API for SingerLab/gac
Genetic Analysis of Cells

Global functions
DepScores Source code
HeatmapCNR Man page Source code
addCells Man page Source code
addInfo Man page Source code
addPheno Man page Source code
addQC Man page Source code
ampCol Man page
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
callCN Man page Source code
callDNA_CN Man page Source code
ccClustCol Man page
chromInfo Man page
cluster_heterogeneity Man page Source code
cluster_representation Source code
cnr Man page
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
exportCNR Man page Source code
export_pval_igv Man page Source code
fgaCol Man page
find_genes Man page Source code
fisher_tree Source code
gac Man page
gene.aggregate Source code
gene.index Man page
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 Source code
get_cluster_profiles Man page Source code
get_del_counts Source code
get_gene_details Source code
get_gene_frequencies Source code
gisticGR Source code
gisticRegions Source code
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
legAmp Man page
legFGA Man page
legLog2R Man page
legPloidy Man page
legSeg Man page
list_genes Man page Source code
lookupCN Man page Source code
lowCol Man page
mapd Man page Source code
mark.genes Man page Source code
merge_lineage_tables 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
parctan Man page Source code
percent_genome_amplified Source code
percent_genome_gain Source code
percent_genome_loss Source code
pheno Man page
phyloCNR Man page Source code
phyloDDRC Man page Source code
plog Source code
ploidyCol Man page
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
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
segCol Man page
setBrayClusters Man page Source code
setKcc Man page Source code
sim_fisherCNR Source code
sinkhornKnopp 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
summaryCNR Man page Source code
symmetricSinkhornKnopp 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
SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.