Files in EngeLab/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/CIMseqConnections.R
R/CIMseqConnections.R~
R/CIMseqData.R
R/CIMseqSwarm.R
R/RcppExports.R
R/circos_arbitrary.R~
R/debugging.R
R/initialize-methods.R
R/plotCounts.R
R/plotExtras.R
R/plotSwarm.R
R/plotSwarm.R~
R/plotSwarm.txt
R/show-methods.R
R/testData.R
R/test_dup_trip.R~
R/test_self_connections.R~
R/tidyFunctions.R
R/utlis.R
README.Rmd
README.md
codecov.yml
data/SmallIntest.marker.genes.rda
data/SmallIntest.multiplets.counts.rda
data/SmallIntest.singlets.classes.rda
data/SmallIntest.singlets.counts.rda
data/sObj.si.rda
data/testCounts.rda
data/testData.rda
data/testMeta.rda
doc/CIMseq-droplet.R
doc/CIMseq-droplet.Rmd
doc/CIMseq-droplet.html
doc/CIMseq-plotting.R
doc/CIMseq-plotting.Rmd
doc/CIMseq-plotting.html
doc/CIMseq-vignette.R
doc/CIMseq-vignette.Rmd
doc/CIMseq-vignette.html
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/CIMseqConnections.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/plotConnectionCircos.Rd
man/plotCountsData.Rd
man/plotCountsERCC.Rd
man/plotCountsMarkers.Rd
man/plotData.Rd
man/plotSwarmBarBase.Rd
man/plotSwarmCircos.Rd
man/plotSwarmCircos2.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
tmp/circos_arbitrary.R
tmp/test_dup_trip.R
tmp/test_self_connections.R
vignettes/CIMseq-droplet.Rmd
vignettes/CIMseq-plotting.Rmd
vignettes/CIMseq-vignette.Rmd
