Files in MattPM/scglmmr
Sample-level Single-cell Generalized Linear Multilevel Models in R
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/SCGroupContrast_modulefunctions.r
R/SCMixedPoisson.r
R/downstream_deprecated_functions.r
R/dream.wrapper.r
R/enrichment_analysis.r
R/hypergeometric_utility_wrappers.r
R/model_result_interaction.r
R/networks.R
R/pseudobulk_helpers.r
R/sample_zscore.r
R/single_cell_gene_module_scores.r
R/utils-pipe.R
R/voom_limma_fixed.r
R/zzz.r
README.Rmd
README.md
_pkgdown.yml
data-raw/DATASET.R
data/hallmark.rda
data/hallmark.rds
docs/404.html
docs/LICENSE-text.html
docs/articles/index.html
docs/articles/networks.html
docs/articles/pseudobulk_mixed_effects.html
docs/articles/scglmmr_singlecell.html
docs/authors.html
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.0/bootstrap.min.css
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/data-deps.txt
docs/deps/jquery-3.5.1/AUTHORS.txt
docs/deps/jquery-3.5.1/LICENSE.txt
docs/deps/jquery-3.5.1/jquery-1.12.4.js
docs/deps/jquery-3.5.1/jquery-1.12.4.min.js
docs/deps/jquery-3.5.1/jquery-1.12.4.min.map
docs/deps/jquery-3.5.1/jquery-2.2.4.js
docs/deps/jquery-3.5.1/jquery-2.2.4.min.js
docs/deps/jquery-3.5.1/jquery-2.2.4.min.map
docs/deps/jquery-3.5.1/jquery-3.5.1.js
docs/deps/jquery-3.5.1/jquery-3.5.1.min.js
docs/deps/jquery-3.5.1/jquery-3.5.1.min.map
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/man/figures/example_sc.png
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/AggregateCellMetadata.html
docs/reference/AverageSampleModuleZscore.html
docs/reference/BulkDesignMatrix.html
docs/reference/CombineResults.html
docs/reference/EnrichmentJaccard.html
docs/reference/ExtractResult.html
docs/reference/FgseaList.html
docs/reference/FitDream.html
docs/reference/FitLmer.html
docs/reference/FitLmerContrast.html
docs/reference/GSEABarPlot.html
docs/reference/GSEABubblePlot.html
docs/reference/GetContrastResults.html
docs/reference/GetContrastResultsRaw.html
docs/reference/GetGeneMatrix.html
docs/reference/GetLeadingEdgeFull.html
docs/reference/GetLeadingEdgeGenes.html
docs/reference/GetRankResults.html
docs/reference/GetRankResultsRaw.html
docs/reference/GetTidySummary.html
docs/reference/HeatmapDiag.html
docs/reference/LeadEdgeSampleHeatmap.html
docs/reference/LeadEdgeTidySampleExprs.html
docs/reference/LeadingEdgeIndexed.html
docs/reference/Normalize.html
docs/reference/NormalizePseudobulk.html
docs/reference/PlotFgsea.html
docs/reference/PlotGeneDistCohort.html
docs/reference/PlotHypergeometric.html
docs/reference/PseudobulkList.html
docs/reference/RbindGseaResultList.html
docs/reference/Rplot001.png
docs/reference/RunFgseaOnRankList.html
docs/reference/RunHypergeometricTest.html
docs/reference/RunVoomLimma.html
docs/reference/RunVoomLimma_covar.html
docs/reference/SCMixedPoisson.html
docs/reference/SubjectCelltypeTable.html
docs/reference/TidySampleData.html
docs/reference/WeightedCellModuleScore.html
docs/reference/calc_avg_module_zscore.html
docs/reference/figures/example_sc.png
docs/reference/figures/scglmmr.overview.png
docs/reference/figures/scglmmr_workflow_pb.png
docs/reference/index.html
docs/reference/pipe.html
docs/search.json
docs/sitemap.xml
man/AggregateCellMetadata.Rd
man/AverageSampleModuleZscore.Rd
man/BulkDesignMatrix.Rd
man/CombineResults.Rd
man/EnrichmentJaccard.Rd
man/ExtractResult.Rd
man/FgseaList.Rd
man/FitDream.Rd
man/FitLmer.Rd
man/FitLmerContrast.Rd
man/GSEABarPlot.Rd
man/GSEABubblePlot.Rd
man/GetContrastResults.Rd
man/GetContrastResultsRaw.Rd
man/GetGeneMatrix.Rd
man/GetLeadingEdgeFull.Rd
man/GetLeadingEdgeGenes.Rd
man/GetRankResults.Rd
man/GetRankResultsRaw.Rd
man/GetTidySummary.Rd
man/HeatmapDiag.Rd
man/LeadEdgeSampleHeatmap.Rd
man/LeadEdgeTidySampleExprs.Rd
man/LeadingEdgeIndexed.Rd
man/Normalize.Rd
man/NormalizePseudobulk.Rd
man/PlotFgsea.Rd
man/PlotGeneDistCohort.Rd
man/PlotHypergeometric.Rd
man/PseudobulkList.Rd
man/RbindGseaResultList.Rd
man/RunFgseaOnRankList.Rd
man/RunHypergeometricTest.Rd
man/RunVoomLimma.Rd
man/RunVoomLimma_covar.Rd
man/SCMixedPoisson.Rd
man/SubjectCelltypeTable.Rd
man/TidySampleData.Rd
man/WeightedCellModuleScore.Rd
man/calc_avg_module_zscore.Rd
man/figures/example_sc.png
man/figures/scglmmr.overview.png
man/figures/scglmmr_workflow_pb.png
man/pipe.Rd
scglmmr.Rproj
vignettes/.gitignore
vignettes/networks.Rmd
vignettes/pseudobulk_mixed_effects.md
vignettes/pseudobulk_mixed_effects.rmd
vignettes/scglmmr_singlecell.Rmd
vignettes/scglmmr_singlecell.md
