Files in SingerLab/gac
Genetic Analysis of Cells
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/DepScores.R
R/HeatmapCNR.R
R/addCells.R
R/addInfo.R
R/addPheno.R
R/addQC.R
R/add_in_silico_root.R
R/binary.cnr.R
R/buildCNR.R
R/cbioportal_copy_number_states.R
R/chromInfo.R
R/cluster_heterogeneity.R
R/cnr.R
R/consensus_nds.R
R/convert_seg_to_bins.R
R/copynumbers.R
R/create_chromosome_annotations.R
R/depmap_annotate.R
R/dna.R
R/doKSpectral.R
R/excludeCells.R
R/expand2genes.R
R/exportCNR.R
R/gac.R
R/gene.aggregate.R
R/gene_lookups.R
R/genetic_diversity.R
R/genotype_vdj.R
R/get_cluster_profiles.R
R/get_frequencies.R
R/gisticGR.R
R/gisticRegions.R
R/grch37.genes.5k.R
R/hg19_cytoBand.R
R/kSpectral.R
R/keepCells.R
R/logistic_reg_histology.R
R/lookupCN.R
R/mapd.R
R/mark.genes.R
R/merge_lineage_tables.R
R/oncoKB_annotate.R
R/parctan.R
R/pheno.R
R/phylo_cnr.R
R/plotCL.R
R/plot_ccp.R
R/plot_cn_correlations.R
R/plot_frequencies.R
R/pull_gene_copy_numbers.R
R/qc.R
R/roundCNR.R
R/run_consensus_clustering.R
R/scClustCNR.R
R/setClusters.R
R/split_cnr.R
R/subsetCNR.R
R/summary_cnr.R
R/sync_cnr.R
R/ternary.cnr.R
R/vdjBrayClust.R
R/vdjHeatmap.R
README.Rmd
README.md
TODO.md
cran-comments.md
data-raw/DATASET.R
data/chromInfo.rda
data/cnr.rda
data/copynumbers.rda
data/datalist
data/dna.rda
data/grch37.genes.5k.rda
data/hg19_cytoBand.rda
data/pheno.rda
data/qc.rda
figures/CNR.png
figures/ComplexHeatmap.png
figures/la_pase_de_marseille.png
inst/extdata/.keep
man/HeatmapCNR.Rd
man/addBinInfo.Rd
man/addCells.Rd
man/addGeneInfo.Rd
man/addInfo.Rd
man/addPheno.Rd
man/addQC.Rd
man/add_in_silico_root.Rd
man/avg_num_alleles_per_locus.Rd
man/binary.X.Rd
man/binary.cnr.Rd
man/binaryDDRC.Rd
man/buildCNR.Rd
man/cbioportal_copy_number_states.Rd
man/chr_breaks.Rd
man/chr_colors.Rd
man/chromInfo.Rd
man/cluster_heterogeneity.Rd
man/cnr.Rd
man/cnr_data_type.Rd
man/copynumbers.Rd
man/create_chromosome_annotation.Rd
man/create_chromosome_annotation_bottom.Rd
man/create_chromosome_annotation_left.Rd
man/create_chromosome_annotation_right.Rd
man/create_chromosome_annotation_top.Rd
man/dna.Rd
man/doKSpectral.Rd
man/estimate_joint_effects.Rd
man/excludeCells.Rd
man/expand2genes.Rd
man/export_cnr.Rd
man/export_pval_igv.Rd
man/figures/README-example-1.png
man/figures/README-example-2.png
man/gac.Rd
man/genotype_vdj.Rd
man/get_alteration_frequencies.Rd
man/get_cluster_profiles.Rd
man/grch37.genes.5k.Rd
man/hg19_cytoBand.Rd
man/histo_logit.Rd
man/histo_logit_cov.Rd
man/keepCells.Rd
man/list_gene_symbols.Rd
man/list_genes_in_region.Rd
man/lookupCN.Rd
man/mapd.Rd
man/mark.genes.Rd
man/maximum.percentage.Rd
man/mid_chr.Rd
man/minimum.intersect.Rd
man/nbins.Rd
man/ncells.Rd
man/ngenes.Rd
man/npheno.Rd
man/optClust.Rd
man/order_bins.Rd
man/order_genes.Rd
man/parctan.Rd
man/pheno.Rd
man/phylo_cnr.Rd
man/phylo_ddrc.Rd
man/plotCL.Rd
man/plot_ccp.Rd
man/plot_cn_correlations.Rd
man/plot_effect.Rd
man/plot_frequencies.Rd
man/plot_lr.Rd
man/plot_sK.Rd
man/proportion_of_polymorphic_loci.Rd
man/pull_gene_copy_numbers.Rd
man/pull_gene_details.Rd
man/qc.Rd
man/rank_clones.Rd
man/rle_ddrc.Rd
man/roundCNR.Rd
man/run_consensus_clustering.Rd
man/seg2bins.Rd
man/setBrayClusters.Rd
man/setKcc.Rd
man/split_cnr.Rd
man/subsetCNR.Rd
man/summary_cnr.Rd
man/sync_cnr.Rd
man/vdjBrayClust.Rd
man/vdjHeatmap.Rd
man/vdjPlotClust.Rd
tests/testthat.R
vignettes/R
vignettes/data
vignettes/getting_started.Rmd
vignettes/inst
vignettes/tests
