seasoncloud/Alleloscope
Allele-specific copy number genotyping for single cell sequencing data

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Allele-specific copy number genotyping for single cell sequencing data

.DS_Store
.gitignore
Alleloscope.Rproj
DESCRIPTION
NAMESPACE
R/.DS_Store
R/AssignClones_ref.R R/Cov_value.R R/Createobj.R R/EM.R R/Est_regions.R R/Genotype.R R/Genotype_value.R R/Lineage_plot.R R/Matrix_filter.R R/Rundf_dna.R R/Segmentation.R R/Segments_filter.R R/Select_normal.R R/genotype_conf.R R/genotype_neighbor.R R/genotype_ref.R R/plot_scATAC_cnv.R README.md
data-raw/.DS_Store
data-raw/P5847/.DS_Store
data-raw/P5847/scDNA/alt_all_sub.rds
data-raw/P5847/scDNA/barcodes.tsv
data-raw/P5847/scDNA/normal_sub.rds
data-raw/P5847/scDNA/ref_all_sub.rds
data-raw/P5847/scDNA/tumor_sub.rds
data-raw/P5847/scDNA/var_all_sub.rds
data-raw/P5931/scDNA/alt_all_sub.mtx
data-raw/P5931/scDNA/barcodes_sub.tsv
data-raw/P5931/scDNA/normal_sub.txt
data-raw/P5931/scDNA/ref_all_sub.mtx
data-raw/P5931/scDNA/tumor_sub.txt
data-raw/P5931/scDNA/var_all_sub.vcf
data-raw/SNU601/.DS_Store
data-raw/SNU601/scATAC/.DS_Store
data-raw/SNU601/scATAC/SNU601_dna.rds
data-raw/SNU601/scATAC/alt_all.mtx
data-raw/SNU601/scATAC/barcodes.tsv
data-raw/SNU601/scATAC/chr200k_fragments_sub.txt
data-raw/SNU601/scATAC/clone.genotypes.rds
data-raw/SNU601/scATAC/peak_umap.rds
data-raw/SNU601/scATAC/ref_all.mtx
data-raw/SNU601/scATAC/var_all.vcf
data-raw/SNU601/scDNA/.DS_Store
data-raw/SNU601/scDNA/alt_all_sub.mtx
data-raw/SNU601/scDNA/barcodes_sub.tsv
data-raw/SNU601/scDNA/normal_sub.txt
data-raw/SNU601/scDNA/ref_all_sub.mtx
data-raw/SNU601/scDNA/tumor_sub.txt
data-raw/SNU601/scDNA/var_all_sub.vcf
data-raw/SU008/.DS_Store
data-raw/SU008/scATAC/.DS_Store
data-raw/SU008/scATAC/alt_all.mtx
data-raw/SU008/scATAC/barcodes.tsv
data-raw/SU008/scATAC/cell_type_from_peaks.rds
data-raw/SU008/scATAC/chr200k_fragments_sub.txt
data-raw/SU008/scATAC/peak_umap_tumor.rds
data-raw/SU008/scATAC/ref_all.mtx
data-raw/SU008/scATAC/seg_table_WES.rds
data-raw/SU008/scATAC/var_all.vcf
data-raw/hg38.100Kb.windows.sorted.bed
data-raw/sizes.cellranger-GRCh38-1.0.0.txt
data-raw/sizes.cellranger-atac-hg19-1.2.0.txt
data/centromere.GRCh38.RData
data/centromere.hg19.RData
data/telomere.GRCh38.RData
data/telomere.hg19.RData
inst/.DS_Store
inst/plots/.DS_Store
inst/plots/UMAP.png
inst/plots/genotype.png
inst/plots/genotype_SU008.png
inst/plots/genotype_scATAC.png
inst/plots/gtype_pre2.png
inst/plots/gtype_updated.png
inst/plots/lineage.png
inst/plots/overview2.png
inst/plots/peak_theta_SU008.png
inst/plots/scATAC_cov_example.png
inst/plots/segmentation.png
inst/plots/theta_clust_SU008.png
man/.DS_Store
man/AssignClones_ref.Rd man/Cov_value.Rd man/Createobj.Rd man/EM.Rd man/Est_regions.Rd man/Genotype.Rd man/Genotype_value.Rd man/Lineage_plot.Rd man/Matrix_filter.Rd man/Rundf_dna.Rd man/Segmentation.Rd man/Segments_filter.Rd man/Select_normal.Rd man/genotype_conf.Rd man/plot_scATAC_cnv.Rd
samples/.DS_Store
samples/P5847/.DS_Store
samples/P5847/scDNA/.DS_Store
samples/P5847/scDNA/output/.DS_Store
samples/P5847/scDNA/output/Obj_filtered.rds
samples/P5847/scDNA/output/genotype_values.rds
samples/P5847/scDNA/output/genotypes.rds
samples/P5847/scDNA/output/plots/.DS_Store
samples/P5847/scDNA/output/plots/AF_scDNAseq_c5_r10.pdf samples/P5847/scDNA/output/plots/EMresults/EMresult_chr11:0.pdf samples/P5847/scDNA/output/plots/EMresults/EMresult_chr15:17840000.pdf samples/P5847/scDNA/output/plots/EMresults/statistics_scDNAseq_chr11:0.pdf samples/P5847/scDNA/output/plots/EMresults/statistics_scDNAseq_chr15:17840000.pdf samples/P5847/scDNA/output/plots/Sample_seg_hmm.pdf samples/P5847/scDNA/output/plots/Sample_seg_hmm1.pdf samples/P5847/scDNA/output/plots/gtype_scatter_ref_11:0.pdf samples/P5847/scDNA/output/plots/hierarchcial_clustering_theta.pdf samples/P5847/scDNA/output/plots/lineage_ref_11:0.pdf samples/P5847/scDNA/output/plots/statistics.pdf
samples/P5847/scDNA/output/rds/chr11:0.rds
samples/P5847/scDNA/output/rds/chr15:17840000.rds
samples/P5847/scDNA/output/theta_N_seg.rds
samples/P5931/scDNA/README.html
samples/P5931/scDNA/README.md samples/P5931/scDNA/output/plots/AF_scDNAseq_c10_r10.pdf samples/P5931/scDNA/output/plots/EMresults/EMresult_chr1.pdf samples/P5931/scDNA/output/plots/EMresults/EMresult_chr20.pdf samples/P5931/scDNA/output/plots/EMresults/EMresult_chr21.pdf samples/P5931/scDNA/output/plots/EMresults/EMresult_chr3.pdf samples/P5931/scDNA/output/plots/EMresults/EMresult_chr3_sub.pdf samples/P5931/scDNA/output/plots/EMresults/EMresult_chr7.pdf samples/P5931/scDNA/output/plots/EMresults/EMresult_chr8.pdf samples/P5931/scDNA/output/plots/EMresults/statistics_scDNAseq_chr1.pdf samples/P5931/scDNA/output/plots/EMresults/statistics_scDNAseq_chr20.pdf samples/P5931/scDNA/output/plots/EMresults/statistics_scDNAseq_chr21.pdf samples/P5931/scDNA/output/plots/EMresults/statistics_scDNAseq_chr3.pdf samples/P5931/scDNA/output/plots/EMresults/statistics_scDNAseq_chr3_sub.pdf samples/P5931/scDNA/output/plots/EMresults/statistics_scDNAseq_chr7.pdf samples/P5931/scDNA/output/plots/EMresults/statistics_scDNAseq_chr8.pdf samples/P5931/scDNA/output/plots/gtype_pre2.pdf samples/P5931/scDNA/output/plots/gtype_scatter_ref_1.pdf samples/P5931/scDNA/output/plots/gtype_scatter_updated.pdf samples/P5931/scDNA/output/plots/gtype_updated2.pdf samples/P5931/scDNA/output/plots/hierarchcial_clustering_theta.pdf samples/P5931/scDNA/output/plots/lineage_ref_1.pdf samples/P5931/scDNA/output/plots/statistics.pdf
samples/P5931/scDNA/output/rds/EMresults/chr1.rds
samples/P5931/scDNA/output/rds/EMresults/chr20.rds
samples/P5931/scDNA/output/rds/EMresults/chr21.rds
samples/P5931/scDNA/output/rds/EMresults/chr3.rds
samples/P5931/scDNA/output/rds/EMresults/chr3_sub.rds
samples/P5931/scDNA/output/rds/EMresults/chr7.rds
samples/P5931/scDNA/output/rds/EMresults/chr8.rds
samples/P5931/scDNA/output/rds/genotype_values.rds
samples/P5931/scDNA/output/rds/genotypes.rds
samples/P5931/scDNA/output/rds/theta_N_seg.rds
samples/SNU601/.DS_Store
samples/SNU601/scATAC/.DS_Store
samples/SNU601/scATAC/README.html
samples/SNU601/scATAC/README.md
samples/SNU601/scATAC/output/.DS_Store
samples/SNU601/scATAC/output/plots/.DS_Store
samples/SNU601/scATAC/output/plots/AF_scATACseq_c5_r5.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr11:45940000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr13:80640000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr1:218360000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr20:26300000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr20:44820000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr3:147340000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr3:163840000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr3:96160000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr4:57600000.pdf samples/SNU601/scATAC/output/plots/EMresults/EMresult_chr7:0.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr11:45940000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr13:80640000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr1:218360000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr20:26300000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr20:44820000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr3:147340000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr3:163840000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr3:96160000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr4:57600000.pdf samples/SNU601/scATAC/output/plots/EMresults/statistics_scATACseq_chr7:0.pdf samples/SNU601/scATAC/output/plots/gtype_scatter_ref_10:0.pdf samples/SNU601/scATAC/output/plots/statistics.pdf
samples/SNU601/scATAC/output/rds/.DS_Store
samples/SNU601/scATAC/output/rds/EMresults/chr11:45940000.rds
samples/SNU601/scATAC/output/rds/EMresults/chr13:80640000.rds
samples/SNU601/scATAC/output/rds/EMresults/chr1:218360000.rds
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samples/SNU601/scATAC/output/rds/EMresults/chr20:44820000.rds
samples/SNU601/scATAC/output/rds/EMresults/chr3:147340000.rds
samples/SNU601/scATAC/output/rds/EMresults/chr3:163840000.rds
samples/SNU601/scATAC/output/rds/EMresults/chr3:96160000.rds
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samples/SNU601/scATAC/output/rds/EMresults/chr7:0.rds
samples/SNU601/scATAC/output/rds/genotype_values.rds
samples/SNU601/scATAC/output/rds/genotypes.rds
samples/SNU601/scDNA/.DS_Store
samples/SNU601/scDNA/README.html
samples/SNU601/scDNA/README.md
samples/SNU601/scDNA/output/.DS_Store
samples/SNU601/scDNA/output/plots/.DS_Store
samples/SNU601/scDNA/output/plots/AF_scDNAseq_c1000_r20.pdf samples/SNU601/scDNA/output/plots/EMresults/EMresult_chr10:0.pdf samples/SNU601/scDNA/output/plots/EMresults/EMresult_chr20:44820000.pdf samples/SNU601/scDNA/output/plots/EMresults/EMresult_chr3:147340000.pdf samples/SNU601/scDNA/output/plots/EMresults/EMresult_chr3:160140000.pdf samples/SNU601/scDNA/output/plots/EMresults/EMresult_chr4:57600000.pdf samples/SNU601/scDNA/output/plots/EMresults/statistics_scDNAseq_chr10:0.pdf samples/SNU601/scDNA/output/plots/EMresults/statistics_scDNAseq_chr20:44820000.pdf samples/SNU601/scDNA/output/plots/EMresults/statistics_scDNAseq_chr3:147340000.pdf samples/SNU601/scDNA/output/plots/EMresults/statistics_scDNAseq_chr3:160140000.pdf samples/SNU601/scDNA/output/plots/EMresults/statistics_scDNAseq_chr4:57600000.pdf samples/SNU601/scDNA/output/plots/Sample_seg_hmm.pdf samples/SNU601/scDNA/output/plots/gtype_scatter_ref_10:0.pdf samples/SNU601/scDNA/output/plots/gtype_scatter_ref_10:0_2.pdf samples/SNU601/scDNA/output/plots/hierarchcial_clustering_theta.pdf samples/SNU601/scDNA/output/plots/lineage_ref_10:0.pdf samples/SNU601/scDNA/output/plots/statistics.pdf
samples/SNU601/scDNA/output/rds/EMresults/chr10:0.rds
samples/SNU601/scDNA/output/rds/EMresults/chr20:44820000.rds
samples/SNU601/scDNA/output/rds/EMresults/chr3:147340000.rds
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samples/SNU601/scDNA/output/rds/theta_N_seg.rds
samples/SU008/.DS_Store
samples/SU008/scATAC/.DS_Store
samples/SU008/scATAC/Gen_seg_table.html
samples/SU008/scATAC/Gen_seg_table.md
samples/SU008/scATAC/README.html
samples/SU008/scATAC/README.md
samples/SU008/scATAC/output/.DS_Store
samples/SU008/scATAC/output/cov_cna_plot.png
samples/SU008/scATAC/output/plots/.DS_Store
samples/SU008/scATAC/output/plots/AF_scATACseq_c10_r10.pdf samples/SU008/scATAC/output/plots/AF_scATACseq_c20_r20.pdf samples/SU008/scATAC/output/plots/AF_scATACseq_c2_r2.pdf samples/SU008/scATAC/output/plots/AF_scATACseq_c2_r20.pdf samples/SU008/scATAC/output/plots/AF_scATACseq_c5_r20.pdf samples/SU008/scATAC/output/plots/AF_scATACseq_c5_r5.pdf samples/SU008/scATAC/output/plots/EMresults/EMresult_chr12:0.pdf samples/SU008/scATAC/output/plots/EMresults/EMresult_chr15:23467210.pdf samples/SU008/scATAC/output/plots/EMresults/EMresult_chr21:16437159.pdf samples/SU008/scATAC/output/plots/EMresults/EMresult_chr22:0.pdf samples/SU008/scATAC/output/plots/EMresults/EMresult_chr3:97670875.pdf samples/SU008/scATAC/output/plots/EMresults/EMresult_chr4:0.pdf samples/SU008/scATAC/output/plots/EMresults/EMresult_chr6:65612425.pdf samples/SU008/scATAC/output/plots/EMresults/statistics_scATACseq_chr12:0.pdf samples/SU008/scATAC/output/plots/EMresults/statistics_scATACseq_chr15:23467210.pdf samples/SU008/scATAC/output/plots/EMresults/statistics_scATACseq_chr21:16437159.pdf samples/SU008/scATAC/output/plots/EMresults/statistics_scATACseq_chr22:0.pdf samples/SU008/scATAC/output/plots/EMresults/statistics_scATACseq_chr3:97670875.pdf samples/SU008/scATAC/output/plots/EMresults/statistics_scATACseq_chr4:0.pdf samples/SU008/scATAC/output/plots/EMresults/statistics_scATACseq_chr6:65612425.pdf samples/SU008/scATAC/output/plots/gtype_scatter_ref_22:0.pdf samples/SU008/scATAC/output/plots/hierarchcial_clustering_theta.pdf samples/SU008/scATAC/output/plots/statistics.pdf
samples/SU008/scATAC/output/rds/EMresults/chr12:0.rds
samples/SU008/scATAC/output/rds/EMresults/chr15:23467210.rds
samples/SU008/scATAC/output/rds/EMresults/chr21:16437159.rds
samples/SU008/scATAC/output/rds/EMresults/chr22:0.rds
samples/SU008/scATAC/output/rds/EMresults/chr3:97670875.rds
samples/SU008/scATAC/output/rds/EMresults/chr4:0.rds
samples/SU008/scATAC/output/rds/EMresults/chr6:65612425.rds
samples/SU008/scATAC/output/rds/genotype_values.rds
samples/SU008/scATAC/output/rds/genotypes.rds
samples/SU008/scATAC/output/rds/theta_N_seg.rds
seasoncloud/Alleloscope documentation built on March 17, 2023, 1:14 a.m.

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