Man pages for EngeLab/CIMseq
CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method
| adjustAccordingToFractions | adjustAccordingToFractions |
| adjustFractions | adjustFractions |
| appropriateSinglets | appropriateSinglets |
| calcResiduals | calcResiduals |
| calculateCost | calculateCost |
| calculateCostDensity | calculateCostDensity |
| calculateCosts | calculateCosts |
| calculateEdgeStats | calculateEdgeStats |
| calculateLogRowMeans | calculateLogRowMeans |
| cellNumberPerClass | cellNumberPerClass |
| CIMseqConnections | CIMseqConnections |
| CIMseqMultiplets | CIMseqMultiplets |
| CIMseqMultiplets_test | CIMseqMultiplets object corresponding to test dataset. |
| CIMseq-package | A package for analyzing tissue spatiality in scRNAseq data. |
| CIMseqSinglets | CIMseqSinglets |
| CIMseqSinglets_test | CIMseqSinglets object corresponding to test dataset. |
| CIMseqSwarm | CIMseqSwarm |
| CIMseqSwarm_test | CIMseqSwarm object corresponding to test dataset. |
| classify_louvain | classify_louvain |
| col40 | col40 |
| coloursFromTargets | coloursFromTargets |
| constructGraph | constructGraph |
| convertToERCC | convertToERCC |
| cost | cost |
| costCalc | costCalc |
| costNegSum | costNegSum |
| countsPerClass | countsPerClass |
| divide_by | divide_by |
| draw_legend | draw_legend |
| erccPerClass | erccPerClass |
| estimateCells | estimateCells |
| estimateTotalConnections | estimateTotalConnections |
| expectedInteractionFreq | expectedInteractionFreq |
| fixNegInf | fixNegInf |
| getCellsForMultiplet | getCellsForMultiplet |
| getEdgesForMultiplet | getEdgesForMultiplet |
| getKNN | getKNN |
| getMultipletsForEdge | getMultipletsForEdge |
| gg-class | "gg" class |
| g_legend | g_legend |
| jaccardSimilarity | jaccardSimilarity |
| longFormConnections | longFormConnections |
| matrix_to_tibble | matrix_to_tibble |
| means.dim.red | means.dim.red |
| multipletSums | multipletSums |
| multiply_by | multiply_by |
| namedListToTibble | namedListToTibble |
| normalizeFractions | normalizeFractions |
| normalizeVec | normalizeVec |
| pcByVarPercent | pcByVarPercent |
| pearsonsDist | pearsonsDist |
| plotConnectionCircos | plotConnectionCircos |
| plotCountsData | plotCountsData |
| plotCountsERCC | plotCountsERCC |
| plotCountsMarkers | plotCountsMarkers |
| plotData | plotData |
| plotSwarmBarBase | plotSwarmBarBase |
| plotSwarmCircos | plotSwarmCircos |
| plotSwarmCircos2 | plotSwarmCircos2 |
| plotSwarmEdgeBar | plotSwarmEdgeBar |
| plotSwarmGenes | plotSwarmGenes |
| plotSwarmGraph | plotSwarmGraph |
| plotSwarmHeat | plotSwarmHeat |
| plotSwarmPbar | plotSwarmPbar |
| plotSwarmPosition | plotSwarmPosition |
| plotUnsupervisedClass | plotUnsupervisedClass |
| plotUnsupervisedMarkers | plotUnsupervisedMarkers |
| processMarkers | processMarkers |
| removeOutliers | removeOutliers |
| runPCA | runPCA |
| runTsne | runTsne |
| sampleSinglets | sampleSinglets |
| selectTopMax | selectTopMax |
| selectTopVar | selectTopVar |
| subsetSinglets | subsetSinglets |
| testCounts | Counts data used to demonstrate CIMseq package. |
| testMeta | Meta data for the testCounts dataset. |
| tidySinglets | tidySinglets |
| tidySwarm | tidySwarm |
| vecToMat | vecToMat |
