Man pages for hjunwoo/ccfindR
Cancer Clone Finder

assignCelltypeCell type assignment via GSEA
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
ccfindRccfindR: Cancer Clone FindeR
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-methodSample annotation accessor
colData-set-scNMFSet-ANY-methodCell annotation assignment
counts-scNMFSet-methodAccessor for count matrix
counts-set-scNMFSet-methodAssignment of count matrix
dbasisBasis SD matrix accessor
dbasis-scNMFSet-methodBasis SD matrix accessor
dbasis-setBasis SD matrix assignment
dbasis-set-scNMFSet-methodModify dbasis matrices
dcoeffCoeff SD matrix accessor
dcoeff-scNMFSet-methodCoeffcient SD matrix accessor
dcoeff-setCoeff SD matrix assignment
dcoeff-set-scNMFSet-methodModify dcoeff matrices
factorizeMaximum likelihood factorization
feature_mapPlot heatmap of basis matrix
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_gene.cvMeta gene table with CV
meta_genesFind metagenes from basis matrix
newickGenerate Newick format tree string from tree list object
normalize_countNormalize count data
optimal_rankDetermine optimal rank
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-methodFeature 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
write_metaWrite meta genes to a file
hjunwoo/ccfindR documentation built on Oct. 4, 2019, 10:31 a.m.