods.html │ ├── plotHeatmap,cellSpecificityValues,cellSpecificityValues-method.html │ ├── plotHeatmap,cellSpecificityValues-method.html │ ├── plotHeatmap,data.frame,data.frame-method.html │ ├── plotHeatmap,data.frame-method.html │ ├── plotHeatmap,matrix,matrix-method.html │ ├── plotHeatmap,matrix-method.html │ ├── plotHeatmap-methods-1.png │ ├── plotHeatmap-methods.html │ ├── plotPCA,list-method.html │ ├── plotPCA-1.png │ ├── plotPCA-2.png │ ├── plotPCA.html │ ├── plotPercentBars,cellSpecificityValues,cellSpecificityValues-method.html │ ├── plotPercentBars,cellSpecificityValues-method.html │ ├── plotPercentBars,vpDF,vpDF-method.html │ ├── plotPercentBars-methods-1.png │ ├── plotPercentBars-methods.html │ ├── plotProjection-1.png │ ├── plotProjection.html │ ├── plotVarPart,DataFrame,DataFrame-method.html │ ├── plotVarPart-methods-1.png │ ├── plotVarPart-methods.html │ ├── plotViolin,cellSpecificityValues,cellSpecificityValues-method.html │ ├── plotViolin,cellSpecificityValues-method.html │ ├── plotViolin-methods-1.png │ ├── plotViolin-methods.html │ ├── plotVolcano,MArrayLM,MArrayLM-method.html │ ├── plotVolcano,MArrayLM-method.html │ ├── plotVolcano,dreamlet_mash_result,dreamlet_mash_result-method.html │ ├── plotVolcano,dreamlet_mash_result-method.html │ ├── plotVolcano,list,list-method.html │ ├── plotVolcano,list-method.html │ ├── plotVolcano-methods-1.png │ ├── plotVolcano-methods-2.png │ ├── plotVolcano-methods.html │ ├── plotVoom,EList-method.html │ ├── plotVoom,dreamletProcessedData,dreamletProcessedData-method.html │ ├── plotVoom,dreamletProcessedData-method.html │ ├── plotVoom,list,list-method.html │ ├── plotVoom-methods-1.png │ ├── plotVoom-methods-2.png │ ├── plotVoom-methods.html │ ├── print,dreamletProcessedData,dreamletProcessedData-method.html │ ├── print,dreamletProcessedData-method.html │ ├── print,dreamletResult,dreamletResult-method.html │ ├── print-methods.html │ ├── processAssays.html │ ├── processOneAssay.html │ ├── removeConstantTerms.html │ ├── residuals,dreamletResult,dreamletResult-method.html │ ├── residuals-methods.html │ ├── run_mash-1.png │ ├── run_mash-2.png │ ├── run_mash.html │ ├── seeErrors,dreamletProcessedData-method.html │ ├── seeErrors,dreamletResult-method.html │ ├── seeErrors,vpDF-method.html │ ├── seeErrors-methods.html │ ├── show,dreamletProcessedData,dreamletProcessedData-method.html │ ├── show,dreamletProcessedData-method.html │ ├── show,dreamletResult,dreamletResult-method.html │ ├── show-methods.html │ ├── sortCols-method-1.png │ ├── sortCols-method.html │ ├── stackAssays-1.png │ ├── stackAssays-2.png │ ├── stackAssays-3.png │ ├── stackAssays-4.png │ ├── stackAssays.html │ ├── tabToMatrix.html │ ├── topTable,dreamletResult,dreamletResult-method.html │ ├── topTable-methods.html │ ├── vpDF-class.html │ ├── zenith_gsa,dreamletResult,GeneSetCollection,ANY-method.html │ ├── zenith_gsa,dreamlet_mash_result,GeneSetCollection,ANY-method.html │ ├── zenith_gsa,dreamlet_mash_result,GeneSetCollection-method.html │ ├── zenith_gsa-methods-1.png │ └── zenith_gsa-methods.html ├── search.json └── sitemap.xml ├── inst ├── CITATION ├── REFERENCES.bib └── unitTests │ ├── test_cellCounts.R │ ├── test_computeLogCPM.R │ ├── test_pbWeights.R │ ├── test_processOneAssay.R │ ├── test_pseudobulk.R │ └── test_rowWeightedVarsMatrix.R ├── man ├── aggregateNonCountSignal.Rd ├── aggregateToPseudoBulk.Rd ├── aggregateVar.Rd ├── as.dreamletResult.Rd ├── assay-methods.Rd ├── assayNames-methods.Rd ├── buildClusterTreeFromPB.Rd ├── cellCounts.Rd ├── cellSpecificityValues-class.Rd ├── cellTypeSpecificity.Rd ├── checkFormula.Rd ├── coefNames-methods.Rd ├── colData-dreamletProcessedData-method.Rd ├── colData-set-dreamletProcessedData-ANY-method.Rd ├── compositePosteriorTest.Rd ├── computeCellCounts.Rd ├── computeLogCPM.Rd ├── computeNormCounts.Rd ├── details-methods.Rd ├── diffVar-methods.Rd ├── dreamlet.Rd ├── dreamletCompareClusters.Rd ├── dreamletProcessedData-class.Rd ├── dreamletResult-class.Rd ├── dreamlet_mash_result-class.Rd ├── dropRedundantTerms.Rd ├── equalFormulas.Rd ├── extract-methods.Rd ├── extractData-methods.Rd ├── figures │ ├── diagram.png │ ├── logo.png │ └── logo.svg ├── fitVarPart.Rd ├── getTreat-methods.Rd ├── meta_analysis.Rd ├── metadata-dreamletProcessedData-method.Rd ├── outlier.Rd ├── outlierByAssay.Rd ├── plotBeeswarm.Rd ├── plotCellComposition.Rd ├── plotForest-methods.Rd ├── plotGeneHeatmap-methods.Rd ├── plotHeatmap-methods.Rd ├── plotPCA.Rd ├── plotPercentBars-methods.Rd ├── plotProjection.Rd ├── plotVarPart-methods.Rd ├── plotViolin-methods.Rd ├── plotVolcano-methods.Rd ├── plotVoom-methods.Rd ├── print-methods.Rd ├── processAssays.Rd ├── processOneAssay.Rd ├── removeConstantTerms.Rd ├── residuals-methods.Rd ├── run_mash.Rd ├── seeErrors-methods.Rd ├── show-methods.Rd ├── sortCols-method.Rd ├── stackAssays.Rd ├── tabToMatrix.Rd ├── topTable-methods.Rd ├── vpDF-class.Rd └── zenith_gsa-methods.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp └── colsum_beachmat.cpp ├── tests └── runTests.R └── vignettes ├── .DS_Store ├── cell_covs.Rmd ├── cell_covs.html ├── dreamlet.Rmd ├── dreamlet.html ├── errors.Rmd ├── errors.html ├── figure ├── forest-1.png ├── volcano-1.png └── zenith-1.png ├── h5ad_on_disk.Rmd ├── h5ad_on_disk.html ├── mashr.Rmd 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