Man pages for hjunwoo/ccfindR
Cancer Clone Finder

basisBasis matrices in an Object
basis-scNMFSet-methodBasis matrix accessor
basis-setGenerics for basis matrix assignment
basis-set-scNMFSet-methodModify basis matrices
build_treeBuild tree connecting clusters at different ranks
cell_mapPlot heatmap of clustering coefficient matrix
cluster_idAssign cells into clusters
coeffCoefficient matrices in an Object
coeff-scNMFSet-methodCoefficient matrix accessor
coeff-setGenerics for coefficient matrix assignment
coeff-set-scNMFSet-methodModify coefficient matrices
colData-scNMFSet-methodCell annotation accessor
colData-set-scNMFSet-ANY-methodCell annotation assignment
counts-scNMFSet-methodAccessor for count matrix
counts-set-scNMFSet-methodAssignment of count matrix
factorizeMaximum likelihood factorization
filter_cellsFilter cells with quality control criteria
filter_genesFilter genes with quality control criteria
gene_mapPlot heatmap of metagene matrix
measureFactorization measures in an Object
measure-scNMFSet-methodRank measure accessor
measure-setGenerics for factorization measure assignment
measure-set-scNMFSet-methodModify factorization measure
meta_genesFind metagenes from basis matrix
normalize_countNormalize count data
plot_genesPlot gene variance distributions
plot_treePlot cluster tree
ranksRank values in an Object
ranks-scNMFSet-methodRank accessor
ranks-setGenerics for ranks assignment
ranks-set-scNMFSet-methodModify ranks
read_10xRead 10x data and generate scNMF object
remove_zerosRemove rows or columns that are empty from an object
rename_tipsRename tips of trees with cell types
rowData-scNMFSet-methodGene annotation accessor
rowData-set-scNMFSet-methodGene annotation assignment
scNMFSetCreate 'scNMFSet' object
scNMFSet-classClass 'scNMFSet' for storing input data and results
show-scNMFSet-methodDisplay object
simulate_dataGenerate simulated data for factorization
simulate_whxSimulate factor matrices and data using priors
subset-methodsSubsetting scNMFSet object
vb_factorizeBayesian NMF inference of count matrix
visualize_clustersVisualize clusters
write_10xWrite 10x data files
hjunwoo/ccfindR documentation built on April 14, 2018, 3:02 a.m.