{
"_id": "6a213047cd65a98ecbd24bc8",
"Package": "numbat",
"Title": "Haplotype-Aware CNV Analysis from scRNA-Seq",
"URL": "https://github.com/kharchenkolab/numbat/,\nhttps://kharchenkolab.github.io/numbat/",
"Version": "1.5.2",
"Authors@R": "c(person(\"Teng\",\"Gao\", email=\"tgaoteng@gmail.com\", role=c(\"cre\", \"aut\")), person(\"Ruslan\", \"Soldatov\", email=\"soldatr@mskcc.org\", role=\"aut\"), person(\"Hirak\", \"Sarkar\", email=\"hirak_sarkar@hms.harvard.edu\", role=\"aut\"), person(\"Evan\", \"Biederstedt\", email=\"evan.biederstedt@gmail.com\", role=\"aut\"), person(\"Peter\", \"Kharchenko\", email = \"peter_kharchenko@hms.harvard.edu\", role = \"aut\"))",
"Description": "A computational method that infers copy number variations\n(CNVs) in cancer scRNA-seq data and reconstructs the tumor\nphylogeny. 'numbat' integrates signals from gene expression,\nallelic ratio, and population haplotype structures to\naccurately infer allele-specific CNVs in single cells and\nreconstruct their lineage relationship. 'numbat' can be used\nto: 1. detect allele-specific copy number variations from\nsingle-cells; 2. differentiate tumor versus normal cells in the\ntumor microenvironment; 3. infer the clonal architecture and\nevolutionary history of profiled tumors. 'numbat' does not\nrequire tumor/normal-paired DNA or genotype data, but operates\nsolely on the donor scRNA-data data (for example, 10x Cell\nRanger output). Additional examples and documentations are\navailable at . For\ndetails on the method please see Gao et al. Nature\nBiotechnology (2022) .",
"License": "MIT + file LICENSE",
"Encoding": "UTF-8",
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"Author": "Teng Gao [cre, aut], Ruslan Soldatov [aut], Hirak Sarkar [aut],\nEvan Biederstedt [aut], Peter Kharchenko [aut]",
"Maintainer": "Teng Gao ",
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"Repository": "https://kharchenkolab.r-universe.dev",
"Date/Publication": "2026-02-04 04:56:07 UTC",
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"message": "Fix detect_clonal_loh example error by filtering empty gene names\n\nThe function was failing when encountering genes with empty string names.\nThe filter !is.na(gene) doesn't catch empty strings, causing summarise()\nto fail when unique(na.omit(Y_obs)) returns an empty vector.\n\nFixed by also filtering out empty gene names: gene != \"\"\n\nFixes example error in R CMD check.\n",
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"_exports": [
"aggregate_counts",
"analyze_bulk",
"annotate_genes",
"cnv_heatmap",
"detect_clonal_loh",
"get_bulk",
"get_gtree",
"Numbat",
"plot_bulks",
"plot_consensus",
"plot_exp_roll",
"plot_mut_history",
"plot_phylo_heatmap",
"plot_psbulk",
"plot_sc_tree",
"run_numbat"
],
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{
"name": "acen_hg19",
"title": "centromere regions (hg19)",
"object": "acen_hg19",
"class": [
"tbl_df",
"tbl",
"data.frame"
],
"fields": [
"CHROM",
"start",
"end"
],
"rows": 22,
"table": true,
"tojson": true
},
{
"name": "acen_hg38",
"title": "centromere regions (hg38)",
"object": "acen_hg38",
"class": [
"tbl_df",
"tbl",
"data.frame"
],
"fields": [
"CHROM",
"start",
"end"
],
"rows": 22,
"table": true,
"tojson": true
},
{
"name": "annot_ref",
"title": "example reference cell annotation",
"object": "annot_ref",
"class": [
"data.frame"
],
"fields": [
"cell",
"group"
],
"rows": 50,
"table": true,
"tojson": true
},
{
"name": "bulk_example",
"title": "example pseudobulk dataframe",
"object": "bulk_example",
"class": [
"tbl_df",
"tbl",
"data.frame"
],
"fields": [
"snp_id",
"CHROM",
"POS",
"cM",
"REF",
"ALT",
"GT",
"gene",
"AD",
"DP",
"AR",
"snp_index",
"pBAF",
"pAD",
"inter_snp_cm",
"p_s",
"Y_obs",
"lambda_obs",
"lambda_ref",
"d_obs",
"gene_start",
"gene_end",
"region",
"gene_length",
"gene_index",
"logFC",
"lnFC",
"sse",
"n_cells",
"members",
"sample",
"state",
"boundary",
"seg_start_index",
"seg_end_index",
"loh",
"diploid",
"mu",
"sig",
"state_post",
"haplo_theta_min",
"major_count",
"minor_count",
"nu",
"seg_start",
"seg_end",
"seg_length",
"seg",
"seg_cons",
"cnv_state",
"n_genes",
"n_snps",
"theta_hat",
"theta_mle",
"theta_sigma",
"L_y_n",
"L_y_d",
"L_y_a",
"phi_mle",
"phi_sigma",
"L_x_n",
"L_x_d",
"L_x_a",
"Z_cnv",
"Z_n",
"Z",
"logBF",
"p_neu",
"p_loh",
"p_amp",
"p_del",
"p_bamp",
"p_bdel",
"LLR_x",
"LLR_y",
"LLR",
"cnv_state_post",
"p_up",
"haplo_post",
"haplo_naive",
"theta_hat_roll",
"phi_mle_roll",
"gamma"
],
"rows": 3935,
"table": true,
"tojson": true
},
{
"name": "chrom_sizes_hg19",
"title": "chromosome sizes (hg19)",
"object": "chrom_sizes_hg19",
"class": [
"data.table",
"data.frame"
],
"fields": [
"CHROM",
"size"
],
"rows": 22,
"table": true,
"tojson": true
},
{
"name": "chrom_sizes_hg38",
"title": "chromosome sizes (hg38)",
"object": "chrom_sizes_hg38",
"class": [
"data.table",
"data.frame"
],
"fields": [
"CHROM",
"size"
],
"rows": 22,
"table": true,
"tojson": true
},
{
"name": "count_mat_example",
"title": "example gene expression count matrix",
"object": "count_mat_example",
"class": [
"dgCMatrix"
],
"fields": [],
"table": false,
"tojson": false
},
{
"name": "count_mat_ref",
"title": "example reference count matrix",
"object": "count_mat_ref",
"class": [
"dgCMatrix"
],
"fields": [],
"table": false,
"tojson": false
},
{
"name": "df_allele_example",
"title": "example allele count dataframe",
"object": "df_allele_example",
"class": [
"data.frame"
],
"fields": [
"cell",
"snp_id",
"CHROM",
"POS",
"cM",
"REF",
"ALT",
"AD",
"DP",
"GT",
"gene"
],
"rows": 41167,
"table": true,
"tojson": true
},
{
"name": "gaps_hg19",
"title": "genome gap regions (hg19)",
"object": "gaps_hg19",
"class": [
"data.table",
"data.frame"
],
"fields": [
"CHROM",
"start",
"end"
],
"rows": 28,
"table": true,
"tojson": true
},
{
"name": "gaps_hg38",
"title": "genome gap regions (hg38)",
"object": "gaps_hg38",
"class": [
"data.table",
"data.frame"
],
"fields": [
"CHROM",
"start",
"end"
],
"rows": 30,
"table": true,
"tojson": true
},
{
"name": "gexp_roll_example",
"title": "example smoothed gene expression dataframe",
"object": "gexp_roll_example",
"class": [
"data.frame"
],
"fields": [
"AP3S1",
"OCLN",
"CDK2",
"WDR77",
"BTF3L4",
"PHF20L1",
"NT5C3B",
"UBE2T",
"MED13",
"ITGB2-AS1",
"ZFAND6",
"RALA",
"C16orf70",
"CBR3",
"KDM7A",
"ITGA10",
"PRKAB1",
"REPS1",
"RNF126",
"TTC19",
"DNAJA1",
"CDK13",
"TRAF3IP1",
"TRAPPC8",
"CEP170B",
"BOLA1",
"CRY1",
"RNF44",
"DCTN6",
"ATXN2",
"MUS81",
"ZNF32",
"SGSM2",
"UTP20",
"LRRC41",
"C2orf68",
"DSN1",
"ASS1",
"ANLN",
"NCOA2",
"PTS",
"NFIC",
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"EXOC4",
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"FOXRED1",
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"TIA1",
"RRAGA",
"SND1-IT1",
"ATP6V1G1",
"ETV5",
"PUS7",
"SREK1",
"JRK",
"AKR1C3",
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"VRK1",
"ABCB8",
"ZNF654",
"RASSF3",
"RTKN2",
"P4HTM",
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"BAZ1B",
"RPTOR",
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"CCT4",
"MIR762HG",
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"URB1-AS1",
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"NUDCD2",
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"PSPH",
"WIF1",
"ELL",
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"KNTC1",
"FRZB",
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"RAB40C",
"INSIG1",
"HSPB11",
"PIFO",
"HERC2",
"VPS4B",
"TBC1D9",
"CDK12",
"VPS26B",
"LRP3",
"PTPN22",
"DGKD",
"TTC28",
"PIP5K1C",
"SART3",
"CLEC11A",
"NINL",
"HSP90AA1",
"NDUFC2",
"CCDC86",
"CHPF",
"BLMH",
"DMTN",
"FAM53B",
"DGKE",
"CFAP36",
"SLC35F5",
"ADGRG1",
"SVIP",
"CHKB",
"PEA15",
"TMEM256",
"SNCA",
"ZNF579",
"DVL1",
"CYP20A1",
"APTX",
"EXOSC8",
"MTMR11",
"CDIPT",
"COLGALT1",
"LRRC8C",
"PSMB2",
"PTDSS2",
"TCTN1",
"PPME1",
"CD79B",
"ZNF438",
"PLEKHA1",
"ATL2",
"SEC24C",
"CLN6",
"GLG1",
"NFX1",
"GLIPR1",
"WDR74",
"NEO1",
"NUTM2B-AS1",
"PRKAG1",
"JOSD2",
"SYNE1",
"UPF1",
"SMC4",
"MMS22L",
"SURF6",
"HMGN2",
"STIM1",
"CHD1L",
"PDIA6",
"GLUD1",
"FGFRL1",
"PPP1R2",
"POLR2L",
"METAP2",
"NAV1",
"USP7",
"NUP214",
"DHX40",
"CYB5R4",
"SH2B1",
"DAAM1",
"ICMT",
"ZNF205",
"HM13",
"NABP2",
"ITPA",
"PRKCA",
"PAM",
"DGKA",
"ERI1",
"MAFK",
"STMN1",
"IGSF8",
"FABP3",
"PPP2R5E",
"EPHB4",
"ADAM15",
"LFNG",
"SYS1",
"PICK1",
"RUNX3",
"ARL4D",
"IMP4",
"NTMT1",
"ASB16-AS1",
"NAPG",
"DZIP3",
"AP4E1",
"ANKFY1",
"RPL15",
"CAD",
"PIGO",
"TMEM161A",
"SCD",
"PSMA4",
"SLAIN2",
"ZCRB1",
"SETDB1",
"TTC37",
"ANAPC7",
"MSL1",
"C19orf12",
"DENND4B",
"ZNF251",
"DIAPH1",
"FOLR1",
"NFIA",
"VPS26A",
"SFR1",
"KLHL5",
"TMEM192",
"ACVR1",
"COMMD1",
"BTG2",
"LRP11",
"PODXL2",
"NME7",
"IDH1",
"HOOK1",
"PLBD1",
"BET1L",
"SDR16C5",
"CBFA2T2",
"DPM3",
"TAF9",
"TUBGCP6",
"CHD1",
"INPP5B",
"PRR13",
"ZNF618",
"RGS5",
"TMEM121",
"RNF180",
"LAMTOR3",
"ASPH",
"TJP3",
"ACAP3",
"PTCD3",
"MPLKIP",
"FCHSD1",
"RPL6",
"DDX11",
"QDPR",
"SLC31A2",
"DLGAP1-AS1",
"SLC25A12",
"CHRNB1",
"EVA1C",
"PRCP",
"SNRPD3",
"PECAM1",
"CEP83",
"TIRAP",
"ISOC1",
"HBA2",
"C1orf162",
"ZNF100",
"NSUN2",
"RSAD2",
"TMEM97",
"TMC4",
"STEAP1",
"TRA2B",
"CAT",
"COX18",
"ABI3",
"SLC35E1",
"MLXIP",
"UBE2D3",
"AFF4",
"FOXK1",
"SEMA3C",
"MSRB2",
"TXNRD1",
"TIGD6",
"MBOAT7",
"MMP14",
"RPIA",
"TXNDC15",
"RFC2",
"SUGP1",
"TBC1D12",
"CD52",
"CORO1B",
"SMAD5",
"FPGT",
"FIBIN",
"CDC42SE2",
"CCAR2",
"CCT8",
"MYBBP1A",
"DLL1",
"BRD8",
"DLEU7",
"TGFB1I1",
"AVL9",
"ZMAT5",
"PADI2",
"PARVG",
"DNAJB6",
"C1orf159",
"GAPT",
"CMTM8",
"SLC9A3R1",
"LINC01094",
"RPS20",
"MPHOSPH6",
"SUSD3",
"ZCCHC10",
"EBNA1BP2",
"PRKAG2",
"OGFR",
"KLHL2",
"BRCA2",
"SLC23A2",
"ASRGL1",
"PYCR1",
"HSPA5",
"PEX14",
"RASSF8",
"TUT1",
"ARAP1",
"RPS9",
"GPAT4",
"TIMM13",
"UBE2K",
"CXCL14",
"PRPF39",
"MTA1",
"PRNP",
"SAV1",
"EMC1",
"FGFBP2",
"UBLCP1",
"TOMM7",
"FBXO5",
"EDF1",
"TEAD2",
"NTN4",
"ATP1B3",
"CSF2RB",
"NPC2",
"UTRN",
"ARAP2",
"POLR1E",
"NME1",
"SLC15A3",
"MED28",
"EIF4E2",
"SLX4IP",
"FBXL8",
"ZNF680",
"ZBTB44",
"DPYSL3",
"OTUB1",
"CD55",
"DNAJC11",
"IRAK4",
"ZNF764",
"SP110",
"NAPA",
"COX5A",
"SDCCAG8",
"LRPPRC",
"FOXO3",
"WDR3",
"PLCL1",
"ATXN7L3B",
"SBNO2",
"RASA1",
"CANX",
"ANKRD54",
"ZNF646",
"SCO1",
"ZBTB24",
"CENPP",
"KIF9",
"RHOQ",
"SCIMP",
"TRAF5",
"LYRM1",
"CST3",
"RNF111",
"SMURF2",
"SOCS4",
"TUG1",
"TOR4A",
"CD82",
"GAS8",
"VMP1",
"ZDHHC21",
"ETV1",
"MDH2",
"MYL9",
"AEBP2",
"TOP1",
"TEAD1",
"ZEB1",
"ZNF761",
"SLC50A1",
"COX6B1",
"IFT122",
"ABHD4",
"CALM3",
"ARHGEF7",
"RUFY1",
"PTRH2",
"SFTPD",
"RIC3",
"ATP8B1",
"ATP6V1A",
"EIF4EBP1",
"CXCL3",
"TNFRSF11B",
"HS2ST1",
"RGCC",
"CCDC117",
"MBNL1",
"MLH1",
"ZNF559",
"LRRC45",
"TDRKH",
"UNC119B",
"MAN2C1",
"EIF3M",
"BCDIN3D",
"SMAD1",
"LRIF1",
"NUDT19",
"TBC1D19",
"PSMA6",
"ATF7IP",
"CALML4",
"RAB38",
"CNOT1",
"PAQR8",
"ECHDC3",
"FKBP4",
"ZFAND5",
"ZNF783",
"C8orf33",
"ARHGAP15",
"SUPT5H",
"POLA2",
"EXOC5",
"PSMG4",
"CHCHD4",
"GART",
"RPL19",
"DUSP1",
"SENP6",
"CRNKL1",
"FUCA1",
"PDS5B",
"RBM42",
"DMKN",
"SETD2",
"EBF1",
"PCYOX1",
"KMT2E",
"TUSC1",
"MIIP",
"TCF25",
"TMEM43",
"FUZ",
"SNX24",
"PCDH7",
"NOLC1",
"AEN",
"L3MBTL2",
"ZNF276",
"MON1A",
"CCAR1",
"MED17",
"PTPRA",
"HSBP1L1",
"RPN2",
"PIK3R5",
"FN1",
"SLC35E3",
"RNF19A",
"FBXW8",
"PARP9",
"FEM1B",
"ALDH6A1",
"ATP6V1E1",
"MRRF",
"PRRG4",
"IL6R",
"TIMP3",
"RALB",
"CLUAP1",
"OCIAD1",
"ZBTB4",
"MPHOSPH8",
"ARHGEF17",
"IRF9",
"SLC25A22",
"PHC2",
"FAM110A",
"PSMC1",
"LCMT1",
"AQP3",
"LENG1",
"UTP6",
"KEAP1",
"DDX60",
"ARF5",
"RAD54L2",
"FAHD2A",
"WDR35",
"MBD4",
"ALDH3A2",
"EXO5",
"CNRIP1",
"RPL14",
"ZNF600",
"BCL2L2",
"DUS3L",
"ITSN2",
"PARL",
"RRM1",
"TRIM5",
"ALDOC",
"EDEM3",
"CYB5R3",
"COL9A3",
"RPL11",
"RAD23A",
"TCF7L2",
"PEX11B",
"PPP4R3B",
"ACVR2A",
"GCNT2",
"RNF8",
"MCUR1",
"SF3B4",
"OTUD4",
"HIVEP2",
"CD300A",
"EIF3E",
"ZBTB20",
"LIMD1",
"SRSF5",
"TMEM25",
"TNFRSF4",
"LDHD",
"ZNF101",
"STAT2",
"HNMT",
"CUTC",
"DGKQ",
"RBM33",
"SETD9",
"SPOPL",
"TBC1D17",
"NCLN",
"SMAD6",
"ZNF687",
"MRPS25",
"SERBP1",
"PMPCA",
"SLC35B2",
"TXNL4B",
"TTC1",
"IDH3B",
"TMEM140",
"SLC16A1",
"MRAS",
"MXD4",
"BRPF1",
"CCDC91",
"PIK3R3",
"DDX42",
"CDK7",
"ATG12",
"FBL",
"EWSR1",
"C18orf32",
"BET1",
"STOM",
"CHPF2",
"DIXDC1",
"KIAA1109",
"IRF5",
"ZDBF2",
"USP31",
"THUMPD2",
"CGRRF1",
"TJP2",
"ATP13A3",
"CTSO",
"CARHSP1",
"GSTO1",
"UBA7",
"ATP6V0B",
"SURF1",
"RBMS3",
"COL4A2",
"GALNT3",
"MRPL39",
"CCSER2",
"RPUSD2",
"CSTF3",
"ENTPD4",
"SMU1",
"SCAI",
"MLPH",
"MRPL51",
"MAP4K2",
"SPIRE1",
"ZNF644",
"TBCB",
"LRRC28",
"SLC22A15",
"STX16",
"SLC9A3R2",
"MTRF1L",
"NFIL3",
"ZCCHC24",
"ADARB1",
"ELAC2",
"DRG2",
"TRIB1",
"ZNF219",
"WDR24",
"FDXACB1",
"DDX20",
"CHCHD6",
"SMARCE1",
"ASCL2",
"ANAPC1",
"COL4A1",
"CERS4",
"HPS5",
"TTC17",
"ZNF180",
"DNAJA4",
"TIMMDC1",
"CIT",
"NME3",
"KIF5B",
"IMMP2L",
"RUVBL1",
"KCMF1",
"C9orf64",
"GPR180",
"BTN3A1",
"SIRT7",
"MIEF1",
"INSR",
"ZBTB43",
"TBC1D24",
"FEN1",
"RHNO1",
"AGPAT5",
"EIF4G1",
"LRRC27",
"CMPK1",
"CLEC10A",
"JUP",
"DECR2",
"MAPK8IP3",
"APC",
"LTC4S",
"NFYC",
"UQCC3",
"HTATIP2",
"GTF3C2",
"COPS5",
"CENPF",
"SESN3",
"PCGF1",
"ZNF420",
"C1orf54",
"SPAG9",
"BANF1",
"ACOX1",
"RAB5B",
"RRM2",
"LARP4B",
"IGFBP6",
"SCRN2",
"TIMM10B",
"RPS23",
"GTF3A",
"NCAPD2",
"MAT2A",
"RABGGTA",
"PNMA1",
"MNDA",
"RC3H2",
"HEXB",
"LRRC59",
"IER3IP1",
"MED29",
"PLS1",
"PFN2",
"CD109",
"ZNF622",
"PFKP",
"PPP1R14C",
"MRPS18C",
"ZFP36L1",
"ILK",
"ADIPOR1",
"CREB3L4",
"KCNQ1",
"PNRC2",
"CDV3",
"HIP1R",
"MOCS3",
"CEP70",
"NES",
"BABAM1",
"IMP3",
"DIMT1",
"ZNF473",
"UBQLN1",
"NR4A1",
"NAPSA",
"HERC6",
"CDCA8",
"PARP2",
"CST6",
"DPP9",
"RBM26",
"DIDO1",
"TMED1",
"PEX11A",
"SLC5A6",
"C3orf62",
"CDKN2AIPNL",
"ALDH1A3",
"HINFP",
"TOR3A",
"NFAM1",
"H6PD",
"CNOT10",
"RANGRF",
"PPHLN1",
"CRKL",
"RNF217",
"MZT2A",
"PTGIS",
"ACOT7",
"ZDHHC14",
"MIEF2",
"FANCD2",
"RASGRP2",
"DHRS7B",
"ACIN1",
"PDE4DIP",
"ZNF765",
"GALNS",
"MYLIP",
"NHSL1",
"PDCD1LG2",
"RABEP2",
"RBP1",
"SCARB1",
"TRIM65",
"EMC2",
"PLEKHF2",
"PIAS3",
"ASAH1",
"MYH11",
"BCL11A",
"RAB6A",
"ZNF189",
"COPS4",
"CDC42EP5",
"MAEA",
"TRDMT1",
"CHMP1B",
"BLM",
"RAP1A",
"GUCD1",
"ZNF738",
"PCGF6",
"CLPTM1L",
"RAB40B",
"KIF21A",
"RIN2",
"SLC16A3",
"ACE",
"KHSRP",
"SKP1",
"PLPP1",
"C9orf78",
"TBC1D23",
"GATAD2B",
"NBAS",
"MDM1",
"RPS17",
"IMPA2",
"WDR45B",
"CHEK1",
"CLMN",
"TRAPPC3",
"ERCC6L2",
"POLR2K",
"P3H3",
"UBE2D2",
"MAPRE2",
"DHTKD1",
"COQ7",
"KDELR2",
"PRPF4B",
"RMDN1",
"CERS6",
"ZBTB8A",
"CFD",
"GGCX",
"CDKN1B",
"MPZL2",
"AGAP1",
"DHX15",
"RNASEH2B",
"GYG1",
"YTHDF3",
"HNRNPL",
"MPC2",
"TMX1",
"S100P",
"F2RL3",
"COMMD6",
"ARPC1A",
"CDC27",
"TLR1",
"ZSCAN32",
"KLHL42",
"ANKRD9",
"LZIC",
"NUDT14",
"SMCR5",
"RUBCN",
"AMOTL1",
"RPS6KA5",
"COMMD2",
"MRPS21",
"IMMT",
"PDZRN3",
"SLC16A11",
"SP100",
"GBE1",
"KBTBD4",
"SLC27A3",
"HECTD1",
"MED25",
"RHBDD1",
"MZT1",
"IVNS1ABP",
"ATP6V0E1",
"DCAF11",
"TOR1A",
"ZRANB2",
"PARD3",
"TMEM50B",
"EPG5",
"TELO2",
"HPS3",
"HPN",
"SAR1A",
"ASB1",
"KAT7",
"ARHGEF26",
"DTX3L",
"ALG10",
"EBLN2",
"PER3",
"GEN1",
"IL1RAP",
"OAZ1",
"KIF16B",
"SLC25A4",
"TPX2",
"L3HYPDH",
"AKIRIN2",
"CDKN2AIP",
"S100A11",
"FAAH",
"FZD1",
"FBXO11",
"KPNA2",
"CYB561A3",
"KBTBD2",
"VCAN",
"ERAL1",
"FRA10AC1",
"ZNF226",
"VDAC3",
"KMT2B",
"MFAP2",
"MTMR4",
"PRSS36",
"PLK1",
"PTRH1",
"SERPINA1",
"MRPL35",
"ARRDC1-AS1",
"TOM1L2",
"NUP133",
"CSTF2T",
"TXNL1",
"MAP3K2",
"CTNND1",
"HOTAIRM1",
"ARSK",
"FBXO34",
"PXN",
"DYRK2",
"MASTL",
"CNOT6L",
"CPNE2",
"BLVRB",
"COA6",
"TMEM200A",
"SLC41A1",
"AAR2",
"NUDT1",
"TNFRSF1A",
"LGALS9",
"TRMT2A",
"NDUFAF7",
"IQCH-AS1",
"PEX2",
"LRR1",
"AIDA",
"RAB3IL1",
"RSPO3",
"AURKB",
"SAMD12",
"TRAM1",
"KLHDC3",
"MIER2",
"R3HDM4",
"ERCC6",
"NMI",
"CTBP1",
"DICER1",
"TNPO3",
"YIF1A",
"COPG2",
"PLXNA1",
"SMG7",
"SPEN",
"TRNAU1AP",
"SATB1",
"USP39",
"USB1",
"RPL37",
"CTSH",
"SLC25A38",
"ELP4",
"SLC1A3",
"SARNP",
"AKT1",
"SASH1",
"BBX",
"DOCK1",
"SIGMAR1",
"TSNAX",
"TMEM154",
"GTF2I",
"ACAT2",
"SEC62",
"CLEC3B",
"PAPOLG",
"NAIP",
"TDP2",
"IER5L",
"MFN2",
"C19orf48",
"SNX13",
"CENPC",
"PKIG",
"POGK",
"TMF1",
"TMEM128",
"MRPL52",
"USP37",
"KLHL18",
"TMEM70",
"SESTD1",
"SURF4",
"CD276",
"TSHZ3",
"NPTN",
"WASL",
"USP16",
"AASS",
"GALM",
"CPXM1",
"TRIM32",
"RASA4",
"NTHL1",
"STK3",
"SEC31A",
"PLEK2",
"CNKSR3",
"SNN",
"TCEANC2",
"IFRD2",
"BAMBI",
"RBM19",
"PTX3",
"JMJD6",
"E2F1",
"IQCE",
"ATP6V0D1",
"POLB",
"GORASP1",
"RPUSD1",
"TRIM44",
"ANAPC15",
"SERTAD2",
"PCMTD2",
"ZNF791",
"SUDS3",
"TAOK1",
"NOD1",
"RTN4",
"GNGT2",
"SFMBT1",
"ARFIP1",
"ETFB",
"PHKB",
"PDP2",
"SLC38A7",
"TBCC",
"P3H4",
"ADAL",
"ADNP2",
"CAPRIN1",
"MRPL10",
"PIK3C3",
"ARHGAP9",
"SF3A1",
"GMPR2",
"ANKRD65",
"SULT1A1",
"TRIT1",
"PGGT1B",
"ACBD3",
"MIER3",
"ZDHHC4",
"ARHGAP29",
"TPST2",
"SYNGR2",
"FBXO22",
"ADAMTS2",
"CWC27",
"FRMD4B",
"RILPL2",
"PLEKHG1",
"PIGR",
"ZNF430",
"MAP7D1",
"CHCHD5",
"PUSL1",
"MXI1",
"FAM160B2",
"IRF8",
"ARMC9",
"DHX57",
"TNFRSF18",
"PLOD2",
"NDUFA11",
"ITGBL1",
"CDK1",
"TRIM59",
"TRIO",
"INPP1",
"COMMD7",
"CHD9",
"ZNF467",
"RAD51AP1",
"MAP3K7",
"NT5E",
"METTL3",
"UCK1",
"STXBP3",
"APMAP",
"UBIAD1",
"SFRP1",
"NCAPG2",
"UTP4",
"PACSIN2",
"PSMB6",
"MLH3",
"MINCR",
"KBTBD3",
"NOP2",
"USP13",
"EPSTI1",
"FABP4",
"CCDC127",
"ANKAR",
"SMAP2",
"PEBP4",
"ITGB1",
"CIRBP",
"G3BP2",
"LSM10",
"RANBP9",
"MINK1",
"DEPDC5",
"SPR",
"DDT",
"UBAC2",
"ADA",
"TTC5",
"CREBL2",
"RTCA",
"SAFB2",
"C11orf58",
"TBC1D10A",
"AGPAT2",
"TMEM106B",
"FOXP1",
"HAUS6",
"SLC33A1",
"LEO1",
"LACTB",
"SREK1IP1",
"TMEM167B",
"ZFR",
"RRP7A",
"CCT7",
"ABCA3",
"VAT1",
"RALY",
"KLHL6",
"ATRAID",
"CEP57L1",
"SRA1",
"NDUFA2",
"TTC7A",
"PIGW",
"NCBP1",
"PRDX2",
"PGM3",
"TRMT10B",
"GLO1",
"MEF2A",
"SIK1",
"CDK5RAP2",
"FCER1G",
"FER",
"CYLD",
"EMC10",
"TANGO6",
"SRPRB",
"CLTA",
"MALSU1",
"CYTH3",
"UTP15",
"ZNF584",
"ECD",
"ANKH",
"SDC3",
"EIF1AD",
"BTN3A2",
"SESN1",
"NDC80",
"SF3B2",
"DECR1",
"PHF11",
"OSBPL1A",
"ACBD4",
"HSF1",
"TMED4",
"TXLNA",
"CCNG1",
"LMCD1",
"MKS1",
"ARID3A",
"S100A4",
"TGFBR2",
"C2CD2",
"TNFRSF21",
"CCDC90B",
"NFU1",
"C1orf21",
"SIPA1L1",
"FAM234A",
"SAMHD1",
"ZNRF2",
"SASS6",
"TMEM101",
"USP54",
"ZDHHC18",
"CCNK",
"APBB1",
"IQCG",
"PLSCR1",
"UBE2O",
"LRIG2",
"MRPS27",
"CCZ1",
"NEK8",
"YTHDC1",
"BCL2",
"CYSTM1",
"ATMIN",
"PYGL",
"BID",
"ZNF343",
"TMEM41A",
"IRF2BPL",
"UHRF1BP1L",
"SCRN1",
"RPS3",
"CCL8",
"INTS10",
"NSG1",
"MGP",
"FBXW11",
"CRLS1",
"NOP14-AS1",
"HSPA13",
"STX2",
"LDLRAD3",
"ZNF823",
"ADGRF5",
"TOR2A",
"LTBP2",
"FMOD",
"LDHB",
"MTO1",
"TAOK3",
"RAI14",
"SIGLEC1",
"TYROBP",
"SEMA4A",
"EAPP",
"ZMYM6",
"PLCG2",
"MRPL32",
"STARD4-AS1",
"FBXL6",
"FAM20C",
"MAFF",
"DRAM2",
"SHROOM3",
"C22orf46",
"NUAK1",
"IMPDH1",
"WRAP53",
"INMT",
"PDE6D",
"RPL31",
"TMED9",
"ACD",
"PI4K2B",
"SDHC",
"LMO3",
"B4GAT1",
"DFFA",
"POLR3C",
"PTPRN2",
"UCHL5",
"HOMEZ",
"UBALD2",
"MAP4",
"CD320",
"TAF5L",
"CHURC1",
"LCP1",
"GMNN",
"DLEU1",
"PTBP1",
"SNRPD2",
"CRNDE",
"SETD1A",
"PTGS2",
"MAN1A1",
"HAPLN3",
"NQO2",
"WDR61",
"ANXA1",
"KIF15",
"FKBP10",
"TBCCD1",
"KIF2A",
"IL11RA",
"POMZP3",
"STK17B",
"SENP7",
"RGS18",
"TBC1D13",
"PEMT",
"PLAG1",
"ADAMTSL4",
"FDFT1",
"OGFOD1",
"MGAT1",
"EXOG",
"IRF2BP2",
"RRP36",
"PSMB5",
"TIGD2",
"SETD7",
"HARS2",
"MARCKS",
"PAXIP1",
"SLC26A6",
"PPP1R3E",
"POMT1",
"ME2",
"APIP",
"NOP16",
"PIAS2",
"FAM126A",
"TAGAP",
"NAGPA",
"P3H1",
"KHDRBS1",
"BBS2",
"SMIM10L1",
"AVPI1",
"NDUFAF3",
"KDM2A",
"DSE",
"TOPORS",
"CLK4",
"HNRNPK",
"PDCL3",
"P4HB",
"TMEM45A",
"ASF1A",
"XPNPEP1",
"ACAD10",
"GALNT1",
"GSK3B",
"NSUN6",
"CDKN2A",
"AP1M1",
"POLR2A",
"PPAT",
"HOXB7",
"RPL13",
"COPG1",
"PLBD2",
"ZNF747",
"PFDN5",
"ALG2",
"NAA25",
"CPM",
"NIP7",
"LRRK1",
"MRPS30",
"COL27A1",
"PAQR3",
"HSP90B1",
"CLEC4E",
"MRPL40",
"ARL14EP",
"RNF6",
"CRAMP1",
"IST1",
"CHCHD2",
"EVL",
"METTL8",
"SETD5",
"SHROOM1",
"KIF11",
"ZNF678",
"GLIS2",
"TCP1",
"FKBP9",
"ANAPC16",
"RAB2B",
"C2orf74",
"RNF149",
"FRYL",
"ZNF337",
"C16orf87",
"MLLT10",
"RBM14",
"SMARCA5",
"ALDH9A1",
"NCF2",
"EVI5",
"CLSPN",
"FUCA2",
"FSD1L",
"MEN1",
"RPP25",
"PARP10",
"POU2F1",
"C2CD2L",
"DHX32",
"ANKRD52",
"MDK",
"STRBP",
"ARG2",
"EED",
"SNX6",
"SNTB1",
"CENPW",
"B4GALT5",
"NAT14",
"DUSP4",
"TAGLN",
"UTP14C",
"CLIC3",
"RTKN",
"RBM15",
"HAUS4",
"NUDT6",
"ORAI2",
"CYB5R1",
"CLPTM1",
"NUBP1",
"TRPV2",
"NCBP3",
"LY75",
"PIAS1",
"TBC1D15",
"CREB5",
"PPP3CA",
"ZNF133",
"CD4",
"B3GAT3",
"TMEM123",
"TRAPPC2L",
"LINC00294",
"ORC4",
"LIN7C",
"TMEM258",
"PANK2",
"IFI44L",
"PLXNB1",
"SLFN13",
"AK3",
"ARL6IP6",
"PAN2",
"SLC20A1",
"SEC23B",
"PITPNA",
"MAP3K1",
"ARL3",
"DCTN5",
"ENTPD7",
"THEM6",
"MTHFD2",
"SYDE1",
"ROCK2",
"IGIP",
"UQCR10",
"ANKRD36C",
"FZR1",
"POLR2I",
"HP1BP3",
"CDC5L",
"GNA11",
"LINC00869",
"TPM2",
"GPR153",
"KRIT1",
"TSPAN9",
"UGP2",
"FIBP",
"TMEM42",
"MARK2",
"RHOBTB3",
"MYH10",
"TBC1D14",
"PPM1G",
"C11orf49",
"ACSL1",
"PPFIBP2",
"UBE2D1",
"DIP2B",
"ARHGAP35",
"PEBP1",
"CNN3",
"KLF9",
"DESI2",
"EPS15",
"KIAA0930",
"GPR89A",
"LTN1",
"GLUL",
"TRNT1",
"AMD1",
"CYGB",
"ARHGEF3",
"PLEKHM3",
"C9orf16",
"PTPRS",
"ACACB",
"MTERF3",
"AP3M2",
"ZNF846",
"MRM1",
"FAM20B",
"HNRNPU",
"EXD2",
"LOX",
"JMJD1C",
"ANGPTL4",
"CCDC149",
"DEAF1",
"RBPMS-AS1",
"TRMT6",
"ZNF138",
"PLEKHJ1",
"GRAMD1A",
"VAPA",
"GAMT",
"PACRGL",
"TARS2",
"TRAPPC12",
"PML",
"NUTF2",
"VIPAS39",
"P2RX4",
"FEZ2",
"MED4",
"RAB34",
"SUMO3",
"ORAI1",
"KCNQ1OT1",
"DNAJC17",
"GAREM1",
"TINAGL1",
"MARK4",
"EMP2",
"RRP1",
"TMEM14C",
"OMA1",
"PCGF3",
"SCAP",
"UBE3A",
"STOML2",
"HSD3B7",
"COL5A2",
"GMEB1",
"LATS2",
"CROT",
"PEX7",
"NOD2",
"TMEM50A",
"RALGAPA1",
"PIK3CB",
"PRPF31",
"GLB1L",
"STRAP",
"ACBD5",
"FUBP3",
"GNB2",
"S100A16",
"PDZD8",
"CDC16",
"DNAJC27",
"MLYCD",
"STXBP6",
"MTHFSD",
"SUGT1",
"TRAPPC4",
"AP1B1",
"CHI3L2",
"AFTPH",
"BNIP3L",
"SULF2",
"GPR68",
"METRNL",
"PRR7",
"DDX60L",
"NELFCD",
"TNFSF13B",
"GMEB2",
"FAM207A",
"ZNF521",
"NPHP1",
"KIAA0586",
"MAML2",
"IRF2",
"BAZ2B",
"SLC30A7",
"JOSD1",
"HAUS2",
"CIR1",
"WNT7B",
"COLEC12",
"NATD1",
"SLC36A1",
"DUT",
"UBTD2",
"SMG9",
"MAP3K11",
"PDCD4",
"EGR1",
"MAN2A1",
"ARRB2",
"IMPACT",
"LPIN2",
"GEM",
"GCFC2",
"G3BP1",
"SOX4",
"FAM160A2",
"WDR70",
"PHC1",
"MORC2",
"ABHD2",
"DPP7",
"RIT1",
"UBN1",
"PGAP3",
"TNFRSF12A",
"TET2",
"SDF2",
"RCE1",
"RNF170",
"MTMR14",
"AGO4",
"FTO",
"FKBP7",
"ETFA",
"FAM219A",
"KRTCAP3",
"DPP3",
"A1BG-AS1",
"RRN3",
"UGGT1",
"RDX",
"DDIT4",
"UBE2E3",
"GTF3C5",
"GGT1",
"ST3GAL4",
"SFXN1",
"RPL41",
"WDFY2",
"SRFBP1",
"TCAIM",
"PLAC9",
"CARS2",
"TXNRD2",
"MVB12A",
"ASH1L-AS1",
"ADPRH",
"PANK3",
"POMP",
"CALD1",
"SERPINB9",
"BCL7C",
"NLK",
"IRF6",
"DTD2",
"ST13",
"DNAJC21",
"UNC5B",
"RETN",
"ITGB7",
"PER2",
"RAD23B",
"FZD3",
"BPIFB1",
"MET",
"CSF1",
"NF1",
"MEIS2",
"MRPS2",
"FASTKD5",
"IFIH1",
"LRRC32",
"ANAPC13",
"OXCT1",
"POP7",
"SMIM20",
"RCC1",
"KCNMB1",
"TAMM41",
"NDUFA4",
"GPX1",
"NINJ2",
"CCDC59",
"WEE1",
"SMPDL3B",
"SPTY2D1",
"GPATCH11",
"EVI2B",
"SIGLEC14",
"ZNF362",
"COA5",
"FBXO25",
"WDR91",
"LATS1",
"WDR75",
"EML3",
"MTAP",
"PHF5A",
"IPO5",
"PTBP2",
"HNRNPAB",
"TAF6L",
"ZNF568",
"ITSN1",
"IWS1",
"DTX2",
"ZMAT2",
"GKN2",
"TCIRG1",
"CHN1",
"ZNF264",
"FBXW4",
"DOCK6",
"FAM214A",
"TIAL1",
"SLCO3A1",
"ALKBH8",
"HNRNPM",
"PLEKHM2",
"POLR1B",
"BMP2K",
"EFCAB2",
"PDCD11",
"ZNRF1",
"ADAMTS9",
"PSMB3",
"GLMP",
"NCOR2",
"EGFR",
"ZNF780B",
"CSRNP1",
"SCCPDH",
"ESCO2",
"ALPK1",
"SUMF2",
"FGGY",
"RIF1",
"SLC34A2",
"RANBP2",
"DOK1",
"LPAR6",
"FBXO33",
"TCTN2",
"MITD1",
"MMAB",
"HHEX",
"ZDHHC16",
"EIF2S2",
"PHYKPL",
"CD48",
"KCNJ2",
"MSL2",
"ANAPC11",
"IPO4",
"VCL",
"AKR7A2",
"CRIP1",
"EEF1A1",
"TGFBR1",
"BZW1",
"MRPS23",
"DBI",
"AAAS",
"MVK",
"PTPRE",
"ARHGAP5",
"CCNYL1",
"CHPT1",
"SS18",
"TNFAIP1",
"SLC52A2",
"CBX1",
"HIF1AN",
"RAB13",
"ANKDD1A",
"CALB2",
"FAM98B",
"ARL6IP1",
"SKA2",
"C12orf43",
"FLOT2",
"RASD1",
"PRR34-AS1",
"SUSD2",
"ARID5B",
"TMEM17",
"ZNF585A",
"MRPL53",
"GSTM4",
"PPP1R26",
"ERMP1",
"HS6ST1",
"TMEM263",
"INPP5E",
"MRPS33",
"STK38L",
"AXIN1",
"RHPN1",
"RRP9",
"UBXN6",
"RASSF1",
"GNPAT",
"DDRGK1",
"RPRD1B",
"CLN8",
"REL",
"CCNL2",
"LMBR1",
"NFATC1",
"UBE2J2",
"TMED3",
"EFNB2",
"FNIP1",
"EMC9",
"POLH",
"SRPK1",
"IL1R1",
"SCARF2",
"TUBGCP3",
"PRR5",
"GHDC",
"C12orf73",
"UQCRQ",
"CPT1A",
"MCAT",
"LRCH1",
"EMC8",
"GNPTAB",
"PPP2R5C",
"LRRFIP1",
"TUSC2",
"CWC15",
"NUDT9",
"SLC25A36",
"TYW3",
"SPPL2A",
"GNAI2",
"NR4A3",
"GNB5",
"KLHL7",
"PPP1R37",
"EVA1A",
"MT1E",
"PDGFRL",
"VAMP5",
"APOBEC3A",
"YWHAG",
"USF2",
"ZNF317",
"SLC25A29",
"LARP1",
"DSP",
"PPP1R14A",
"PHF20",
"PALD1",
"FADD",
"APEX1",
"SLC12A9",
"AZIN2",
"SGK1",
"ZMYND15",
"WDR92",
"ARL2",
"C6orf120",
"SERP1",
"SLC22A5",
"ENKD1",
"CTC1",
"ALG6",
"WBP1L",
"EIF2A",
"ENPP5",
"SLC35E4",
"SHOC2",
"RASSF5",
"ORMDL1",
"NFATC2IP",
"THADA",
"ZNF629",
"LRIG3",
"SMARCC2",
"TFG",
"CCDC102B",
"CRADD",
"SSB",
"PLEKHH2",
"TATDN1",
"NENF",
"RARG",
"CCDC51",
"DDX52",
"IKBKE",
"UBXN11",
"CNTRL",
"GZMK",
"C21orf91",
"TSEN2",
"DCTN3",
"RASEF",
"PCCA",
"TMEM9",
"PDGFD"
],
"rows": 10,
"table": true,
"tojson": true
},
{
"name": "gtf_hg19",
"title": "gene model (hg19)",
"object": "gtf_hg19",
"class": [
"data.table",
"data.frame"
],
"fields": [
"gene",
"gene_start",
"gene_end",
"CHROM",
"gene_length"
],
"rows": 26841,
"table": true,
"tojson": true
},
{
"name": "gtf_hg38",
"title": "gene model (hg38)",
"object": "gtf_hg38",
"class": [
"data.table",
"data.frame"
],
"fields": [
"gene",
"gene_start",
"gene_end",
"CHROM",
"gene_length"
],
"rows": 26807,
"table": true,
"tojson": true
},
{
"name": "gtf_mm10",
"title": "gene model (mm10)",
"object": "gtf_mm10",
"class": [
"data.table",
"data.frame"
],
"fields": [
"gene",
"gene_start",
"gene_end",
"CHROM",
"gene_length"
],
"rows": 30336,
"table": true,
"tojson": true
},
{
"name": "hc_example",
"title": "example hclust tree",
"object": "hc_example",
"class": [
"hclust"
],
"fields": [],
"table": false,
"tojson": false
},
{
"name": "joint_post_example",
"title": "example joint single-cell cnv posterior dataframe",
"object": "joint_post_example",
"class": [
"data.table",
"data.frame"
],
"fields": [
"cell",
"CHROM",
"seg",
"cnv_state",
"l11_x",
"l20_x",
"l10_x",
"l21_x",
"l31_x",
"l22_x",
"l00_x",
"Z_x",
"Z_cnv_x",
"Z_n_x",
"logBF_x",
"l11_y",
"l20_y",
"l10_y",
"l21_y",
"l31_y",
"l22_y",
"l00_y",
"Z_y",
"Z_cnv_y",
"Z_n_y",
"logBF_y",
"n_snp",
"MAF",
"major",
"seg_start",
"seg_end",
"n_genes",
"n_snps",
"prior_loh",
"prior_amp",
"prior_del",
"prior_bamp",
"prior_bdel",
"LLR",
"LLR_x",
"LLR_y",
"l11",
"l20",
"l10",
"l21",
"l31",
"l22",
"l00",
"Z_amp",
"Z_loh",
"Z_del",
"Z_bamp",
"Z_bdel",
"Z_n",
"Z",
"Z_cnv",
"p_amp",
"p_neu",
"p_del",
"p_loh",
"p_bamp",
"p_bdel",
"logBF",
"p_cnv",
"p_n",
"p_cnv_x",
"p_cnv_y",
"cnv_state_mle",
"cnv_state_map",
"seg_label",
"avg_entropy"
],
"rows": 3806,
"table": true,
"tojson": true
},
{
"name": "mut_graph_example",
"title": "example mutation graph",
"object": "mut_graph_example",
"class": [
"igraph"
],
"fields": [],
"table": false,
"tojson": false
},
{
"name": "phylogeny_example",
"title": "example single-cell phylogeny",
"object": "phylogeny_example",
"class": [
"tbl_graph",
"igraph"
],
"fields": [],
"table": false,
"tojson": false
},
{
"name": "pre_likelihood_hmm",
"title": "HMM object for unit tests",
"object": "pre_likelihood_hmm",
"class": [
"list"
],
"fields": [],
"table": false,
"tojson": true
},
{
"name": "ref_hca",
"title": "reference expression magnitudes from HCA",
"object": "ref_hca",
"class": [
"matrix",
"array"
],
"fields": [
"NK",
"Fibroblast",
"Macrophage",
"CD4+T",
"CD8+T",
"Endothelial",
"Myeloid",
"Monocyte",
"Dendritic",
"Plasma",
"B",
"Epithelial"
],
"rows": 24756,
"table": true,
"tojson": true
},
{
"name": "ref_hca_counts",
"title": "reference expression counts from HCA",
"object": "ref_hca_counts",
"class": [
"matrix",
"array"
],
"fields": [
"NK",
"Fibroblast",
"Macrophage",
"CD4+T",
"CD8+T",
"Endothelial",
"Myeloid",
"Monocyte",
"Dendritic",
"Plasma",
"B",
"Epithelial"
],
"rows": 24857,
"table": true,
"tojson": true
},
{
"name": "segs_example",
"title": "example CNV segments dataframe",
"object": "segs_example",
"class": [
"data.table",
"data.frame"
],
"fields": [
"sample",
"CHROM",
"seg",
"cnv_state",
"cnv_state_post",
"seg_start",
"seg_end",
"seg_start_index",
"seg_end_index",
"theta_mle",
"theta_sigma",
"phi_mle",
"phi_sigma",
"p_loh",
"p_del",
"p_amp",
"p_bamp",
"p_bdel",
"LLR",
"LLR_y",
"LLR_x",
"n_genes",
"n_snps",
"component",
"LLR_sample",
"seg_length",
"seg_cons",
"n_states",
"cnv_states",
"group"
],
"rows": 27,
"table": true,
"tojson": true
},
{
"name": "vcf_meta",
"title": "example VCF header",
"object": "vcf_meta",
"class": [
"character"
],
"fields": [],
"table": false,
"tojson": true
}
],
"_help": [
{
"page": "acen_hg19",
"title": "centromere regions (hg19)",
"topics": [
"acen_hg19"
]
},
{
"page": "acen_hg38",
"title": "centromere regions (hg38)",
"topics": [
"acen_hg38"
]
},
{
"page": "aggregate_counts",
"title": "Utility function to make reference gene expression profiles",
"topics": [
"aggregate_counts"
]
},
{
"page": "analyze_bulk",
"title": "Call CNVs in a pseudobulk profile using the Numbat joint HMM",
"topics": [
"analyze_bulk"
]
},
{
"page": "annot_ref",
"title": "example reference cell annotation",
"topics": [
"annot_ref"
]
},
{
"page": "annotate_genes",
"title": "Annotate genes on allele dataframe",
"topics": [
"annotate_genes"
]
},
{
"page": "bulk_example",
"title": "example pseudobulk dataframe",
"topics": [
"bulk_example"
]
},
{
"page": "chrom_sizes_hg19",
"title": "chromosome sizes (hg19)",
"topics": [
"chrom_sizes_hg19"
]
},
{
"page": "chrom_sizes_hg38",
"title": "chromosome sizes (hg38)",
"topics": [
"chrom_sizes_hg38"
]
},
{
"page": "cnv_heatmap",
"title": "Plot CNV heatmap",
"topics": [
"cnv_heatmap"
]
},
{
"page": "count_mat_example",
"title": "example gene expression count matrix",
"topics": [
"count_mat_example"
]
},
{
"page": "count_mat_ref",
"title": "example reference count matrix",
"topics": [
"count_mat_ref"
]
},
{
"page": "detect_clonal_loh",
"title": "Call clonal LOH using SNP density. Rcommended for cell lines or tumor samples with no normal cells.",
"topics": [
"detect_clonal_loh"
]
},
{
"page": "df_allele_example",
"title": "example allele count dataframe",
"topics": [
"df_allele_example"
]
},
{
"page": "gaps_hg19",
"title": "genome gap regions (hg19)",
"topics": [
"gaps_hg19"
]
},
{
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