MOVARSim presets
Authors/Creators
- 1. University of Padova
-
2.
Ab Analitica (Italy)
Description
This page contains cancer-specific presets derived from COSMIC and TCGA to inform MOVARSim's parameters for 21 cancer types.
The presets contain the information needed to derive realistic and cancer-specific values for the characteristics of variants (total number of variants per sample, number of variants per type, variants zigosity, variants lengths, variants positions) which are specified in the main input format of MOVARSim, i.e. the VAR file.
Files are named using the following format: <database_name>_mutations_workspace_<tumor_type>.RData.
- <database_name> can be either "cosmic_core" or "tgca".
- <tumor_type> can be: "adrenal_gland", "biliary_tract","bone", "cervix", "eye", "kidney", "liver", "esophagus", "ovary", "pancreas", "pleura", "prostate", "skin", "soft_tissue", "stomach", "testis", "thymus", "thyroid".
Files
Files
(461.2 MB)
| Name | Size | Download all |
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md5:583f462d7b0655003e4f7b21dbd4c4bc
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198.9 kB | Download |
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md5:0ee3b880018002897d1e9716eea07e96
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13.9 MB | Download |
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md5:a4269fa12d61c1860cc67be87734355a
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1.2 MB | Download |
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md5:e48451f6b745ffb85b173466db77163b
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39.5 MB | Download |
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md5:9e07c6ffa6ff703c41b5c5f46a8ef1dd
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2.7 MB | Download |
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md5:0c163e01fbb2459610a8842c6893b3b5
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44.7 MB | Download |
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md5:0de4726279dd64031151ccb8df0825bb
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26.1 MB | Download |
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md5:2f03de9fe400d2d55e58088410d3de3c
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57.0 kB | Download |
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md5:661e7076cdc08af0ef2b42a13ef7c43d
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9.8 MB | Download |
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md5:4bdb9772207b4251073fb32ac59b4196
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60.7 MB | Download |
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md5:c6e7461e9c1ad8e82b49cdafbcedbb57
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32.0 MB | Download |
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md5:6f009f4b2fbc0a34f85ad5eeb6a33bf5
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13.9 MB | Download |
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md5:a3cc6bded23cb0d94997dda693394942
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33.8 MB | Download |
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md5:413533ecfee8c5f1f252735713a24137
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59.6 kB | Download |
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md5:e754d8abf91a04230fe7f95dff17d1bd
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28.0 MB | Download |
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md5:eb9174da3fcb8d4bddf899b5fa933103
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52.3 MB | Download |
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md5:77030cddbf968209ff4ae51bde6ef9a9
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10.1 MB | Download |
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md5:3d9637cb4de54688b5c83d5cda314ace
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26.0 MB | Download |
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md5:b05a0598f3d1549049da61160eef5b42
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51.4 kB | Download |
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md5:99556dfdf45701ab26a4662e9e2dbbbb
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27.7 kB | Download |
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md5:8f0b91df4129912b72d965fd750c6d9b
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5.3 MB | Download |
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md5:701788e19ad38d64c11b943a2d4bce65
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342.6 kB | Download |
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md5:eff4c0875aa7e10d4edd79e72315ad62
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24.8 kB | Download |
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md5:15fd45fe1ec7c8c33fc69294ea5f7219
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56.9 kB | Download |
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md5:27686ccad15e371f76e1bf23995e1a50
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3.4 MB | Download |
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md5:819323d498f05fec87586c5bf41bba20
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2.3 MB | Download |
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md5:9e1d9e41c95b84f437ca43725c21467d
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11.2 MB | Download |
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md5:912c5e8f659655b1d84fb73b7211ac47
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1.1 MB | Download |
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md5:730cd1fac38bf0dfa4846b5cdcbc9ce0
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24.7 kB | Download |
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md5:4a7d53b162255ad9f90103ce5b43f179
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1.9 MB | Download |
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md5:6b13926c4ab2da5743e57c3178596578
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1.5 MB | Download |
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md5:b28cfb7e8b71979728bebf2184408354
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15.7 MB | Download |
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md5:ba982a3bf9f3ab86d6a2ae4750e8a44c
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1.9 MB | Download |
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md5:a79689334908a22ce31072609a9b7d4b
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1.2 MB | Download |
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md5:6c1825f259c25cad5759a57a91028cc2
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45.5 kB | Download |
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md5:87509ee59a868c4ab9f5b42ea626072b
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732.0 kB | Download |
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md5:1e12cabf7e5266fc236b266d0ec31af2
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12.5 MB | Download |
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md5:c0c9f24127bcf4e222acb3c7913a01c3
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383.6 kB | Download |
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md5:48f110b4ded306ce4a9cca311cd9b862
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6.3 MB | Download |
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md5:1aea56f811ca20210049bbced023d656
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33.8 kB | Download |
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md5:c405023105c83c2f91393466c6f184f2
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31.7 kB | Download |
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md5:079433d3a430bbb4f5c08cc748e6b774
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59.9 kB | Download |
Additional details
Software
- Repository URL
- https://gitlab.com/sysbiobig/movarsim
- Programming language
- Python , R , C
References
- Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E, Fish P, Harsha B, Hathaway C, Jupe SC, Kok CY, Noble K, Ponting L, Ramshaw CC, Rye CE, Speedy HE, Stefancsik R, Thompson SL, Wang S, Ward S, Campbell PJ, Forbes SA. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947. doi: 10.1093/nar/gky1015. PMID: 30371878; PMCID: PMC6323903.
- Cancer Genome Atlas Research Network; Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764. PMID: 24071849; PMCID: PMC3919969.