Files in jasonserviss/CIMseq
CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

.Rbuildignore
.gitignore
.travis.yml
CIMseq.Rproj
DESCRIPTION
NAMESPACE
NEWS
R/All-classes.R R/CIMseq-package.R R/CIMseqData.R R/CIMseqSwarm.R R/RcppExports.R R/debugging.R R/initialize-methods.R R/plotCounts.R R/plotExtras.R R/plotSwarm.R R/show-methods.R R/testData.R R/tidyFunctions.R R/utlis.R README.Rmd README.md
codecov.yml
data/testCounts.rda
data/testData.rda
data/testMeta.rda
inst/containers/Dockerfile
inst/containers/Singularity
inst/include/CIMseq.h
inst/rawData/testCounts.R inst/rawData/testData.R inst/simplifyPkg.R man/CIMseq-package.Rd man/CIMseqMultiplets.Rd man/CIMseqMultiplets_test.Rd man/CIMseqSinglets.Rd man/CIMseqSinglets_test.Rd man/CIMseqSwarm.Rd man/CIMseqSwarm_test.Rd man/adjustAccordingToFractions.Rd man/adjustFractions.Rd man/appropriateSinglets.Rd man/calcResiduals.Rd man/calculateCost.Rd man/calculateCostDensity.Rd man/calculateCosts.Rd man/calculateEdgeStats.Rd man/calculateLogRowMeans.Rd man/cellNumberPerClass.Rd man/classify_louvain.Rd man/col40.Rd man/coloursFromTargets.Rd man/constructGraph.Rd man/convertToERCC.Rd man/cost.Rd man/costCalc.Rd man/costNegSum.Rd man/countsPerClass.Rd man/divide_by.Rd man/draw_legend.Rd man/erccPerClass.Rd man/estimateCells.Rd man/estimateTotalConnections.Rd man/expectedInteractionFreq.Rd man/fixNegInf.Rd man/g_legend.Rd man/getCellsForMultiplet.Rd man/getEdgesForMultiplet.Rd man/getKNN.Rd man/getMultipletsForEdge.Rd man/gg-class.Rd man/jaccardSimilarity.Rd man/longFormConnections.Rd man/matrix_to_tibble.Rd man/means.dim.red.Rd man/multipletSums.Rd man/multiply_by.Rd man/namedListToTibble.Rd man/normalizeFractions.Rd man/normalizeVec.Rd man/pcByVarPercent.Rd man/pearsonsDist.Rd man/plotCountsData.Rd man/plotCountsERCC.Rd man/plotCountsMarkers.Rd man/plotData.Rd man/plotSwarmBarBase.Rd man/plotSwarmCircos.Rd man/plotSwarmEdgeBar.Rd man/plotSwarmGenes.Rd man/plotSwarmGraph.Rd man/plotSwarmHeat.Rd man/plotSwarmPbar.Rd man/plotSwarmPosition.Rd man/plotUnsupervisedClass.Rd man/plotUnsupervisedMarkers.Rd man/processMarkers.Rd man/removeOutliers.Rd man/runPCA.Rd man/runTsne.Rd man/sampleSinglets.Rd man/selectTopMax.Rd man/selectTopVar.Rd man/subsetSinglets.Rd man/testCounts.Rd man/testMeta.Rd man/tidySinglets.Rd man/tidySwarm.Rd man/vecToMat.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/calculateCost.cpp
tests/testthat.R tests/testthat/test_All-classes.R tests/testthat/test_data.R tests/testthat/test_plotCounts.R tests/testthat/test_plotExtras.R tests/testthat/test_plotSwarm.R tests/testthat/test_showMethods.R tests/testthat/test_swarm.R tests/testthat/test_tidyFunctions.R vignettes/CIMseq-plotting.Rmd vignettes/CIMseq-vignette.Rmd
jasonserviss/CIMseq documentation built on May 8, 2019, 9:55 p.m.