Files in GabrielHoffman/dreamlet

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

.Rbuildignore

.github/.gitignore

.github/workflows/pkgdown.yaml

DESCRIPTION

NAMESPACE

NEWS.md R/RcppExports.R R/aggregateNonCountSignal.R R/aggregateToPseudoBulk.R R/aggregateVar.R R/buildClusterTreeFromPB.R R/cellCounts.R R/cellTypeSpecificity.R R/colsum2.R R/colsum_fast.R R/compositePosteriorTest.R R/computeLogCPM.R R/da_to_sparseMatrix.R R/diffVar.R R/dreamlet.R R/dreamletCompareClusters.R R/dreamletProcessedData.R R/dropRedundantTerms.R R/fitVarPart.R R/getExprGeneNames.R R/initialPrecisionWeights.R R/mash.R R/meta_analysis.R R/misc.R R/outlier.R R/plotBeeswarm.R R/plotCellComposition.R R/plotForest.R R/plotGeneHeatmap.R R/plotHeatmap.R R/plotPCA.R R/plotPercentBars.R R/plotProjection.R R/plotVarPart.R R/plotViolin.R R/plotVolcano.R R/plotVoom.R R/processAssays.R R/removeConstantTerms.R R/stackAssays.R R/vpDF.R R/zenith_gsa.R README.md

TODO

_pkgdown.yml

docs/404.html

docs/apple-touch-icon-120x120.png

docs/apple-touch-icon-152x152.png

docs/apple-touch-icon-180x180.png

docs/apple-touch-icon-60x60.png

docs/apple-touch-icon-76x76.png

docs/apple-touch-icon.png

docs/articles/cell_covs.html

docs/articles/cell_covs_files/figure-html/processAssays-1.png

docs/articles/dreamlet.html

docs/articles/dreamlet_files/figure-html/boxplot-1.png

docs/articles/dreamlet_files/figure-html/cellTypeSpecificity-1.png

docs/articles/dreamlet_files/figure-html/dreamlet.contrasts-1.png

docs/articles/dreamlet_files/figure-html/forrest-1.png

docs/articles/dreamlet_files/figure-html/heatmap-1.png

docs/articles/dreamlet_files/figure-html/heatmap2-1.png

docs/articles/dreamlet_files/figure-html/plotGeneHeatmap-1.png

docs/articles/dreamlet_files/figure-html/plotPercentBars-1.png

docs/articles/dreamlet_files/figure-html/plotPercentBars-2.png

docs/articles/dreamlet_files/figure-html/plotVolcano-1.png

docs/articles/dreamlet_files/figure-html/voom.plots-1.png

docs/articles/dreamlet_files/figure-html/vp.barplt-1.png

docs/articles/dreamlet_files/figure-html/vp.violin-1.png

docs/articles/errors.html

docs/articles/figure/forest-1.png

docs/articles/figure/volcano-1.png

docs/articles/figure/zenith-1.png

docs/articles/h5ad_on_disk.html

docs/articles/index.html

docs/articles/mashr.html

docs/articles/non_lin_eff.html

docs/authors.html

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/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/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/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-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-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/pe03MImSLYBIv1o4X1M8cc9iB_5p.woff

docs/deps/bootstrap-5.2.2/fonts/pe0qMImSLYBIv1o4X1M8cfe5.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/favicon-16x16.png

docs/favicon-32x32.png

docs/favicon.ico

docs/index.html

docs/link.svg

docs/logo.svg

docs/news/index.html

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/Rplot002.png

docs/reference/Rplot003.png

docs/reference/aggregateNonCountSignal.html

docs/reference/aggregateToPseudoBulk.html

docs/reference/aggregateVar.html

docs/reference/as.dreamletResult.html

docs/reference/assay-methods.html

docs/reference/assayNames-methods.html

docs/reference/buildClusterTreeFromPB-1.png

docs/reference/buildClusterTreeFromPB.html

docs/reference/cellCounts.html

docs/reference/cellSpecificityValues-class.html

docs/reference/cellTypeSpecificity-1.png

docs/reference/cellTypeSpecificity-2.png

docs/reference/cellTypeSpecificity-3.png

docs/reference/cellTypeSpecificity.html

docs/reference/checkFormula.html

docs/reference/coefNames-methods.html

docs/reference/colData-dreamletProcessedData-method.html

docs/reference/colData-set-dreamletProcessedData-ANY-method.html

docs/reference/compositePosteriorTest.html

docs/reference/computeCellCounts.html

docs/reference/computeLogCPM.html

docs/reference/computeNormCounts.html

docs/reference/details-methods.html

docs/reference/diffVar-method-1.png

docs/reference/diffVar-method.html

docs/reference/diffVar-methods-1.png

docs/reference/diffVar-methods.html

docs/reference/dreamlet.html

docs/reference/dreamletCompareClusters-1.png

docs/reference/dreamletCompareClusters-2.png

docs/reference/dreamletCompareClusters-3.png

docs/reference/dreamletCompareClusters.html

docs/reference/dreamletProcessedData-class.html

docs/reference/dreamletResult-class.html

docs/reference/dreamlet_mash_result-class.html

docs/reference/dropRedundantTerms.html

docs/reference/equalFormulas.html

docs/reference/extract-methods.html

docs/reference/extractData-methods-1.png

docs/reference/extractData-methods.html

docs/reference/figures/diagram.png

docs/reference/figures/logo.png

docs/reference/figures/logo.svg

docs/reference/fitVarPart-1.png

docs/reference/fitVarPart-2.png

docs/reference/fitVarPart.html

docs/reference/getExprGeneNames.html

docs/reference/getTreat-methods.html

docs/reference/index.html

docs/reference/meta_analysis.html

docs/reference/metadata-dreamletProcessedData-method.html

docs/reference/outlier.html

docs/reference/outlierByAssay.html

docs/reference/pbWeights.html

docs/reference/plotBeeswarm-1.png

docs/reference/plotBeeswarm.html

docs/reference/plotCellComposition-1.png

docs/reference/plotCellComposition-2.png

docs/reference/plotCellComposition.html

docs/reference/plotForest-methods-1.png

docs/reference/plotForest-methods.html

docs/reference/plotGeneHeatmap-methods-1.png

docs/reference/plotGeneHeatmap-methods.html

docs/reference/plotHeatmap-methods-1.png

docs/reference/plotHeatmap-methods.html

docs/reference/plotPCA-1.png

docs/reference/plotPCA-2.png

docs/reference/plotPCA.html

docs/reference/plotPercentBars-methods-1.png

docs/reference/plotPercentBars-methods.html

docs/reference/plotProjection-1.png

docs/reference/plotProjection.html

docs/reference/plotVarPart-methods-1.png

docs/reference/plotVarPart-methods.html

docs/reference/plotViolin-methods-1.png

docs/reference/plotViolin-methods.html

docs/reference/plotVolcano-methods-1.png

docs/reference/plotVolcano-methods-2.png

docs/reference/plotVolcano-methods.html

docs/reference/plotVoom-methods-1.png

docs/reference/plotVoom-methods-2.png

docs/reference/plotVoom-methods.html

docs/reference/print-methods.html

docs/reference/processAssays.html

docs/reference/processOneAssay.html

docs/reference/removeConstantTerms.html

docs/reference/residuals-methods.html

docs/reference/run_mash-1.png

docs/reference/run_mash-2.png

docs/reference/run_mash.html

docs/reference/seeErrors-methods.html

docs/reference/show-methods.html

docs/reference/sortCols-method-1.png

docs/reference/sortCols-method.html

docs/reference/stackAssays-1.png

docs/reference/stackAssays-2.png

docs/reference/stackAssays.html

docs/reference/tabToMatrix.html

docs/reference/topTable-methods.html

docs/reference/vpDF-class.html

docs/reference/zenith_gsa-methods-1.png

docs/reference/zenith_gsa-methods.html

docs/search.json

docs/sitemap.xml

inst/CITATION

inst/REFERENCES.bib

inst/unitTests/test_cellCounts.R inst/unitTests/test_computeLogCPM.R inst/unitTests/test_pbWeights.R inst/unitTests/test_processOneAssay.R inst/unitTests/test_pseudobulk.R inst/unitTests/test_rowWeightedVarsMatrix.R man/aggregateNonCountSignal.Rd man/aggregateToPseudoBulk.Rd man/aggregateVar.Rd man/as.dreamletResult.Rd man/assay-methods.Rd man/assayNames-methods.Rd man/buildClusterTreeFromPB.Rd man/cellCounts.Rd man/cellSpecificityValues-class.Rd man/cellTypeSpecificity.Rd man/checkFormula.Rd man/coefNames-methods.Rd man/colData-dreamletProcessedData-method.Rd man/colData-set-dreamletProcessedData-ANY-method.Rd man/compositePosteriorTest.Rd man/computeCellCounts.Rd man/computeLogCPM.Rd man/computeNormCounts.Rd man/details-methods.Rd man/diffVar-methods.Rd man/dreamlet.Rd man/dreamletCompareClusters.Rd man/dreamletProcessedData-class.Rd man/dreamletResult-class.Rd man/dreamlet_mash_result-class.Rd man/dropRedundantTerms.Rd man/equalFormulas.Rd man/extract-methods.Rd man/extractData-methods.Rd

man/figures/diagram.png

man/figures/logo.png

man/figures/logo.svg

man/fitVarPart.Rd man/getExprGeneNames.Rd man/getTreat-methods.Rd man/meta_analysis.Rd man/metadata-dreamletProcessedData-method.Rd man/outlier.Rd man/outlierByAssay.Rd man/pbWeights.Rd man/plotBeeswarm.Rd man/plotCellComposition.Rd man/plotForest-methods.Rd man/plotGeneHeatmap-methods.Rd man/plotHeatmap-methods.Rd man/plotPCA.Rd man/plotPercentBars-methods.Rd man/plotProjection.Rd man/plotVarPart-methods.Rd man/plotViolin-methods.Rd man/plotVolcano-methods.Rd man/plotVoom-methods.Rd man/print-methods.Rd man/processAssays.Rd man/processOneAssay.Rd man/removeConstantTerms.Rd man/residuals-methods.Rd man/run_mash.Rd man/seeErrors-methods.Rd man/show-methods.Rd man/sortCols-method.Rd man/stackAssays.Rd man/tabToMatrix.Rd man/topTable-methods.Rd man/vpDF-class.Rd man/zenith_gsa-methods.Rd

src/Makevars

src/Makevars.win

src/RcppExports.cpp

src/colsum_beachmat.cpp

tests/runTests.R

vignettes/.DS_Store

vignettes/cell_covs.Rmd

vignettes/cell_covs.html

vignettes/dreamlet.Rmd

vignettes/dreamlet.html

vignettes/errors.Rmd

vignettes/errors.html

vignettes/figure/forest-1.png

vignettes/figure/volcano-1.png

vignettes/figure/zenith-1.png

vignettes/h5ad_on_disk.Rmd

vignettes/h5ad_on_disk.html

vignettes/mashr.Rmd vignettes/non_lin_eff.Rmd

vignettes/old_txt.txt

vignettes/run_vigs.txt

GabrielHoffman/dreamlet documentation built on May 20, 2024, 2:05 p.m.