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Web Supplement: Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression

John Wiedenhoeft, Eric Brugel, Alexander Schliep


Software

Software

Results on Additional Data Sets

GSE23949

Edgren, H., Murumagi, A., et al. (2011). Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biology, 12(1), R6. doi:10.1186/gb-2011-12-1-r6

Snijders

Snijders, A. M., Nowak, N., et al. (2001). Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genetics, 29(3), 263–264. doi:10.1038/ng754

Willenbrock and Fridlyand

Willenbrock, H., & Fridlyand, J. (2005). A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics, 21(22), 4084–91. doi:10.1093/bioinformatics/bti677

Breakpoint Detection and Merging

Results from both CBS and HaMMLET on 500 samples: Samples 1-10, Samples 11-20, Samples 21-30, Samples 31-40, Samples 41-50, Samples 51-60, Samples 61-70, Samples 71-80, Samples 81-90, Samples 91-100, Samples 101-110, Samples 111-120, Samples 121-130, Samples 131-140, Samples 141-150, Samples 151-160, Samples 161-170, Samples 171-180, Samples 181-190, Samples 191-200, Samples 201-210, Samples 211-220, Samples 221-230, Samples 231-240, Samples 241-250, Samples 251-260, Samples 261-270, Samples 271-280, Samples 281-290, Samples 291-300, Samples 301-310, Samples 311-320, Samples 321-330, Samples 331-340, Samples 341-350, Samples 351-360, Samples 361-370, Samples 371-380, Samples 381-390, Samples 391-400, Samples 401-410, Samples 411-420, Samples 421-430, Samples 431-440, Samples 441-450, Samples 451-460, Samples 461-470, Samples 471-480, Samples 481-490, Samples 491-500.

Spatial Resolution Study Testing Study

Results from both CBS and HaMMLET on 500 samples: Dataset 1, Dataset 2, Dataset 3, Dataset 4, Dataset 5, Dataset 6, Dataset 7, Dataset 8, Dataset 9, Dataset 10, Dataset 11, Dataset 12, Dataset 13, Dataset 14, Dataset 15, Dataset 16, Dataset 17, Dataset 18, Dataset 19, Dataset 20, Dataset 21, Dataset 22, Dataset 23, Dataset 24, Dataset 25, Dataset 26, Dataset 27, Dataset 28, Dataset 29, Dataset 30, Dataset 31, Dataset 32, Dataset 33, Dataset 34, Dataset 35, Dataset 36, Dataset 37, Dataset 38, Dataset 39, Dataset 40, Dataset 41, Dataset 42, Dataset 43, Dataset 44, Dataset 45, Dataset 46, Dataset 47, Dataset 48, Dataset 49, Dataset 50, Dataset 51, Dataset 52, Dataset 53, Dataset 54, Dataset 55, Dataset 56, Dataset 57, Dataset 58, Dataset 59, Dataset 60, Dataset 61, Dataset 62, Dataset 63, Dataset 64, Dataset 65, Dataset 66, Dataset 67, Dataset 68, Dataset 69, Dataset 70, Dataset 71, Dataset 72, Dataset 73, Dataset 74, Dataset 75, Dataset 76, Dataset 77, Dataset 78, Dataset 79, Dataset 80, Dataset 81, Dataset 82, Dataset 83, Dataset 84, Dataset 85, Dataset 86, Dataset 87, Dataset 88, Dataset 89, Dataset 90, Dataset 91, Dataset 92, Dataset 93, Dataset 94, Dataset 95, Dataset 96, Dataset 97, Dataset 98, Dataset 99, Dataset 100, Dataset 101, Dataset 102, Dataset 103, Dataset 104, Dataset 105, Dataset 106, Dataset 107, Dataset 108, Dataset 109, Dataset 110, Dataset 111, Dataset 112, Dataset 113, Dataset 114, Dataset 115, Dataset 116, Dataset 117, Dataset 118, Dataset 119, Dataset 120, Dataset 121, Dataset 122, Dataset 123, Dataset 124, Dataset 125, Dataset 126, Dataset 127, Dataset 128, Dataset 129, Dataset 130, Dataset 131, Dataset 132, Dataset 133, Dataset 134, Dataset 135, Dataset 136, Dataset 137, Dataset 138, Dataset 139, Dataset 140, Dataset 141, Dataset 142, Dataset 143, Dataset 144, Dataset 145, Dataset 146, Dataset 147, Dataset 148, Dataset 149, Dataset 150, Dataset 151, Dataset 152, Dataset 153, Dataset 154, Dataset 155, Dataset 156, Dataset 157, Dataset 158, Dataset 159, Dataset 160, Dataset 161, Dataset 162, Dataset 163, Dataset 164, Dataset 165, Dataset 166, Dataset 167, Dataset 168, Dataset 169, Dataset 170, Dataset 171, Dataset 172, Dataset 173, Dataset 174, Dataset 175, Dataset 176, Dataset 177, Dataset 178, Dataset 179, Dataset 180, Dataset 181, Dataset 182, Dataset 183, Dataset 184, Dataset 185, Dataset 186, Dataset 187, Dataset 188, Dataset 189, Dataset 190, Dataset 191, Dataset 192, Dataset 193, Dataset 194, Dataset 195, Dataset 196, Dataset 197, Dataset 198, Dataset 199, Dataset 200, Dataset 201, Dataset 202, Dataset 203, Dataset 204, Dataset 205, Dataset 206, Dataset 207, Dataset 208, Dataset 209, Dataset 210, Dataset 211, Dataset 212, Dataset 213, Dataset 214, Dataset 215, Dataset 216, Dataset 217, Dataset 218, Dataset 219, Dataset 220, Dataset 221, Dataset 222, Dataset 223, Dataset 224, Dataset 225, Dataset 226, Dataset 227, Dataset 228, Dataset 229, Dataset 230, Dataset 231, Dataset 232, Dataset 233, Dataset 234, Dataset 235, Dataset 236, Dataset 237, Dataset 238, Dataset 239, Dataset 240, Dataset 241, Dataset 242, Dataset 243, Dataset 244, Dataset 245, Dataset 246, Dataset 247, Dataset 248, Dataset 249, Dataset 250, Dataset 251, Dataset 252, Dataset 253, Dataset 254, Dataset 255, Dataset 256, Dataset 257, Dataset 258, Dataset 259, Dataset 260, Dataset 261, Dataset 262, Dataset 263, Dataset 264, Dataset 265, Dataset 266, Dataset 267, Dataset 268, Dataset 269, Dataset 270, Dataset 271, Dataset 272, Dataset 273, Dataset 274, Dataset 275, Dataset 276, Dataset 277, Dataset 278, Dataset 279, Dataset 280, Dataset 281, Dataset 282, Dataset 283, Dataset 284, Dataset 285, Dataset 286, Dataset 287, Dataset 288, Dataset 289, Dataset 290, Dataset 291, Dataset 292, Dataset 293, Dataset 294, Dataset 295, Dataset 296, Dataset 297, Dataset 298, Dataset 299, Dataset 300, Dataset 301, Dataset 302, Dataset 303, Dataset 304, Dataset 305, Dataset 306, Dataset 307, Dataset 308, Dataset 309, Dataset 310, Dataset 311, Dataset 312, Dataset 313, Dataset 314, Dataset 315, Dataset 316, Dataset 317, Dataset 318, Dataset 319, Dataset 320, Dataset 321, Dataset 322, Dataset 323, Dataset 324, Dataset 325, Dataset 326, Dataset 327, Dataset 328, Dataset 329, Dataset 330, Dataset 331, Dataset 332, Dataset 333, Dataset 334, Dataset 335, Dataset 336, Dataset 337, Dataset 338, Dataset 339, Dataset 340, Dataset 341, Dataset 342, Dataset 343, Dataset 344, Dataset 345, Dataset 346, Dataset 347, Dataset 348, Dataset 349, Dataset 350, Dataset 351, Dataset 352, Dataset 353, Dataset 354, Dataset 355, Dataset 356, Dataset 357, Dataset 358, Dataset 359, Dataset 360, Dataset 361, Dataset 362, Dataset 363, Dataset 364, Dataset 365, Dataset 366, Dataset 367, Dataset 368, Dataset 369, Dataset 370, Dataset 371, Dataset 372, Dataset 373, Dataset 374, Dataset 375, Dataset 376, Dataset 377, Dataset 378, Dataset 379, Dataset 380, Dataset 381, Dataset 382, Dataset 383, Dataset 384, Dataset 385, Dataset 386, Dataset 387, Dataset 388, Dataset 389, Dataset 390, Dataset 391, Dataset 392, Dataset 393, Dataset 394, Dataset 395, Dataset 396, Dataset 397, Dataset 398, Dataset 399, Dataset 400, Dataset 401, Dataset 402, Dataset 403, Dataset 404, Dataset 405, Dataset 406, Dataset 407, Dataset 408, Dataset 409, Dataset 410, Dataset 411, Dataset 412, Dataset 413, Dataset 414, Dataset 415, Dataset 416, Dataset 417, Dataset 418, Dataset 419, Dataset 420, Dataset 421, Dataset 422, Dataset 423, Dataset 424, Dataset 425, Dataset 426, Dataset 427, Dataset 428, Dataset 429, Dataset 430, Dataset 431, Dataset 432, Dataset 433, Dataset 434, Dataset 435, Dataset 436, Dataset 437, Dataset 438, Dataset 439, Dataset 440, Dataset 441, Dataset 442, Dataset 443, Dataset 444, Dataset 445, Dataset 446, Dataset 447, Dataset 448, Dataset 449, Dataset 450, Dataset 451, Dataset 452, Dataset 453, Dataset 454, Dataset 455, Dataset 456, Dataset 457, Dataset 458, Dataset 459, Dataset 460, Dataset 461, Dataset 462, Dataset 463, Dataset 464, Dataset 465, Dataset 466, Dataset 467, Dataset 468, Dataset 469, Dataset 470, Dataset 471, Dataset 472, Dataset 473, Dataset 474, Dataset 475, Dataset 476, Dataset 477, Dataset 478, Dataset 479, Dataset 480, Dataset 481, Dataset 482, Dataset 483, Dataset 484, Dataset 485, Dataset 486, Dataset 487, Dataset 488, Dataset 489, Dataset 490, Dataset 491, Dataset 492, Dataset 493, Dataset 494, Dataset 495, Dataset 496, Dataset 497, Dataset 498, Dataset 499, Dataset 500