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Jump to navigationJump to search- 00:24, 20 October 2014 diff hist -49 Abecasis Lab →Research Fellows
- 13:56, 22 September 2014 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
- 21:11, 18 September 2014 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
- 21:11, 18 September 2014 diff hist +3 Biostatistics 830: Main Page →Class Worksheets
- 21:09, 18 September 2014 diff hist 0 N File:Question Sheet - Menelaou et al (2013) Bioinformatics.pdf current
- 21:08, 18 September 2014 diff hist +517 Biostatistics 830: Main Page →Class Worksheets
- 15:18, 15 September 2014 diff hist +125 Biostatistics 830: Main Page →Scheduling
- 15:14, 9 September 2014 diff hist +38 Biostatistics 830: Main Page →Class Worksheets
- 15:12, 9 September 2014 diff hist +178 Biostatistics 830: Main Page →Required Reading
- 18:02, 4 September 2014 diff hist +1 Xiaowei Zhan current
- 18:02, 4 September 2014 diff hist +4 Abecasis Lab →Former Doctoral Students
- 17:59, 4 September 2014 diff hist +100 ChunkChromosome
- 17:59, 4 September 2014 diff hist +100 Minimac →Additional Sources of Information
- 15:49, 2 September 2014 diff hist 0 Biostatistics 830: Main Page →Required Reading
- 15:28, 2 September 2014 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
- 14:49, 2 September 2014 diff hist +101 Biostatistics 830: Main Page →Required Reading
- 14:48, 2 September 2014 diff hist +543 Biostatistics 830: Main Page →Required Reading
- 14:39, 2 September 2014 diff hist 0 Biostatistics 830: Main Page →Required Reading
- 14:39, 2 September 2014 diff hist +150 Biostatistics 830: Main Page →Required Reading
- 14:36, 2 September 2014 diff hist 0 Biostatistics 830: Main Page →Required Reading
- 14:35, 2 September 2014 diff hist +227 Biostatistics 830: Main Page →Required Reading
- 14:34, 2 September 2014 diff hist +531 Biostatistics 830: Main Page →Required Reading
- 14:04, 2 September 2014 diff hist -3,830 Biostatistics 830: Main Page
- 13:59, 2 September 2014 diff hist +8,505 N Biostatistics 830: Fall 2013 Edition Created page with "This is an archive of the Biostatistics 830 class page, as taught in the Fall of 2013. For the current edition of the course see Biostatistics 830: Main Page. == Objectiv..." current
- 11:06, 20 June 2014 diff hist -2 SeqShop: June 2014
- 11:05, 20 June 2014 diff hist +2 SeqShop: June 2014
- 11:04, 20 June 2014 diff hist +97 SeqShop: June 2014
- 11:01, 20 June 2014 diff hist 0 N File:2014.06 - Workshop Closing.pdf current
- 05:31, 16 June 2014 diff hist +55 SeqShop: June 2014
- 05:30, 16 June 2014 diff hist 0 N File:2014.06 - Abecasis Workshop Introduction.pdf current
- 10:32, 25 April 2014 diff hist +256 Abecasis Lab →Alumni
- 10:25, 25 April 2014 diff hist -16 Abecasis Lab →Graduate Students
- 10:02, 27 March 2014 diff hist -95 RAREMETALWORKER METHOD →Single Variant Score Tests
- 09:58, 27 March 2014 diff hist +167 RAREMETALWORKER METHOD →Single Variant Score Tests
- 09:56, 27 March 2014 diff hist 0 RAREMETALWORKER METHOD
- 09:56, 27 March 2014 diff hist -101 RAREMETALWORKER METHOD →Brief Introduction
- 17:55, 31 January 2014 diff hist +50 Abecasis Lab →Former Research Fellows
- 17:23, 31 January 2014 diff hist +19 Abecasis Lab →Staff
- 17:22, 31 January 2014 diff hist +64 Abecasis Lab →Former Staff
- 17:20, 31 January 2014 diff hist -30 Abecasis Lab →Staff
- 17:20, 31 January 2014 diff hist +22 Abecasis Lab →Former Masters Students
- 17:18, 31 January 2014 diff hist +150 Abecasis Lab →Former Research Fellows
- 17:17, 31 January 2014 diff hist -18 Abecasis Lab →Research Fellows
- 17:17, 31 January 2014 diff hist -20 Abecasis Lab →Graduate Students
- 17:15, 31 January 2014 diff hist +14 Abecasis Lab →Former Masters Students
- 16:48, 29 January 2014 diff hist +1 Tutorial: RAREMETAL →STEP 3: Run RAREMETAL for Meta-Analysis
- 16:48, 29 January 2014 diff hist +1 Tutorial: RAREMETAL →STEP 2: Analyze individual samples using RAREMETALWORKER
- 16:47, 29 January 2014 diff hist +17 Tutorial: RAREMETAL →STEP 3: Run RAREMETAL for Meta-Analysis
- 16:44, 29 January 2014 diff hist +1 Tutorial: RAREMETAL →STEP 2: Analyze individual samples using RAREMETALWORKER
- 09:51, 29 January 2014 diff hist 0 Minimac →using a MaCH reference panel
- 09:51, 29 January 2014 diff hist -7 Minimac →using a VCF reference panel
- 08:46, 29 January 2014 diff hist +541 Tutorial: RAREMETAL
- 18:19, 16 January 2014 diff hist +21 Abecasis Lab →Graduate Students
- 11:38, 16 December 2013 diff hist +13 Abecasis Lab →Former Masters Students
- 11:37, 16 December 2013 diff hist -1 Abecasis Lab →Graduate Students
- 16:08, 6 December 2013 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
- 16:08, 6 December 2013 diff hist +83 Biostatistics 830: Main Page →Class Worksheets
- 16:08, 6 December 2013 diff hist 0 N File:Question Sheet - Jun et al (2012) American Journal of Human Genetics.pdf current
- 16:07, 4 December 2013 diff hist 0 Rvtests →Genotyep filters
- 15:44, 4 December 2013 diff hist +1 RAREMETAL Documentation →Where to Download
- 13:30, 4 December 2013 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
- 13:30, 4 December 2013 diff hist +82 Biostatistics 830: Main Page →Class Worksheets
- 13:29, 4 December 2013 diff hist 0 N File:Question Sheet - Wu et al (2011) American Journal of Human Genetics.pdf current
- 18:03, 26 November 2013 diff hist +64 Biostatistics 830: Main Page →Class Worksheets
- 17:55, 26 November 2013 diff hist 0 N File:Question Sheet - Liu et al (2013) Nature Genetics.pdf
- 16:33, 25 November 2013 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
- 16:33, 25 November 2013 diff hist +93 Biostatistics 830: Main Page →Class Worksheets
- 16:10, 25 November 2013 diff hist +94 Biostatistics 830: Main Page →Class Worksheets
- 16:01, 25 November 2013 diff hist 0 N File:Question Sheet - Li and Durbin (2011) Nature.pdf current
- 18:19, 18 November 2013 diff hist +28 Abecasis Group Awards
- 18:19, 18 November 2013 diff hist +152 Abecasis Group Awards →International Genetic Epidemiology Society
- 16:10, 12 November 2013 diff hist -1 Biostatistics 830: Main Page →Class Worksheets
- 16:09, 12 November 2013 diff hist +7 Biostatistics 830: Main Page →Class Worksheets
- 16:09, 12 November 2013 diff hist +60 Biostatistics 830: Main Page →Class Worksheets
- 16:09, 12 November 2013 diff hist 0 N File:Question Sheet - Iqbal et al (2012) Nature Genetics.pdf
- 04:01, 7 November 2013 diff hist +146 Biostatistics 830: Main Page →Class Worksheets
- 04:00, 7 November 2013 diff hist 0 File:Question Sheet - Zerbino and Birney (2008) Bioinformatics.pdf Goncalo uploaded a new version of "File:Question Sheet - Zerbino and Birney (2008) Bioinformatics.pdf": Removed unnecessary second page. current
- 03:58, 7 November 2013 diff hist 0 File:Question Sheet - Li and Durbin (2009) Bioinformatics.pdf Goncalo uploaded a new version of "File:Question Sheet - Li and Durbin (2009) Bioinformatics.pdf": Fixed typos in code example. current
- 03:57, 7 November 2013 diff hist 0 N File:Question Sheet - Zerbino and Birney (2008) Bioinformatics.pdf
- 12:19, 30 October 2013 diff hist +78 Biostatistics 830: Main Page →Class Worksheets
- 12:19, 30 October 2013 diff hist 0 N File:Question Sheet - Li and Durbin (2009) Bioinformatics.pdf
- 12:18, 30 October 2013 diff hist +24 Biostatistics 830: Main Page →Class Worksheets
- 16:09, 28 October 2013 diff hist +6 830 - MaqIndex::LookupWord() current
- 13:58, 28 October 2013 diff hist +268 N 830 - BestAlignment::IterateCache() Created page with "<source lang="cpp"> unsigned int BestAlignment::IterateCache(unsigned int key) { int h = (key * PRIME) % cacheSize; while (cache[h] != -1 && cache[h] ..." current
- 13:53, 28 October 2013 diff hist +4 Biostatistics 830 - Code Snippets →Code Snippets current
- 13:53, 28 October 2013 diff hist +51 N 830 - BestAlignment::ClearCache() Goncalo moved page 830 - BestAlignment::ClearCache() to 830 - BestAlignment::ClearPositions() current
- 13:53, 28 October 2013 diff hist 0 m 830 - BestAlignment::ClearPositions() Goncalo moved page 830 - BestAlignment::ClearCache() to 830 - BestAlignment::ClearPositions() current
- 13:52, 28 October 2013 diff hist +142 N 830 - BestAlignment::ClearPositions() Created page with "<source lang="cpp"> void BestAlignment::ClearPositions() { cacheItems = 0; for (int i = 0; i < cacheSize; i++) cache[i] = -1; } </source>"
- 13:51, 28 October 2013 diff hist +265 N 830 - BestAlignment::isNewPosition() Created page with "<source lang="cpp"> bool BestAlignment::isNewPosition(unsigned int pos) { int h = IterateCache(pos); if (cache[h] == pos) return false; cache[h] = pos; cacheItems++; ..." current
- 13:49, 28 October 2013 diff hist +122 Biostatistics 830 - Code Snippets →Code Snippets
- 13:47, 28 October 2013 diff hist +32 830 - BestAlignment::EvaluateAlignment() (detailed comparison) current
- 13:47, 28 October 2013 diff hist +584 N 830 - BestAlignment::EvaluateAlignment() (detailed comparison) Created page with "void BestAlignment::EvaluateAlignment(String & reference, FastQ & read, unsigned int pos, bool fwd) { if (pos < 0 || read.Length() + pos > reference.Length()) return; if ..."
- 13:46, 28 October 2013 diff hist +350 N 830 - BestAlignment::EvaluateAlignment() (main loop) Created page with "<source lang="cpp"> void BestAlignment::EvaluateAlignment(MaqIndex & index, FastQ & read, unsigned int offset, bool fwd) { unsigned int start, stop; index.LookupWord(read...." current
- 13:45, 28 October 2013 diff hist +32 830 - BestAlignment::MaqAlignment() current
- 13:44, 28 October 2013 diff hist +1,224 N 830 - BestAlignment::MaqAlignment() Created page with "void BestAlignment::MaqAlignment(MaqIndex & index1, MaqIndex & index2, MaqIndex & index3, FastQ & read) { position = -1; sumQ = mapQ = 0; mismatches = read.Length(); forwa..."
- 13:44, 28 October 2013 diff hist +167 Biostatistics 830 - Code Snippets →Code Snippets
- 13:39, 28 October 2013 diff hist +500 N 830 - MaqIndex::GetWord() Created page with "<source lang="cpp"> long long MaqIndex::GetWord(String & sequence, unsigned int position) { long long word = 0; if (position + mask.Length() > sequence.Length()) return -..." current
- 13:38, 28 October 2013 diff hist +613 N 830 - MaqIndex::BuildIndex() Created page with "<source lang="cpp"> void MaqIndex::BuildIndex() { // This function could use quite a lot of memory ... // 4 bytes per word // 4 bytes per position // 4 bytes per ..." current
- 13:36, 28 October 2013 diff hist +1,079 N 830 - MaqIndex::LookupWord() Created page with "<source lang="cpp"> bool MaqIndex::LookupWord(String & sequence, int offset, unsigned int & firstOccurrence, unsigned int & lastOccurrence) { firstOccurrence = 0; lastOccurr..."
- 13:34, 28 October 2013 diff hist -2 830 - MaqIndex::CompareToIndex() current