API for SingerLab/gac
Genetic Analysis of Cells
| Global functions | |
|---|---|
| DepScores | Source code |
| HeatmapCNR | Man page Source code |
| addBinInfo | Man page Source code |
| addCells | Man page Source code |
| addGeneInfo | Man page Source code |
| addInfo | Man page Source code |
| addPheno | Man page Source code |
| addQC | Man page Source code |
| add_in_silico_root | Man page Source code |
| avg_num_alleles_per_locus | Man page Source code |
| binary.X | Man page Source code |
| binary.cnr | Man page Source code |
| binary.mat | Source code |
| binaryDDRC | Man page Source code |
| buildCNR | Man page Source code |
| callX | Source code |
| cbioportal_copy_number_states | Man page Source code |
| cbioportal_states_from_integer_cn | Source code |
| cbioportal_states_from_log2_ratio | Source code |
| chr_breaks | Man page Source code |
| chr_colors | Man page Source code |
| chromInfo | Man page |
| cluster_heterogeneity | Man page Source code |
| cluster_representation | Source code |
| cnr | Man page |
| cnr_data_type | Man page Source code |
| convert_coord | Source code |
| copynumbers | Man page |
| create_chromosome_annotation | Man page Source code |
| create_chromosome_annotation_bottom | Man page Source code |
| create_chromosome_annotation_left | Man page Source code |
| create_chromosome_annotation_right | Man page Source code |
| create_chromosome_annotation_top | Man page Source code |
| depmap_annotate | Source code |
| distCNR | Source code |
| dna | Man page |
| doKSpectral | Man page Source code |
| eps | Source code |
| estimate_joint_effects | Man page Source code |
| estimate_joint_effects_bin | Source code |
| estimate_joint_effects_gene | Source code |
| excludeCells | Man page Source code |
| expand2genes | Man page Source code |
| export_cnr | Man page Source code |
| export_pval_igv | Man page Source code |
| fisher_tree | Source code |
| gac | Man page |
| gac-package | Man page |
| gene.aggregate | Source code |
| genotype_vdj | Man page Source code |
| getSubclonesCNR | Source code |
| get_alt_counts | Source code |
| get_alteration_frequencies | Man page Source code |
| get_amp_counts | Source code |
| get_bin_frequencies_cn | Source code |
| get_cluster_profiles | Man page Source code |
| get_del_counts | Source code |
| get_gene_details | Source code |
| get_gene_frequencies_cn | Source code |
| gisticGR | Source code |
| gisticRegions | Source code |
| grch37.genes.5k | Man page |
| hclustCNR | Source code |
| hg19_cytoBand | Man page |
| histo_logit | Man page Source code |
| histo_logit_bin | Source code |
| histo_logit_bin_cov | Source code |
| histo_logit_cov | Man page Source code |
| histo_logit_gene | Source code |
| histo_logit_gene_cov | Source code |
| kSpectral | Source code |
| keepCells | Man page Source code |
| list_gene_symbols | Man page Source code |
| list_genes_in_region | Man page Source code |
| lookupCN | Man page Source code |
| mapd | Man page Source code |
| mark.genes | Man page Source code |
| maximum.percentage | Man page Source code |
| merge_lineage_tables | Source code |
| mid_chr | Man page Source code |
| minimum.intersect | Man page Source code |
| nbins | Man page Source code |
| ncells | Man page Source code |
| ngenes | Man page Source code |
| npheno | Man page Source code |
| oncoKB_annotate | Source code |
| optClust | Man page Source code |
| order_bins | Man page Source code |
| order_genes | Man page Source code |
| parctan | Man page Source code |
| percent_genome_amplified | Source code |
| percent_genome_gain | Source code |
| percent_genome_loss | Source code |
| pheno | Man page |
| phylo_cnr | Man page Source code |
| phylo_ddrc | Man page Source code |
| plog | Source code |
| plotCL | Man page Source code |
| plot_ccp | Man page Source code |
| plot_cn_correlations | Man page Source code |
| plot_effect | Man page Source code |
| plot_frequencies | Man page Source code |
| plot_lr | Man page Source code |
| plot_sK | Man page Source code |
| proportion_of_polymorphic_loci | Man page Source code |
| pull_gene_copy_numbers | Man page Source code |
| pull_gene_details | Man page Source code |
| qc | Man page |
| rank_clones | Man page Source code |
| rle_ddrc | Man page Source code |
| roundCNR | Man page Source code |
| run_consensus_clustering | Man page Source code |
| scClustCNR | Source code |
| seg2bins | Man page Source code |
| setBrayClusters | Man page Source code |
| setKcc | Man page Source code |
| sim_fisherCNR | Source code |
| sinkhornKnopp | Source code |
| split_cnr | Man page Source code |
| subsetCNR | Man page Source code |
| subset_ci | Source code |
| subset_on_bins | Source code |
| subset_on_chrom | Source code |
| subset_on_coordinates | Source code |
| subset_on_genes | Source code |
| summary_cnr | Man page Source code |
| symmetricSinkhornKnopp | Source code |
| sync_cnr | Man page Source code |
| ternary.cnr | Source code |
| use_clusters | Source code |
| vdjBrayClust | Man page Source code |
| vdjHeatmap | Man page Source code |
| vdjPlotClust | Man page Source code |
