├── 10X_cross_validation.cfg ├── CONICS.cfg ├── CONICSmat ├── CONICSmat.Rproj ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── AutoReceiveData.R │ ├── BinarizeMatrix.R │ ├── GetPositions.R │ ├── InferBreakpoints.R │ ├── Preprocess.R │ ├── Tsne.R │ └── VisualizePosterior.R ├── data │ └── ensembl_genes_human.RData └── man │ ├── BIC.mix.Rd │ ├── binarizeCalls.Rd │ ├── binarizeMatrix.Rd │ ├── calcNormFactors.Rd │ ├── calcPvalue.Rd │ ├── calculateTsne.Rd │ ├── detectBreakPoints.Rd │ ├── detectVarGenes.Rd │ ├── filterMatrix.Rd │ ├── generatePvalMat.Rd │ ├── getGenePositions.Rd │ ├── likelihoodRatioTest.Rd │ ├── loadPublicData.Rd │ ├── normMat.Rd │ ├── plotAll.Rd │ ├── plotAllChromosomes.Rd │ ├── plotBinaryMat.Rd │ ├── plotChrEnichment.Rd │ ├── plotChromosomeHeatmap.Rd │ ├── plotHistogram.Rd │ ├── plotTsneGene.Rd │ ├── plotTsneProbabilities.Rd │ └── removeLogScale.Rd ├── CompareExomeSeq_vs_ScRNAseq.cfg ├── CorrelationNetwork.cfg ├── Empirical_validation.cfg ├── README.md ├── SF10281c.cnv.merged_gt1500000_20percent.bed ├── Tree.cfg ├── backend ├── CalculateCoverageMatrix.py ├── CalculateCoverageMatrix_10X.py ├── CalculateCoverageMatrix_empirical.py ├── CompareExomeSeq_vs_ScRNAseq.R ├── CorrelationNetwork.R ├── FilterSNVsFromVCF.py ├── MkBedFromSequenza.pl ├── mk_10_random_sample.pl ├── plotVAFs.R ├── plotVAFs.r ├── plot_Boxplot.R ├── plot_Tree.R ├── plot_bean_CPM.R ├── plot_bean_CPM_validation.R ├── process_10x_crossVal_result.pl ├── process_empirical_Val_result.pl └── summarizeSNVs.py ├── chromosome_arm_positions_grch38.txt ├── chromosome_full_positions_grch38.txt ├── chromosome_full_positions_mm10.txt ├── images ├── 10X_boxplot.jpg ├── 1p.jpg ├── 1p_res.jpg ├── 1p_result.jpg ├── 1q.jpg ├── BCH869.jpg ├── BCH869.png ├── BT_S2genotypes_awesome.png ├── BT_S2genotypes_awesome_marked.jpg ├── BT_S4clusterplot.png ├── CONICS_chromosome_maps.jpg ├── Compare_200.jpg ├── Darmanis.png ├── Empirical_boxplot.jpg ├── MGH97.jpg ├── PTEN_topCorr.jpg ├── Phyngle_dendrogram.jpg ├── Phyngle_violin.jpg ├── Trees_cluster.jpg ├── Tutorial1_CNVs.pdf ├── adj_p_distr.jpg ├── breakpoints.jpg ├── chr7_darmanis.png ├── chr_1p_with_assignment.jpg ├── conics_overview.jpg ├── heatmap_all.jpg ├── heatmap_filtered.jpg ├── heatmap_sf10345.jpg ├── heatmap_sf10345.pdf ├── log_likelihood.jpg ├── tsne_chr1q.jpg ├── tsne_darmanis.png └── tsne_genes.jpg ├── run_10X_cross_validation.sh ├── run_BAf_analysis.sh ├── run_CONICS.sh ├── run_CorrelationNetwork.sh ├── run_Tree.sh ├── run_compareExomeSeq_vs_ScRNAseq.sh └── run_empirical_validation.sh /10X_cross_validation.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neurosurgery-Brain-Tumor-Center-DiazLab/CONICS/HEAD/10X_cross_validation.cfg -------------------------------------------------------------------------------- /CONICS.cfg: -------------------------------------------------------------------------------- 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