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 | 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 |
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 |
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 | 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 |
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