API for monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Global functions
BEAM Man page Source code
CellDataSet Man page
CellDataSet,ANY,ANY-method Man page Man page Man page Man page
CellDataSet-class Man page
CellDataSet-methods Man page
CellType Man page
CellType-class Man page
CellTypeHierarchy Man page
CellTypeHierarchy-class Man page
`cellPairwiseDistances<-` Source code
`minSpanningTree<-` Source code
`reducedDimA<-` Source code
`reducedDimK<-` Source code
`reducedDimS<-` Source code
`reducedDimW<-` Source code
addCellType Man page Source code
branchTest Man page Source code
buildBranchCellDataSet Man page Source code
calABCs Man page Source code
calILRs Man page
calculateMarkerSpecificity Man page Source code
calculate_NB_dispersion_hint Source code
calculate_QP_dispersion_hint Source code
calibrate_per_cell_total_proposal Man page Source code
cellPairwiseDistances Man page Source code
cellPairwiseDistances<- Man page
checkSizeFactors Source code
classifyCells Man page Source code
classifyCellsHelperCds Source code
classifyCellsHelperCell Source code
clusterCells Man page Source code
clusterGenes Man page Source code
compareModels Man page Source code
cth_classifier_cds Source code
cth_classifier_cell Source code
detectBifurcationPoint Man page Source code
detectGenes Man page Source code
diff_test_helper Man page Source code
differentialGeneTest Man page Source code
disp_calc_helper_NB Source code
dispersionTable Man page Source code
dmode Source code
estimateDispersions,CellDataSet-method Man page
estimateDispersionsForCellDataSet Man page Source code
estimateSizeFactors,CellDataSet-method Man page
estimateSizeFactorsForDenseMatrix Source code
estimateSizeFactorsForMatrix Man page Source code
estimateSizeFactorsForSparseMatrix Source code
estimate_t Man page Source code
exportCDS Man page Source code
extract_good_branched_ordering Man page
fitModel Man page Source code
fit_model_helper Man page Source code
genSmoothCurveResiduals Man page Source code
genSmoothCurves Man page Source code
get_classic_muscle_markers Man page Source code
importCDS Man page Source code
isSparseMatrix Source code
jaccard_coeff Source code
load_HSMM Man page Source code
load_HSMM_markers Man page Source code
load_lung Man page Source code
makeprobs Source code
makeprobsvec Source code
markerDiffTable Man page
mcesApply Man page Source code
minSpanningTree Man page Source code
minSpanningTree<- Man page
monocle_theme_opts Source code
newCellDataSet Man page Source code
newCellTypeHierarchy Man page Source code
norm_kb Source code
opt_norm_kb Source code
opt_norm_t Source code
orderCells Man page
order_p_node Man page
parametricDispersionFit Source code
plot_cell_clusters Man page
plot_cell_trajectory Man page Source code
plot_clusters Man page
plot_coexpression_matrix Man page
plot_complex_cell_trajectory Man page
plot_genes_branched_heatmap Man page
plot_genes_branched_pseudotime Man page
plot_genes_in_pseudotime Man page
plot_genes_jitter Man page
plot_genes_positive_cells Man page
plot_genes_violin Man page
plot_multiple_branches_heatmap Man page
plot_multiple_branches_pseudotime Man page
plot_ordering_genes Man page
plot_pc_variance_explained Man page
plot_pseudotime_heatmap Man page
plot_rho_delta Man page
plot_spanning_tree Man page
pq_helper Man page
reduceDimension Man page
reducedDimA Man page Source code
reducedDimA<- Man page
reducedDimK Man page Source code
reducedDimK<- Man page
reducedDimS Man page Source code
reducedDimS<- Man page
reducedDimW Man page Source code
reducedDimW<- Man page
relative2abs Man page Source code
residualMatrix Man page Source code
responseMatrix Man page Source code
run_pca Source code
scale_pseudotime Source code
selectTopMarkers Man page Source code
setOrderingFilter Man page
shannon.entropy Source code
sizeFactors,CellDataSet-method Man page
sizeFactors<-,CellDataSet,numeric-method Man page
smartEsApply Source code
sparseApply Source code
spike_df Man page
vstExprs Man page Source code
monocle documentation built on Oct. 31, 2019, 2:19 a.m.