Files in MarioniLab/scran

Methods for Single-Cell RNA-Seq Data Analysis

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/DM.R R/RcppExports.R R/buildSNNGraph.R R/clusterCells.R R/combineBlocks.R R/combineMarkers.R R/combinePValues.R R/combineVar.R R/computeMinRank.R R/computeSumFactors.R R/convertTo.R R/correlateGenes.R R/correlateNull.R R/correlatePairs.R R/cyclone.R R/decideTestsPerLabel.R R/defunct.R R/denoisePCA.R R/expandPairings.R R/findMarkers.R R/fitTrendCV2.R R/fitTrendPoisson.R R/fitTrendVar.R R/fixedPCA.R R/getClusteredPCs.R R/getMarkerEffects.R R/getTopHVGs.R R/getTopMarkers.R R/modelGeneCV2.R R/modelGeneCV2WithSpikes.R R/modelGeneVar.R R/modelGeneVarByPoisson.R R/modelGeneVarWithSpikes.R R/multiMarkerStats.R R/namespace.R R/pairwiseBinom.R R/pairwiseTTests.R R/pairwiseWilcox.R R/pseudoBulkDGE.R R/pseudoBulkSpecific.R R/quickCluster.R R/quickSubCluster.R R/rhoToPValue.R R/sandbag.R R/scaledColRanks.R R/scoreMarkers.R R/summaryMarkerStats.R R/testLinearModel.R R/utils_markers.R R/utils_parallel.R R/utils_pca.R R/utils_tricube.R R/utils_variance.R

inst/CITATION

inst/NEWS.Rd

inst/exdata/generate_markers.R

inst/exdata/human_cycle_markers.rds

inst/exdata/mouse_cycle_markers.rds

man/DM.Rd man/buildSNNGraph.Rd man/clusterCells.Rd man/combineBlocks.Rd man/combineMarkers.Rd man/combinePValues.Rd man/combineVar.Rd man/computeMinRank.Rd man/computeSumFactors.Rd man/convertTo.Rd man/correlateGenes.Rd man/correlateNull.Rd man/correlatePairs.Rd man/cyclone.Rd man/decideTestsPerLabel.Rd man/defunct.Rd man/denoisePCA.Rd man/findMarkers.Rd man/fitTrendCV2.Rd man/fitTrendPoisson.Rd man/fitTrendVar.Rd man/fixedPCA.Rd man/gene_selection.Rd man/getClusteredPCs.Rd man/getMarkerEffects.Rd man/getTopHVGs.Rd man/getTopMarkers.Rd man/logBH.Rd man/modelGeneCV2.Rd man/modelGeneCV2WithSpikes.Rd man/modelGeneVar.Rd man/modelGeneVarByPoisson.Rd man/modelGeneVarWithSpikes.Rd man/multiMarkerStats.Rd man/pairwiseBinom.Rd man/pairwiseTTests.Rd man/pairwiseWilcox.Rd man/pseudoBulkDGE.Rd man/pseudoBulkSpecific.Rd man/quickCluster.Rd man/quickSubCluster.Rd man/rhoToPValue.Rd man/sandbag.Rd man/scaledColRanks.Rd man/scoreMarkers.Rd man/summaryMarkerStats.Rd man/testLinearModel.Rd

src/Makevars

src/RcppExports.cpp

src/choose_effect_size.cpp

src/combine_rho.cpp

src/compute_blocked_stats.cpp

src/compute_residual_stats.cpp

src/compute_rho_null.cpp

src/cyclone_scores.cpp

src/overlap_exprs.cpp

src/rand_custom.cpp

src/rand_custom.h

src/utils.h

tests/testthat.R tests/testthat/setup.R tests/testthat/test-altrep.R tests/testthat/test-build-snn.R tests/testthat/test-colranks.R tests/testthat/test-combine-markers.R tests/testthat/test-combine-p.R tests/testthat/test-combine-var.R tests/testthat/test-convert.R tests/testthat/test-correlate-genes.R tests/testthat/test-correlate-pairs.R tests/testthat/test-cyclone.R tests/testthat/test-denoise-pca.R tests/testthat/test-expand-pairings.R tests/testthat/test-fixed-pca.R tests/testthat/test-linear-test.R tests/testthat/test-markers.R tests/testthat/test-model-cv2.R tests/testthat/test-model-var.R tests/testthat/test-multi-markers.R tests/testthat/test-pairwise-binom.R tests/testthat/test-pairwise-t.R tests/testthat/test-pairwise-wilcox.R tests/testthat/test-pseudo-dge.R tests/testthat/test-pseudo-spec.R tests/testthat/test-quickclust.R tests/testthat/test-sandbag.R tests/testthat/test-score-markers.R tests/testthat/test-subclust.R tests/testthat/test-top-hvgs.R tests/testthat/test-trend-cv2.R tests/testthat/test-trend-var.R

vignettes/ref.bib

vignettes/scran.Rmd

MarioniLab/scran documentation built on March 7, 2024, 1:45 p.m.