minwoopak
/ Clonal_Evolution_Analysis.R
Created
October 7, 2024 01:42
— forked from chrisamiller/run.R
Fishplot - Updated Clonevol Integration in Additional File 2
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| library(sciClone) | |
| library(clonevol) | |
| library(fishplot) | |
| ## read in the data - copy number | |
| cn1 = read.table("tumor.cn",sep="\t",stringsAsFactors=F) | |
| cn2 = read.table("relapse.cn",sep="\t",stringsAsFactors=F) | |
| cn1 = cn1[,c(1,2,3,5)] | |
| cn2 = cn2[,c(1,2,3,5)] | |
| ## read in vaf data |
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| id,value,category | |
| Diversity Panel,58,Diversity Panel | |
| Focused Cancer,76,Related Disease | |
| Leukemia & |Lymphoma,29,Related Disease | |
| Inflammation,21,Related Disease | |
| Cardiovascular,22,Related Disease | |
| Diabetes,26,Related Disease | |
| Neurological,24,Related Disease | |
| Broad |Oncology,104,Related Disease | |
| Focussed |Safety,40,Related Disease |
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minwoopak
/ Brca_Basal_Tumor_Proteomics.exp.labeled
Last active
August 19, 2021 13:58
210819_ALPACA_v6
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| symbol location kegg exprs | |
| A1BG Extracellular space Summary 2.2901439787779974 | |
| A2M Extracellular space Complement and coagulation cascades 2.698718542339477 | |
| A2ML1 Extracellular space Summary 2.186132512127215 | |
| AAAS Cytoskeleton RNA transport 1.8528998484948849 | |
| AAAS Cytosol RNA transport 1.8528998484948849 | |
| AAAS Nucleus RNA transport 1.8528998484948849 | |
| AACS Cytosol Summary 0.6476449198836426 | |
| AADAT Cytosol Summary 1.4419559318834678 | |
| AADAT Mitochondrion Summary 1.4419559318834678 |
minwoopak
/ Brca_Basal_proteomics.exp.labeled
Last active
July 15, 2021 07:50
Protein Location Analyzer Input Data
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| symbol location kegg exprs | |
| A1BG Extracellular space none 2.2901439787779974 | |
| A2M Extracellular space Complement and coagulation cascades 2.698718542339477 | |
| A2ML1 Extracellular space none 2.186132512127215 | |
| AAAS Nucleus RNA transport 1.8528998484948849 | |
| AAAS Cytoskeleton RNA transport 1.8528998484948849 | |
| AAAS Cytosol RNA transport 1.8528998484948849 | |
| AACS Cytosol none 0.6476449198836426 | |
| AADAT Plasma membrane none 1.4419559318834678 | |
| AADAT Cytosol none 1.4419559318834678 |
minwoopak
/ protein_localization_cell_graphics.svg
Created
June 22, 2021 11:49
Protein Localization Cell Graphics
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minwoopak
/ OV.tumor.locFiltered.itraq.tsv
Created
June 22, 2021 00:28
OV Tumor Protein Quantification Data (Only proteins with location info)
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| symbol 09-1664-01A 61-2094-01A 25-1312-01A 13-1409-01A 24-1416-01A 29-1769-01A 13-1489-01A 13-1482-01A 13-1504-01A 13-1492-01A 36-2530-01A 25-2409-01A 13-1497-01A 61-1995-01A 13-2065-01A 61-1918-01A 61-2613-01A 23-1122-01A 24-1464-01A 25-1322-01A 24-1103-01A 24-2289-01A 13-1511-01A 24-1431-01A 36-1570-01A 13-1488-01A 24-1435-01A 30-1887-01A 23-1121-01A 24-1436-01A 13-2061-01A 36-2537-01A 24-1474-01A 13-1501-01A 24-1555-01A 24-1562-01A 25-1628-01A 24-1558-01A 29-1705-01A 24-1920-01A 30-1891-01A 61-2008-01A 24-1927-01A 36-2544-01A 24-2024-01A 29-1693-01A 13-1485-01A 24-2030-01A 29-1702-01A 24-2033-01A 24-2298-01A 24-1544-01A 61-1914-01A 25-1313-01A 29-1766-01A 24-2261-01A 25-1318-01A 36-2532-01A 13-2059-01A 25-2399-01A 29-1698-01A 29-1688-01A 13-1494-01A 13-1507-01A 29-1690-01A 25-1631-01A 13-1500-01A 29-1696-01A 29-1771-01A 13-2066-01A 29-1711-01A 13-1483-01A 24-1422-01A 29-1763-01A 25-2397-01A 29-2427-01A 29-1785-01A 61-2088-01A 25-1623-01A 36-1577-01A 29-1768-01A 36-1569-01A 36-2534-01A 36-2549-01A 36-2547-0 |
minwoopak
/ OV.normal.locFiltered.itraq.tsv
Created
June 22, 2021 00:27
OV Tumor Protein Quantification (Only proteins with location info)
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| symbol OVARIAN-CONTROL.1 OVARIAN-CONTROL.2 OVARIAN-CONTROL.3 OVARIAN-CONTROL.4 OVARIAN-CONTROL.5 OVARIAN-CONTROL.10 OVARIAN-CONTROL.6 OVARIAN-CONTROL.7 OVARIAN-CONTROL.8 OVARIAN-CONTROL.9 locations | |
| A1BG -0.1502189571456849 -0.0805052914950944 -0.246012807167401 -0.1486755030457313 -0.2090813845585678 -0.1286595513641955 -0.21453257721525895 -0.1724390717496462 -0.0808057417033928 -0.1358528383106838 Extracellular space | |
| A2M 0.0322562173619065 0.0227316355852755 -0.0189972131528324 0.0024661393590733 0.0200353476500812 -0.0128471221220725 0.034152247569455 -0.0081028045038869 0.0293355777519887 0.0120498314776176 Extracellular space | |
| A2ML1 -1.1616679957132512 -0.2886171307526257 -1.6161633631494177 -1.4301008404748228 -1.5322875804249998 -0.2167305514389663 -1.5017342186773466 -1.6189438611192986 -0.9860303844628444 -1.232298381993477 Extracellular space | |
| AAAS -0.0315266495465002 -0.2486881245945418 0.0 -0.1948123701315119 -0.1377493447799542 -0.0541702057584495 -0.0203395324759425 0.0628264223477427 -0.049407409 |
minwoopak
/ BRCA.normal.locFiltered.itraq.tsv
Created
June 22, 2021 00:23
BRCA Normal Protein Quantification Data (Only proteins with location info)
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| symbol | 263d3f-I | blcdb9-I | c4155b-C | locations | |
|---|---|---|---|---|---|
| A1BG | 1.5590886979306997 | 2.0746586868427017 | 2.4645703348221004 | Extracellular space | |
| A2M | 1.4395596593570654 | 2.5973614456722345 | 2.4825596265315366 | Extracellular space | |
| A2ML1 | 0.046995424688689 | 0.7294229150755784 | 0.28687585864791965 | Extracellular space | |
| AAAS | 0.36214045157430336 | 0.6069440532670369 | 0.11147673796775104 | Nucleus | |
| AAK1 | 0.08157590278758063 | 0.3927102507745711 | 0.10695312516942844 | Plasma membrane | |
| AAMP | -0.6139005051146706 | -1.5938469931922992 | -1.0858577430570375 | Plasma membrane | |
| AARS2 | -0.30404714495261365 | 0.16250487098259425 | -0.004348031820326615 | Mitochondrion | |
| ABAT | -0.11359125497813236 | 1.8550469831812133 | -0.2283415565723348 | Mitochondrion | |
| ABCA2 | -1.4747112486919738 | -3.910245261520092 | -1.4669611229747108 | Endosome,Lysosome |
minwoopak
/ symbols_to_KEGG_location_available.tsv
Last active
June 24, 2021 05:22
Symbols to KEGG Location
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| symbol kegg_terms | |
| CS 2-Oxocarboxylic acid metabolism,Biosynthesis of amino acids,Carbon metabolism,Citrate cycle (TCA cycle),Glyoxylate and dicarboxylate metabolism,Metabolic pathways | |
| NAGS 2-Oxocarboxylic acid metabolism,Arginine biosynthesis,Biosynthesis of amino acids,Metabolic pathways | |
| GOT2 2-Oxocarboxylic acid metabolism,Alanine aspartate and glutamate metabolism,Arginine and proline metabolism,Arginine biosynthesis,Biosynthesis of amino acids,Carbon metabolism,Cysteine and methionine metabolism,Fat digestion and absorption,Metabolic pathways,Phenylalanine metabolism,Phenylalanine tyrosine and tryptophan biosynthesis,Tyrosine metabolism | |
| IDH1 2-Oxocarboxylic acid metabolism,Biosynthesis of amino acids,Carbon metabolism,Central carbon metabolism in cancer,Citrate cycle (TCA cycle),Glutathione metabolism,Metabolic pathways,Peroxisome | |
| IDH2 2-Oxocarboxylic acid metabolism,Biosynthesis of amino acids,Carbon metabolism,Central carbon metabolism in cancer,Citrate cycle (TCA cycle),Glutathione metabolism,Metabolic |
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