API for cole-trapnell-lab/monocle-release
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
JSdistVec Source code
SubSet_cds Source code
addCellType Man page Source code
asSlamMatrix Source code
asSparseMatrix Source code
assign_cell_lineage Source code
branchTest Man page Source code
buildBranchCellDataSet Man page Source code
calABCs Man page Source code
calILRs Man page Source code
cal_ncenter Source code
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
count_leaf_descendents 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_ddrtree_ordering Source code
extract_good_branched_ordering Man page Source code
extract_good_ordering Source code
findNearestPointOnMST Source code
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
get_next_node_id Source code
ica_helper Source code
importCDS Man page Source code
isSparseMatrix Source code
load_HSMM Man page Source code
load_HSMM_markers Man page Source code
load_lung Man page Source code
make_canonical Source code
makeprobs Source code
makeprobsvec Source code
markerDiffTable Man page Source code
matlab.like Source code
matlab.like2 Source code
mcesApply Man page Source code
measure_diameter_path 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
normalize_expr_data Source code
opt_norm_kb Source code
opt_norm_t Source code
orderCells Man page Source code
order_p_node Man page Source code
order_q_node Source code
parametricDispersionFit Source code
plot_cell_clusters Man page Source code
plot_cell_trajectory Man page Source code
plot_clusters Man page Source code
plot_coexpression_matrix Man page Source code
plot_complex_cell_trajectory Man page Source code
plot_genes_branched_heatmap Man page Source code
plot_genes_branched_pseudotime Man page Source code
plot_genes_heatmap Source code
plot_genes_in_pseudotime Man page Source code
plot_genes_jitter Man page Source code
plot_genes_positive_cells Man page Source code
plot_genes_violin Man page Source code
plot_multiple_branches_heatmap Man page Source code
plot_multiple_branches_pseudotime Man page Source code
plot_ordering_genes Man page Source code
plot_pc_variance_explained Man page Source code
plot_pseudotime_heatmap Man page Source code
plot_rho_delta Man page Source code
plot_spanning_tree Man page Source code
pq_helper Man page Source code
projPointOnLine Source code
project2MST Source code
project_point_to_line_segment Source code
reduceDimension Man page Source code
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
reverseEmbeddingCDS Source code
reverse_ordering Source code
rgb.tables Source code
run_pca Source code
scale_pseudotime Source code
selectNegentropyGenes Man page Source code
selectTopMarkers Man page Source code
select_root_cell Source code
setOrderingFilter Man page Source code
shannon.entropy Source code
sizeFactors,CellDataSet-method Man page
sizeFactors<-,CellDataSet,numeric-method Man page
smartEsApply Source code
sparseApply Source code
sparseParCApply Source code
sparseParRApply Source code
spike_df Man page
splitCols Source code
splitRows Source code
table.ramp Source code
traverseTree Source code Source code
traverseTreeCDS Source code
vstExprs Man page Source code
weight_of_ordering Source code
cole-trapnell-lab/monocle-release documentation built on Nov. 21, 2017, 6:49 a.m.