addBinInfo | Adds new columns to the chromInfo |
addCells | Add cells to an existing cnr |
addGeneInfo | Adds Gene Information to the gene.index |
addInfo | Adds new columns to the chromInfo and gene.index |
add_in_silico_root | build an in-silico root cell and clone profile |
addPheno | Adds additional phenotypes for a new trait |
addQC | addQC |
avg_num_alleles_per_locus | Estimate the estimated number of alleles (copies) per locus |
binary.cnr | build binary CNR from integer copy number data |
binaryDDRC | binaryDDRC |
binary.X | build binary matrix from integer copy number data |
buildCNR | Build a CNR bundle (Copy Number, -Rounded) |
cbioportal_copy_number_states | Copy number call categories from ratio data |
chr_breaks | Estimate chromosome end locations along a continuous genome |
chr_colors | Generate chromosome sidebar colors |
chromInfo | Chromosome coordinates and additional data of the bins |
cluster_heterogeneity | cluster heterogeneity across the sample |
cnr | cnr: copy number, rounded |
cnr_data_type | data type in CNR |
copynumbers | Copy number quantal matrix (copynumbers) |
create_chromosome_annotation | Create chromosome annotations for custom heatmaps |
create_chromosome_annotation_bottom | Create chromosome annotations for custom heatmaps |
create_chromosome_annotation_left | Create chromosome annotations for custom heatmaps |
create_chromosome_annotation_right | Create chromosome annotations for custom heatmaps |
create_chromosome_annotation_top | Create chromosome annotations for custom heatmaps |
dna | dna: a cnr with bulk DNA like copy number data |
doKSpectral | Run Specral K to select optimum and maximum K from Consensus... |
estimate_joint_effects | Wrapper to joint CNA effect estimation using GLMNet |
excludeCells | exclude cells from CNR bundle |
expand2genes | Expands the bins to genes |
export_cnr | export CNR to flat text files |
export_pval_igv | Export the p-values for comparisons of interest to visualize... |
gac | gac |
genotype_vdj | Genotype cells at the VDJ recombination sites |
get_alteration_frequencies | estimate bin and gene alteration frequencies |
get_cluster_profiles | Build a consensus copy number profile for each cluster or... |
grch37.genes.5k | Bin-to-gene index |
HeatmapCNR | HeatmapCNR |
hg19_cytoBand | HG19 cytoband file from UCSC genome browser |
histo_logit | Perform logistic regression for a binary/binarized trait |
histo_logit_cov | perform logistic regression for a binary/binarized trait with... |
keepCells | keep cells from CNR bundle |
list_genes_in_region | finds genes within one chromosome interval |
list_gene_symbols | list out genes |
lookupCN | Lookup copy number data from bins |
mapd | Median absolute pairwise deviance (MAPD) |
mark.genes | Mark genes |
maximum.percentage | Max percent |
mid_chr | Estimate chromosome midpoint locations along a continuous... |
minimum.intersect | Minimum tree.height at the intersect of one-cell and... |
nbins | number of bins |
ncells | number of cells in cnr |
ngenes | number of genes in gene.index |
npheno | number of phenotypes |
optClust | Optimizing clustering for single-cell copy number |
order_bins | order genome bins based on chromosome and starting position |
order_genes | order gene.index based on chromosome and starting coordinate |
parctan | Peter Andrew's arctan transformation for visualizing copy... |
pheno | Single-cell phenotype annotation |
phylo_cnr | Calculating cell-to-cell distances, heirarchical clustering,... |
phylo_ddrc | Calculating clone-to-clone distances, and estimating a... |
plot_ccp | plot consensus clustering |
plotCL | plot cluster optimization |
plot_cn_correlations | plot genome wide correlations |
plot_effect | Genome-wide effects plot |
plot_frequencies | plot genome-wide amplification and deletion frequencies |
plot_lr | Manhattan plot of logistic regression output |
plot_sK | plot kCC vs sK plot kParameter, and stable K from kStats |
proportion_of_polymorphic_loci | proportion of polymorphic alleles as subclonal |
pull_gene_copy_numbers | pull a set of copy numbers from a cnr into a data.frame |
pull_gene_details | Pull gene details for a set of genes |
qc | Quality control annotation |
rank_clones | rank clones |
rle_ddrc | run length encoding to create segment files from DDRC.df |
roundCNR | rounded quantal matrix |
run_consensus_clustering | run consensus clustering |
seg2bins | convert .seg files to match a chromInfo matrix |
setBrayClusters | Set Bray clusters |
setKcc | Set cluster membership for K clusters |
split_cnr | split a cnr by one variable |
subsetCNR | Subset a set of bins or genes from a CNR object |
summary_cnr | summary of cnr bundle |
sync_cnr | sync cnr cells to those in the phenotype annotation |
vdjBrayClust | VDJ cells clustering based on Bray-Curtis Dissimilarity |
vdjHeatmap | Heatmap of cells with VDJ recombination |
vdjPlotClust | plot VDJ clustering |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.