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/ampCol.R R/binary.cnr.R R/buildCNR.R R/callCN.R R/ccClustCol.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_chromAnno.R R/depmap_annotate.R R/distCNR.R R/dna.R R/doKSpectral.R R/excludeCells.R R/expand2genes.R R/exportCNR.R R/fgaCol.R R/gac.R R/gene.aggregate.R R/gene.index.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/hg19_cytoBand.R R/kSpectral.R R/keepCells.R R/legAmp.R R/legFGA.R R/legLog2R.R R/legPloidy.R R/legSeg.R R/logistic_reg_histology.R R/lookupCN.R R/lowCol.R R/mapd.R R/mark.genes.R R/merge_lineage_tables.R R/oncoKB_annotate.R R/optClust.R R/parctan.R R/pheno.R R/phyloCNR.R R/ploidyCol.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/segCol.R R/setClusters.R R/subsetCNR.R R/summaryCNR.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/ampCol.rda
data/ccClustCol.rda
data/chromInfo.rda
data/cnr.rda
data/copynumbers.rda
data/datalist
data/dna.rda
data/fgaCol.rda
data/gene.index.rda
data/hg19_cytoBand.rda
data/legAmp.rda
data/legFGA.rda
data/legLog2R.rda
data/legPloidy.rda
data/legSeg.rda
data/lowCol.rda
data/pheno.rda
data/ploidyCol.rda
data/qc.rda
data/segCol.rda
figures/CNR.png
figures/ComplexHeatmap.png
figures/la_pase_de_marseille.png
inst/extdata/.keep
man/HeatmapCNR.Rd man/addCells.Rd man/addInfo.Rd man/addPheno.Rd man/addQC.Rd man/ampCol.Rd man/avg_num_alleles_per_locus.Rd man/binary.X.Rd man/binary.cnr.Rd man/binaryDDRC.Rd man/buildCNR.Rd man/callCN.Rd man/callDNA_CN.Rd man/ccClustCol.Rd man/chromInfo.Rd man/cluster_heterogeneity.Rd man/cnr.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/exportCNR.Rd man/export_pval_igv.Rd man/fgaCol.Rd
man/figures/README-example-1.png
man/figures/README-example-2.png
man/find_genes.Rd man/gac.Rd man/gene.index.Rd man/genotype_vdj.Rd man/get_alteration_frequencies.Rd man/get_cluster_profiles.Rd man/hg19_cytoBand.Rd man/histo_logit.Rd man/histo_logit_cov.Rd man/keepCells.Rd man/legAmp.Rd man/legFGA.Rd man/legLog2R.Rd man/legPloidy.Rd man/legSeg.Rd man/list_genes.Rd man/lookupCN.Rd man/lowCol.Rd man/mapd.Rd man/mark.genes.Rd man/minimum.intersect.Rd man/nbins.Rd man/ncells.Rd man/ngenes.Rd man/npheno.Rd man/optClust.Rd man/parctan.Rd man/pheno.Rd man/phyloCNR.Rd man/phyloDDRC.Rd man/ploidyCol.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/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/segCol.Rd man/setBrayClusters.Rd man/setKcc.Rd man/subsetCNR.Rd man/summaryCNR.Rd man/vdjBrayClust.Rd man/vdjHeatmap.Rd man/vdjPlotClust.Rd tests/testthat.R
vignettes/R
vignettes/data
vignettes/getting_started.Rmd
vignettes/getting_started.html
vignettes/inst
vignettes/tests
SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.