User contributions
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Jump to navigationJump to search- 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
- 13:34, 28 October 2013 diff hist +345 N 830 - MaqIndex::CompareToIndex() Created page with "<source lang="cpp"> int MaqIndex::CompareToIndex(String & sequence, unsigned int offset, unsigned int index) { index = sortedPositions[index]; for (unsigned int i = 0; i <..."
- 13:33, 28 October 2013 diff hist +137 Biostatistics 830 - Code Snippets →Code Snippets
- 13:29, 28 October 2013 diff hist +2,285 N 830 - BasicMapper::main() Created page with "<source lang="cpp"> int main(int argc, char ** argv) { // Record start time for this run time_t start = time(NULL); // This function summarizes available options and proc..." current
- 13:28, 28 October 2013 diff hist +266 Biostatistics 830 - Code Snippets →Howie et al (2012) Nat Genet
- 13:26, 28 October 2013 diff hist +54 Biostatistics 830: Main Page →Required Reading
- 12:45, 25 October 2013 diff hist +220 Abecasis Lab →Former Doctoral Students
- 14:48, 14 October 2013 diff hist +95 RAREMETAL Documentation →Useful Wiki Pages
- 05:11, 11 October 2013 diff hist +93 Biostatistics 830: Main Page →Class Worksheets
- 05:10, 11 October 2013 diff hist 0 N File:Question Sheet - Li et al (2008) Genome Research.pdf current
- 11:13, 3 October 2013 diff hist +53 N RAREMETAL-SOFTWARE Goncalo moved page RAREMETAL-SOFTWARE to Rare Variant Analysis and Meta-Analysis current
- 11:13, 3 October 2013 diff hist 0 m Rare Variant Analysis and Meta-Analysis Goncalo moved page RAREMETAL-SOFTWARE to Rare Variant Analysis and Meta-Analysis current
- 16:16, 2 October 2013 diff hist 0 830 - Haplotyper::ImputeGenotypes() (edge) current
- 16:15, 2 October 2013 diff hist 0 830 - Haplotyper::ImputeGenotypes() (internal) current
- 16:03, 2 October 2013 diff hist 0 830 - Haplotyper::SampleOneHaplotype() current
- 15:55, 2 October 2013 diff hist -1 830 - Haplotyper::SummarizeOptions() current
- 15:06, 2 October 2013 diff hist +574 830 - MINIMAC::main() current
- 14:57, 2 October 2013 diff hist +421 830 - MINIMAC::main()
- 14:52, 2 October 2013 diff hist -1 830 - MINIMAC::main()
- 14:52, 2 October 2013 diff hist +11,013 N 830 - MINIMAC::main() Created page with "</source lang="cpp"> int main(int argc, char ** argv) { time_t start = time(NULL); printf("MiniMac - Imputation into phased haplotypes\n" "(c) 2010-2011 Goncalo..."
- 14:51, 2 October 2013 diff hist +27 Biostatistics 830 - Code Snippets →Code Snippets
- 14:31, 2 October 2013 diff hist +15 Biostatistics 830 - Code Snippets →Code Snippets
- 14:31, 2 October 2013 diff hist +75 N 830 - Haplotyper::ScoreLeftConditional smart() Goncalo moved page 830 - Haplotyper::ScoreLeftConditional smart() to 830 - Haplotyper::ScoreLeftConditional() (smart, complicated): Consistency. current
- 14:31, 2 October 2013 diff hist 0 m 830 - Haplotyper::ScoreLeftConditional() (smart, complicated) Goncalo moved page 830 - Haplotyper::ScoreLeftConditional smart() to 830 - Haplotyper::ScoreLeftConditional() (smart, complicated): Consistency. current
- 14:29, 2 October 2013 diff hist +215 830 - Haplotyper::ImputeGenotypes() (internal)
- 14:28, 2 October 2013 diff hist +645 N 830 - Haplotyper::ImputeGenotypes() (internal) Created page with "void Haplotyper::ImputeGenotypes(float * matrix1, float * matrix2, int marker) { posterior[0][marker] = posterior[1][marker] = posterior[2][marker] = 0.0; for (int i..."
- 14:26, 2 October 2013 diff hist +673 N 830 - Haplotyper::ImputeGenotypes() (edge) Created page with "<source lang="cpp"> void Haplotyper::ImputeGenotypes(float * matrix, int marker) { posterior[0][marker] = posterior[1][marker] = posterior[2][marker] = 0.0; for (in..."
- 14:25, 2 October 2013 diff hist +100 Biostatistics 830 - Code Snippets →Code Snippets
- 14:19, 2 October 2013 diff hist -498 830 - Haplotyper::ImputeGenotypes() current
- 14:16, 2 October 2013 diff hist -1 830 - Haplotyper::SampleOneHaplotype()
- 14:15, 2 October 2013 diff hist +198 830 - Haplotyper::SampleOneHaplotype()
- 14:14, 2 October 2013 diff hist +316 N 830 - Haplotyper::SampleOneHaplotype() Created page with "<source lang="cpp"> float Haplotyper::SampleOneHaplotype(float * vector, double first, double & second, float & choice) { for (second = 0; second < states; second++) ..."
- 14:14, 2 October 2013 diff hist +44 Biostatistics 830 - Code Snippets →Code Snippets
- 14:13, 2 October 2013 diff hist +2 830 - Haplotyper::SummarizeOptions()
- 14:13, 2 October 2013 diff hist +1,150 N 830 - Haplotyper::SummarizeOptions() Created page with "<code lang="cpp"> float Haplotyper::SummarizeOptions(float * vector, float ** left, float ** right, float theta, int first, int second) { right[0][0] = (1. - theta) * (..."
- 14:12, 2 October 2013 diff hist +42 Biostatistics 830 - Code Snippets →Code Snippets
- 14:11, 2 October 2013 diff hist +30 830 - Haplotyper::SampleChromosomes() current
- 14:11, 2 October 2013 diff hist +1,350 N 830 - Haplotyper::SampleChromosomes() Created page with " void Haplotyper::SampleChromosomes(Random * rand) { RewindMemoryPool(); RetrieveMemoryBlock(markers - 1); int first = 0, second = 0; SampleHaplotypes(leftMat..."
- 14:10, 2 October 2013 diff hist +9 830 - Haplotyper::SampleHaplotypes() current
- 14:08, 2 October 2013 diff hist -589 830 - Haplotyper::SampleHaplotypes()
- 14:08, 2 October 2013 diff hist +43 Biostatistics 830 - Code Snippets →Code Snippets
- 14:06, 2 October 2013 diff hist +4 830 - Haplotyper::SampleHaplotypes()
- 14:05, 2 October 2013 diff hist +1,364 N 830 - Haplotyper::SampleHaplotypes() Created page with "<source lang="cpp"> void Haplotyper::SampleChromosomes(Random * rand) { RewindMemoryPool(); RetrieveMemoryBlock(markers - 1); int first = 0, second = 0; Sampl..."
- 14:05, 2 October 2013 diff hist +42 Biostatistics 830 - Code Snippets →Code Snippets
- 13:30, 2 October 2013 diff hist +1 830 - Haplotyper::ScoreLeftConditional() current
- 13:27, 2 October 2013 diff hist -376 830 - Haplotyper::ScoreLeftConditional()
- 13:26, 2 October 2013 diff hist +966 N 830 - Haplotyper::ScoreLeftConditional() (smart, complicated) Created page with "<source lang="cpp"> // This version of the ScoreLeftConditional() function deals with sites // where no genotypes are observed a little more efficiently. // void Haplotyper:..."
- 13:25, 2 October 2013 diff hist +52 Biostatistics 830 - Code Snippets →Code Snippets
- 02:03, 27 September 2013 diff hist -16 Abecasis Lab →Staff
- 01:30, 27 September 2013 diff hist 0 Abecasis Lab →Former Research Fellows
- 15:01, 25 September 2013 diff hist +1,257 N 830 - MarkovModel::CountErrorsAndRecombinants() Created page with "<source lang="cpp"> void MarkovModel::CountErrorsAndRecombinants(char * observed, char ** haplotypes, float ** freq) { float * swap; float * vector = new float [state..." current
- 14:57, 25 September 2013 diff hist +508 N 830 - MarkovModel::CountErrors() Created page with "<source lang="cpp"> double MarkovModel::CountErrors(float * vector, char ** haplotypes, int position, char observed, double e, double freq) { if (observed == 0) re..." current
- 14:54, 25 September 2013 diff hist +487 N 830 - MarkovModel::CountRecombinants() Created page with "<source lang="cpp"> double MarkovModel::CountRecombinants(float * from, float * to, double r) { if (r == 0) return 0.0; double sum = 0.0; for (int i = 0; i ..." current
- 14:53, 25 September 2013 diff hist +135 Biostatistics 830 - Code Snippets →Code Snippets
- 14:50, 25 September 2013 diff hist +1,345 N 830 - MarkovModel::Impute() Created page with "<source lang="cpp"> void MarkovModel::Impute(char * major, char * observed, float * probs, char ** haplotypes, float ** freqs, int position) { d..." current
- 14:45, 25 September 2013 diff hist +33 Biostatistics 830 - Code Snippets →Code Snippets
- 14:45, 25 September 2013 diff hist +974 N 830 - MarkovModel::WalkRight() Created page with "<source lang="cpp"> void MarkovModel::WalkRight(char * major, char * observed, char ** haplotypes, float ** freqs) { float * swap; float * vector = new float [states]..." current
- 14:43, 25 September 2013 diff hist +36 Biostatistics 830 - Code Snippets →Code Snippets
- 14:42, 25 September 2013 diff hist +637 N 830 - MarkovModel::WalkLeft() Created page with "<source lang="cpp"> void MarkovModel::WalkLeft(char * observed, char ** haplotypes, float ** freqs) { // Initialize likelihoods at first position for (int i = 0; i < ..."
- 14:41, 25 September 2013 diff hist +35 Biostatistics 830 - Code Snippets →Code Snippets
- 14:40, 25 September 2013 diff hist -36 830 - MarkovModel::Condition() current
- 14:40, 25 September 2013 diff hist +476 N 830 - MarkovModel::Condition() Created page with "<source lang="cpp"> void MarkovModel::Condition(float * vector, char ** haplotypes, int position, char observed, double e, double freq) { if ..."
- 14:40, 25 September 2013 diff hist +1 Biostatistics 830 - Code Snippets →Code Snippets
- 14:40, 25 September 2013 diff hist +35 Biostatistics 830 - Code Snippets →Code Snippets
- 14:39, 25 September 2013 diff hist -202 830 - MarkovModel::Transpose() current
- 14:37, 25 September 2013 diff hist +767 N 830 - MarkovModel::Transpose() Created page with "<source lang="cpp"> void MarkovModel::Transpose(float * from, float * to, double r) { if (r == 0) for (int i = 0; i < states; i++) to[i] = from[i]; els..."
- 14:36, 25 September 2013 diff hist +2 Biostatistics 830 - Code Snippets →Code Snippets
- 14:36, 25 September 2013 diff hist +34 Biostatistics 830 - Code Snippets →Howie et al (2012) Nat Genet
- 14:33, 25 September 2013 diff hist +72 Biostatistics 830: Main Page →Scheduling
- 14:33, 25 September 2013 diff hist 0 N File:Question Sheet - Li et al (2010) Gen Epid.pdf current
- 14:32, 25 September 2013 diff hist +81 Biostatistics 830: Main Page →Class Worksheets
- 14:32, 25 September 2013 diff hist 0 N File:Question Sheet - Howie et al (2012) Nat Genet.pdf current
- 14:31, 25 September 2013 diff hist +174 Biostatistics 830: Main Page →Scheduling
- 14:29, 25 September 2013 diff hist 0 N File:Question Sheet - Browing and Browning (2012) Am J Hum Genet.pdf current
- 11:00, 25 September 2013 diff hist +208 Biostatistics 830 - Code Snippets →Howie et al (2012) Nat Genet
- 11:00, 25 September 2013 diff hist +54 Biostatistics 830: Main Page →Required Reading
- 10:59, 25 September 2013 diff hist +82 Biostatistics 830 - Code Snippets →Li et al (2010) Genet Epidemiol
- 10:58, 25 September 2013 diff hist +1,613 Biostatistics 830: Main Page →Scheduling
- 15:56, 13 September 2013 diff hist -163 830 - Haplotyper::RandomSetup() current
- 15:07, 13 September 2013 diff hist +16 Biostatistics 830: Main Page →Required Reading
- 15:06, 13 September 2013 diff hist -1 830 - Haplotyper::ImputeGenotypes()
- 15:06, 13 September 2013 diff hist +1,221 N 830 - Haplotyper::ImputeGenotypes() Created page with "</source lang="cpp"> void Haplotyper::ImputeGenotypes() { RewindMemoryPool(); // Process the last position RetrieveMemoryBlock(markers - 1); ImputeGenotypes(le..."
- 15:04, 13 September 2013 diff hist +41 Biostatistics 830 - Code Snippets →Code Snippets
- 15:02, 13 September 2013 diff hist +31 830 - Haplotyper::ScoreLeftConditional()
- 15:01, 13 September 2013 diff hist +797 N 830 - Haplotyper::ScoreLeftConditional() Created page with "void Haplotyper::ScoreLeftConditional() { ResetMemoryPool(); GetMemoryBlock(0); SetupPrior(leftMatrices[0]); ConditionOnData(leftMatrices[0], 0, current_genoty..."
- 15:00, 13 September 2013 diff hist +46 Biostatistics 830 - Code Snippets →Code Snippets
- 14:58, 13 September 2013 diff hist 0 830 - Haplotyper::ConditionOnData() current
- 14:58, 13 September 2013 diff hist +666 N 830 - Haplotyper::ConditionOnData() Created page with "<source code="cpp"> void Haplotyper::ConditionOnData(float * matrix, int marker, char genotype) { // We treat missing genotypes as uninformative about the mosaic's //..."
- 14:56, 13 September 2013 diff hist 0 830 - Haplotyper::SetupPrior() current
- 14:56, 13 September 2013 diff hist +324 N 830 - Haplotyper::SetupPrior() Created page with "<source code="cpp"> void Haplotyper::SetupPrior(float * matrix) { float prior = 1.0 / (states * states); for (int i = 0; i < states; i++) { for (int j = ..."
- 14:55, 13 September 2013 diff hist +77 Biostatistics 830 - Code Snippets →Code Snippets
- 14:52, 13 September 2013 diff hist +1,947 N 830 - Haplotyper::Transpose() Created page with "<source lang="cpp"> void Haplotyper::Transpose(float * source, float * dest, float theta) { // *source and *dest store a vector with likelihood information for each pos..." current
- 14:48, 13 September 2013 diff hist +1 Biostatistics 830 - Code Snippets →Code Snippets
- 14:48, 13 September 2013 diff hist +34 Biostatistics 830 - Code Snippets →Code Snippets
- 14:47, 13 September 2013 diff hist +91 830 - Haplotyper::RandomSetup()
- 14:46, 13 September 2013 diff hist +1,837 N 830 - Haplotyper::RandomSetup() Created page with "<source lang="cpp"> void Haplotyper::RandomSetup(Random * rand) { // access two arrays... // genotypes[i][j] includes genotypes for each individual // i..."
- 14:42, 13 September 2013 diff hist +37 Biostatistics 830 - Code Snippets →Code Snippets
- 14:38, 13 September 2013 diff hist +263 N Biostatistics 830 - Code Snippets Created page with "== Li et al (2010) Genet Epidemiol == === Full Citation === Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotyp..."
- 14:37, 13 September 2013 diff hist +16 Biostatistics 830: Main Page →Required Reading
- 14:37, 13 September 2013 diff hist +22 Biostatistics 830: Main Page →Required Reading
- 10:50, 9 September 2013 diff hist -2 Abecasis Group Awards
- 10:50, 9 September 2013 diff hist +129 Abecasis Group Awards →Goncalo's Awards
- 15:10, 4 September 2013 diff hist -12 Biostatistics 830: Main Page →Required Reading
- 15:09, 4 September 2013 diff hist +175 Biostatistics 830: Main Page →Required Reading
- 15:08, 4 September 2013 diff hist +162 Biostatistics 830: Main Page →Required Reading
- 15:05, 4 September 2013 diff hist +51 Biostatistics 830: Main Page →Required Reading
- 10:32, 4 September 2013 diff hist -3 Biostatistics 830: Main Page →Required Reading
- 10:31, 4 September 2013 diff hist +26 Biostatistics 830: Main Page →Required Reading
- 10:30, 4 September 2013 diff hist +130 Biostatistics 830: Main Page →Required Reading
- 10:25, 4 September 2013 diff hist +2,526 Biostatistics 830: Main Page →Required Reading
- 09:27, 4 September 2013 diff hist +2,396 N Biostatistics 830: Core Competencies Created page with "The Council for Education in Public Health recommends that every course document the Public Health competencies covered in its syllabus. This is the list of competencies cover..." current
- 09:24, 4 September 2013 diff hist -198 Biostatistics 666: Main Page
- 09:22, 4 September 2013 diff hist +2,344 N Biostatistics 830: Main Page Created page with "== Objective == Gene mapping studies study the relationship between genetic variation and susceptibility to human disease. These studies are changing rapidly with the availab..."
- 09:15, 4 September 2013 diff hist +42 N 830 Redirected page to Biostatistics 830: Main Page current
- 09:15, 4 September 2013 diff hist +42 N Biostatistics 830 Redirected page to Biostatistics 830: Main Page current
- 09:13, 4 September 2013 diff hist +39 MediaWiki:Sidebar
- 12:33, 12 August 2013 diff hist +27 Short Workshops →Low Pass Whole Genomes
- 12:32, 12 August 2013 diff hist +137 Short Workshops
- 01:51, 3 August 2013 diff hist +44 Goncalo Abecasis →2013 Overton Prize current
- 01:50, 3 August 2013 diff hist -2 Goncalo Abecasis
- 01:50, 3 August 2013 diff hist +66 Goncalo Abecasis →2013 Overton Prize
- 12:10, 2 August 2013 diff hist +100 Goncalo Abecasis →See Also
- 12:07, 2 August 2013 diff hist 0 N File:2013.07 - Overton Award Final.pdf current
- 10:17, 2 August 2013 diff hist +114 Abecasis Group Awards →American Society of Human Genetics
- 15:24, 12 June 2013 diff hist +37 Dajiang Liu →Rare Metal and Rare Metal Worker
- 15:23, 12 June 2013 diff hist +228 Dajiang Liu
- 15:21, 12 June 2013 diff hist +40 Scott Vrieze
- 15:20, 12 June 2013 diff hist 0 N File:Scott Vrieze.jpg current
- 12:14, 12 June 2013 diff hist +17 Dajiang Liu
- 03:30, 12 June 2013 diff hist +324 Exome Chip Design →Cautious Sites
- 11:42, 11 June 2013 diff hist +187 N Dajiang Liu Created page with 'Dajiang Liu is currently a research fellow working on rare variant analysis methods with Goncalo Abecasis. Previously, he completed his Ph.D. at Rice University working with Suza…'
- 11:41, 11 June 2013 diff hist +4 Abecasis Lab →Research Fellows
- 04:29, 10 June 2013 diff hist +12 Abecasis Lab →Staff
- 04:28, 10 June 2013 diff hist +13 Abecasis Lab →Graduate Students
- 14:56, 7 June 2013 diff hist +118 Goncalo Abecasis: Interview with Christiana Fogg current
- 12:24, 5 June 2013 diff hist +6 Abecasis Group Awards →Goncalo's Awards
- 12:22, 5 June 2013 diff hist -8 Abecasis Group Awards →Goncalo's Awards
- 12:21, 5 June 2013 diff hist +115 Abecasis Group Awards →Goncalo's Awards
- 18:28, 21 May 2013 diff hist -9 Trial Enrichment →Download current
- 18:27, 21 May 2013 diff hist +48 VerifyBamID →Interpreting output files
- 21:08, 15 May 2013 diff hist +874 Goncalo Abecasis
- 18:32, 15 May 2013 diff hist +18,913 N Goncalo Abecasis: Interview with Christiana Fogg Created page with 'In March 2013, I was awarded the Overton Prize by the International Society for Computational Biology (ISCB). I am not sure I deserve it and, perhaps to double check if they had …'
- 18:23, 15 May 2013 diff hist +70 Goncalo Abecasis
- 18:22, 15 May 2013 diff hist +1 Goncalo Abecasis
- 18:22, 15 May 2013 diff hist -2 Goncalo Abecasis
- 00:20, 13 May 2013 diff hist +6 TrioCaller →Introduction
- 00:19, 13 May 2013 diff hist +16 TrioCaller →Note: if you are interesting in detecting de novo mutations, or are working on a small number of families with high coverage data (e.g. exome sequencing), please first try our sister program Polymutt .
- 00:14, 13 May 2013 diff hist -34 TrioCaller →Introduction
- 10:08, 8 March 2013 diff hist +231 Nm User talk:Dajiang Liu Welcome! current
- 10:08, 8 March 2013 diff hist +1,163 Nm User:Dajiang Liu Creating user page with biography of new user. current
- 21:51, 7 March 2013 diff hist -83 Tutorial: RAREMETAL →STEP 1: Install Software and Download Example Data Sets
- 21:47, 7 March 2013 diff hist -319 Tutorial: RAREMETAL →Introduction
- 13:36, 5 March 2013 diff hist +3 Minimac: Tutorial →Getting Started
- 13:35, 5 March 2013 diff hist +1 Minimac: Tutorial →Getting Started
- 13:30, 5 March 2013 diff hist +10 Minimac: Tutorial →Getting Started
- 00:05, 4 March 2013 diff hist +15 Abecasis Lab →Research Fellows
- 15:32, 31 January 2013 diff hist +89 Minimac: Tutorial →Imputation into Phased Haplotypes - minimac
- 15:29, 31 January 2013 diff hist -88 Minimac: Tutorial →Imputation into Phased Haplotypes - minimac
- 09:10, 31 January 2013 diff hist +955 Minimac Diagnostics →Leave One Out Statistics
- 09:00, 31 January 2013 diff hist +6 Minimac
- 09:00, 31 January 2013 diff hist +446 Minimac
- 12:58, 10 January 2013 diff hist +35 Abecasis Lab →Graduate Students
- 12:57, 10 January 2013 diff hist +16 Abecasis Lab →Former Masters Students
- 12:57, 10 January 2013 diff hist -1 Abecasis Lab →Graduate Students
- 12:56, 10 January 2013 diff hist +133 Abecasis Lab →Former Doctoral Students
- 12:54, 10 January 2013 diff hist -12 Abecasis Lab →Graduate Students
- 15:53, 9 January 2013 diff hist +113 Code Sample: Generating QQ Plots in R
- 15:53, 9 January 2013 diff hist +114 Code Sample: Generating Manhattan Plots in R
- 15:20, 9 January 2013 diff hist 0 N File:Sample-manhattan-plot-B.png current
- 15:20, 9 January 2013 diff hist 0 N File:Sample-manhattan-plot-A.png current
- 15:19, 9 January 2013 diff hist 0 N File:Sample-manhattan-plot.png current
- 15:17, 9 January 2013 diff hist +20,172 N Code Sample: Generating Manhattan Plots in R Created page with 'A useful way to summarize genome-wide association data is with a Manhattan plot. This type of plot has a point for every SNP or location tested with the position in the genome al…'
- 12:50, 9 January 2013 diff hist +9 Exome Chip Design →Second Generation Arrays
- 12:49, 9 January 2013 diff hist 0 Exome Chip Design →Second Generation Arrays
- 12:49, 9 January 2013 diff hist +2,085 Exome Chip Design →Illumina Exome Arrays
- 11:50, 22 December 2012 diff hist +154 Abecasis Lab →Former Research Fellows
- 11:48, 22 December 2012 diff hist -17 Abecasis Lab →Staff
- 11:48, 22 December 2012 diff hist +2 Abecasis Lab →International Visitors
- 11:47, 22 December 2012 diff hist +16 Abecasis Lab →Research Fellows
- 17:06, 21 December 2012 diff hist +235 Nm User talk:Chaolong Wang Welcome! current
- 17:06, 21 December 2012 diff hist +389 Nm User:Chaolong Wang Creating user page with biography of new user. current
- 15:34, 20 December 2012 diff hist -7 Biostatistics 666: Main Page
- 09:19, 5 December 2012 diff hist 0 File:666.24.pdf uploaded a new version of "File:666.24.pdf": →Minor tweaks current
- 06:56, 5 December 2012 diff hist -8 Biostatistics 666: Core Competencies current
- 10:58, 4 December 2012 diff hist +2,404 N Biostatistics 666: Core Competencies Created page with 'The Council for Education in Public Health recommends that every course document the Public Health competencies covered in its subject syllabus. This is the list of competencies …'
- 10:45, 4 December 2012 diff hist +131 Biostatistics 666: Main Page →Objective
- 19:25, 3 December 2012 diff hist +67 Abecasis Lab →Former Doctoral Students
- 19:22, 3 December 2012 diff hist +44 Abecasis Lab →Former Research Fellows
- 19:20, 3 December 2012 diff hist 0 Abecasis Lab →Former Doctoral Students
- 19:18, 3 December 2012 diff hist 0 Abecasis Lab →Former Doctoral Students
- 19:16, 3 December 2012 diff hist +99 Abecasis Lab →Former Research Fellows
- 05:22, 3 December 2012 diff hist 0 File:666.20.pdf uploaded a new version of "File:666.20.pdf": This version adds a tiny bit more detail on the use of empirical kinship coefficients. current
- 04:47, 3 December 2012 diff hist 0 Biostatistics 666: Main Page →Class Notes
- 04:46, 3 December 2012 diff hist +135 Biostatistics 666: Introduction to De Novo Assembly →Recommended Reading
- 04:44, 3 December 2012 diff hist +87 Biostatistics 666: Introduction to De Novo Assembly →Overview
- 04:43, 3 December 2012 diff hist 0 File:666.2012.01.pdf uploaded a new version of "File:666.2012.01.pdf": Added discussion of Lander Waterman results on contig lengths. current
- 14:58, 28 November 2012 diff hist 0 File:666.2011.01.pdf uploaded a new version of "File:666.2011.01.pdf": Typo fixes. current
- 09:28, 28 November 2012 diff hist 0 File:666.2011.01.pdf uploaded a new version of "File:666.2011.01.pdf": Minor updates (for consistency with new preceding lectures); added references for variable threshold test.
- 16:28, 27 November 2012 diff hist +116 Abecasis Group Awards →European Society of Human Genetics
- 09:40, 26 November 2012 diff hist +10 Biostatistics 666: Introduction to De Novo Assembly →Recommended Reading
- 09:39, 26 November 2012 diff hist +399 N Biostatistics 666: Introduction to De Novo Assembly Created page with '== Overview == Introduces the issues surrounding de novo assembly of complex genomes, with a particular focus on issues related to variant discovery. == Slides == [[Media:666.…'
- 09:37, 26 November 2012 diff hist +13 N File:666.2012.01.pdf Version zero!
- 09:37, 26 November 2012 diff hist +89 Biostatistics 666: Main Page →Class Notes
- 02:08, 21 November 2012 diff hist 0 Biostatistics 666: Main Page →Class Notes
- 02:07, 21 November 2012 diff hist 0 File:666.2011.02.pdf uploaded a new version of "File:666.2011.02.pdf": →Minor update; added empirical distribution of read pair distances from QPLOT current
- 02:06, 21 November 2012 diff hist 0 File:666.2010.05.pdf uploaded a new version of "File:666.2010.05.pdf": →Minor typo fixes current
- 21:09, 16 November 2012 diff hist -14 RAREMETALWORKER Minor typos fixed
- 00:32, 14 November 2012 diff hist 0 File:666.2010.04.pdf uploaded a new version of "File:666.2010.04.pdf": Minor updates, adding Ion Torrent as a sequencing technology and adding some specific numbers to illustrate the scale of genetic variation that can be reached by sequencing. current
- 06:33, 12 November 2012 diff hist 0 File:666.2010.03.pdf uploaded a new version of "File:666.2010.03.pdf": Adds a summary slide. current
- 06:26, 12 November 2012 diff hist 0 Biostatistics 666: Main Page →Class Notes
- 03:33, 31 October 2012 diff hist 0 File:666.17.pdf uploaded a new version of "File:666.17.pdf" current
- 03:33, 31 October 2012 diff hist 0 File:666.16.pdf uploaded a new version of "File:666.16.pdf": Minor typo fix. current
- 03:07, 29 October 2012 diff hist 0 File:666.16.pdf uploaded a new version of "File:666.16.pdf": Fixed look of slides with equations.
- 02:08, 29 October 2012 diff hist -3 Biostatistics 666: Linkage Analysis in Sibling Pairs →Recommended Reading
- 05:24, 22 October 2012 diff hist 0 File:666.2010.02.pdf uploaded a new version of "File:666.2010.02.pdf": Updated lecture to include example from an actual affected sibling pair study. The lecture is still far too long. current
- 06:16, 3 October 2012 diff hist 0 File:666.12.pdf uploaded a new version of "File:666.12.pdf": Minor edits. current
- 02:25, 26 September 2012 diff hist 0 File:666.10.pdf uploaded a new version of "File:666.10.pdf": Minor tweaks. Now explicitly mentions use of the E-M algorithm to estimate subpopulations and their frequencies or for calling genotype clusters. current
- 23:05, 18 September 2012 diff hist 0 File:666.06.pdf uploaded a new version of "File:666.06.pdf" current
- 08:40, 10 September 2012 diff hist 0 File:666.03.pdf uploaded a new version of "File:666.03.pdf": Minor updates. current
- 02:15, 5 September 2012 diff hist 0 File:2011.666.01.pdf uploaded a new version of "File:2011.666.01.pdf": Yet more minor edits, this time listing potential group projects. current
- 02:07, 5 September 2012 diff hist 0 File:2011.666.01.pdf uploaded a new version of "File:2011.666.01.pdf": Minor update for 2012, adding more detail to HWE discussion, link to online class notes, and potential discussion of grading scheme
- 02:02, 5 September 2012 diff hist 0 File:2011.666.01.pdf uploaded a new version of "File:2011.666.01.pdf"
- 01:17, 5 September 2012 diff hist +46 Biostatistics 666: Main Page →Course History
- 01:16, 5 September 2012 diff hist +103 Biostatistics 666: Main Page →Course History
- 01:12, 5 September 2012 diff hist +116 Biostatistics 666: Main Page →Standards of Academic Conduct
- 01:11, 5 September 2012 diff hist +12 Biostatistics 666: Main Page →Course History
- 01:11, 5 September 2012 diff hist -16 Biostatistics 666: Main Page →Office Hours
- 01:10, 5 September 2012 diff hist -169 Biostatistics 666: Main Page →Scheduling
- 01:08, 5 September 2012 diff hist +19 Biostatistics 666: Main Page →Objective
- 01:07, 5 September 2012 diff hist -167 Biostatistics 666: Main Page →Problem Set Solutions
- 10:46, 8 June 2012 diff hist -18 Minimac →Running Minimac
- 15:55, 1 June 2012 diff hist +230 Nm User talk:Michael Welcome! current
- 15:55, 1 June 2012 diff hist +318 Nm User:Michael Creating user page with biography of new user. current
- 15:53, 1 June 2012 diff hist +333 Karma
- 10:34, 13 April 2012 diff hist +16 Abecasis Group Awards →Goncalo's Awards
- 10:33, 13 April 2012 diff hist +131 Abecasis Group Awards →Goncalo's Awards
- 15:02, 5 April 2012 diff hist +80 Short Workshops
- 05:27, 8 February 2012 diff hist +1 TrioCaller →Converting Alignments to BAM format
- 05:24, 8 February 2012 diff hist +6 TrioCaller →Genotype Refinement Using Linkage Disequilibrium Information (TrioCaller)
- 05:23, 8 February 2012 diff hist -92 TrioCaller →Genotype Refinement Using Linkage Disequilibrium Information (TrioCaller)
- 05:22, 8 February 2012 diff hist +102 TrioCaller →Genotype Refinement Using Linkage Disequilibrium Information (TrioCaller)
- 05:20, 8 February 2012 diff hist +135 TrioCaller →Alternative way to call variants
- 05:18, 8 February 2012 diff hist -8 TrioCaller →Initial set of variant calls
- 05:16, 8 February 2012 diff hist -405 TrioCaller →Mapping Reads to The Genome
- 05:11, 8 February 2012 diff hist +91 TrioCaller →Building an Index for Short Read Alignment
- 05:09, 8 February 2012 diff hist -61 TrioCaller →Required Software
- 05:02, 8 February 2012 diff hist +9 TrioCaller →Download with example datasets
- 07:42, 23 January 2012 diff hist +380 N ThunderVCF Created page with 'This a modified version of MACH, designed for the accurate genotyping of low pass sequence data from unrelated individuals and included in the UMAKE download. The tool requi…' current
- 07:37, 23 January 2012 diff hist +287 Tutorial: Low Pass Sequence Analysis →Example Dataset
- 07:32, 23 January 2012 diff hist 0 Tutorial: Low Pass Sequence Analysis →Example Dataset
- 17:56, 20 January 2012 diff hist +523 Tutorial: Low Pass Sequence Analysis →Mapping Reads to The Genome
- 05:42, 20 January 2012 diff hist +236 Tutorial: Low Pass Sequence Analysis →Example Dataset
- 04:49, 7 December 2011 diff hist +92 N File:666.24.pdf Introduction to likelihood calculations in large pedigrees and the Elston Stewart algorithm.
- 04:48, 7 December 2011 diff hist +257 N Biostatistics 666: Likelihood Calculations for Large Pedigrees Created page with '== Outline == This lecture introduces an alternative formulation of the pedigree likelihood, that does not rely on summation over IBD states. The lecture also introduces the Els…' current
- 04:47, 7 December 2011 diff hist +95 Biostatistics 666: Main Page →Class Notes
- 04:20, 7 December 2011 diff hist 0 File:666.2011.01.pdf uploaded a new version of "File:666.2011.01.pdf": Corrected small typos.
- 04:19, 7 December 2011 diff hist 0 File:666.2011.02.pdf uploaded a new version of "File:666.2011.02.pdf": Corrected small typos.
- 09:14, 5 December 2011 diff hist +5 Biostatistics 666: Analysis of Copy Number Using Sequence Data →Recommended Reading current
- 09:13, 5 December 2011 diff hist +50 N File:666.2011.02.pdf Copy Number Variation Analysis Using Sequence Data
- 09:13, 5 December 2011 diff hist +524 N Biostatistics 666: Analysis of Copy Number Using Sequence Data Created page with '== Overview == Introduces the analysis of copy number variation using next generation sequence data, discussing the types of evidence that can be observed in one individual and …'
- 09:11, 5 December 2011 diff hist +100 Biostatistics 666: Main Page →Class Notes
- 07:48, 30 November 2011 diff hist +2 Biostatistics 666: Rare Variant Burden Tests →Recommended Reading current
- 07:48, 30 November 2011 diff hist +551 N Biostatistics 666: Rare Variant Burden Tests Created page with '== Objective == Discussion of the challenges involved in the analysis of rare variation. Introduces basic burden tests, discusses the benefits of different variant weighting sch…'
- 07:44, 30 November 2011 diff hist +82 Biostatistics 666: Main Page →Class Notes
- 07:43, 30 November 2011 diff hist +61 N File:666.2011.01.pdf Introduction to Rare Variant Burden Tests and Related Issues.
- 05:59, 28 November 2011 diff hist 0 File:666.2010.05.pdf uploaded a new version of "File:666.2010.05.pdf": Added Sardinia example and discussion of consensus genotype calling.
- 04:25, 28 November 2011 diff hist 0 File:666.2010.03.pdf uploaded a new version of "File:666.2010.03.pdf": Fixes several small typos in worked imputation examples.
- 07:49, 23 November 2011 diff hist 0 File:666.2010.04.pdf uploaded a new version of "File:666.2010.04.pdf": Updates to introduce base quality, mapping quality and base alignment quality.
- 06:55, 21 November 2011 diff hist 0 File:666.17.pdf uploaded a new version of "File:666.17.pdf": Minor updates to figures.
- 06:54, 21 November 2011 diff hist 0 File:666.16.pdf uploaded a new version of "File:666.16.pdf": Minor updates to figures.
- 06:54, 21 November 2011 diff hist 0 File:666.2010.03.pdf uploaded a new version of "File:666.2010.03.pdf": Minor cosmetic updates.
- 07:17, 16 November 2011 diff hist 0 File:666.20.pdf uploaded a new version of "File:666.20.pdf": This version removes page numbers (a visual nuisance) and adds a mention of approaches that use empirical, rather than pedigree based, kinship coefficients.
- 07:15, 16 November 2011 diff hist 0 File:666.20.pdf uploaded a new version of "File:666.20.pdf"
- 08:01, 9 November 2011 diff hist 0 File:666.16.pdf uploaded a new version of "File:666.16.pdf": Fixed typos, added example of age-related macular degeneration linkage study.
- 17:53, 7 November 2011 diff hist +76 Exome Chip Design →Grunt Work
- 05:12, 7 November 2011 diff hist 0 File:666.2010.02.pdf uploaded a new version of "File:666.2010.02.pdf": Simplified lecture to make it fit more easily into one hour.
- 17:43, 3 November 2011 diff hist +31 MediaWiki:Common.css current
- 17:38, 3 November 2011 diff hist +185 Code Sample: Generating QQ Plots in R →Sample Usage
- 17:34, 3 November 2011 diff hist +66 Code Sample: Generating QQ Plots in R →R Lattice Graphics
- 17:30, 3 November 2011 diff hist +31,589 N MediaWiki:Common.css Created page with '→CSS placed here will be applied to all skins: →Copied verbatim from en.wikipedia.org/wiki/MediaWiki:Common.css: #interwiki-completelist { font-weight: bold; } bod…'
- 07:03, 2 November 2011 diff hist +82 Biostatistics 666: Main Page →Older Lectures
- 07:02, 2 November 2011 diff hist -82 Biostatistics 666: Main Page →Class Notes
- 11:49, 1 November 2011 diff hist +7 Code Sample: Generating QQ Plots in R
- 11:44, 1 November 2011 diff hist +209 N MediaWiki:Geshi.css Created page with '→CSS placed here will be applied to GeSHi syntax highlighting: div.mw-geshi div, pre { padding: 1em; margin: 1em 0; border: 1px dashed #2f6fab; font-family: monospa…' current
- 16:41, 31 October 2011 diff hist +8,486 N Code Sample: Generating QQ Plots in R Created page with 'Quantile-quantile plots (qq-plots) can be useful for verifying that a set of values come from a certain distribution. For example in a genome-wide association study, we expect th…'
- 16:40, 31 October 2011 diff hist +14 N File:Pval-qq-sample.png Sample QQ Plot current
- 11:45, 28 October 2011 diff hist +69 Biostatistics 666: Main Page →Problem Set Solutions
- 11:44, 28 October 2011 diff hist +29 Biostatistics 666: Main Page →Office Hours
- 11:43, 28 October 2011 diff hist +34 Biostatistics 666: Main Page →Office Hours
- 11:42, 28 October 2011 diff hist -76 Biostatistics 666: Main Page →Scheduling
- 10:09, 28 October 2011 diff hist +234 Nm User talk:Clement Ma Welcome! current
- 10:09, 28 October 2011 diff hist +353 Nm User:Clement Ma Creating user page with biography of new user. current
- 02:22, 24 October 2011 diff hist 0 File:666.12.pdf uploaded a new version of "File:666.12.pdf": Added ACE gene example
- 09:54, 18 October 2011 diff hist +325 N Talk:Minimac: 1000 Genomes Imputation Cookbook Created page with 'Issues to resolve: * No --prefix in MACH example command line (both for single job and in parallel) * Should make sure MACH output is gzipped (I think Yun has enabled this by de…' current
- 09:50, 18 October 2011 diff hist 0 IMPUTE2: 1000 Genomes Imputation Cookbook →Imputation
- 09:48, 10 October 2011 diff hist -1 Exome Chip Design →Online Content
- 09:47, 10 October 2011 diff hist +314 Exome Chip Design →Online Content
- 09:46, 10 October 2011 diff hist -2 Exome Chip Design →Online Content
- 09:46, 10 October 2011 diff hist 0 Exome Chip Design →Online Content
- 09:45, 10 October 2011 diff hist +33 Exome Chip Design →Online Content
- 09:45, 10 October 2011 diff hist 0 Exome Chip Design →Online Content
- 09:44, 10 October 2011 diff hist +264 Exome Chip Design →Key Credit
- 09:41, 10 October 2011 diff hist +49 N File:2011.09 - Exome Chip.pdf Summary of exome chip design process and content. current
- 17:46, 4 October 2011 diff hist +44 Abecasis Lab →Former Doctoral Students
- 10:32, 3 October 2011 diff hist 0 Abecasis Lab →Alumni
- 07:00, 3 October 2011 diff hist +28 Abecasis Lab →Former Masters Students
- 07:00, 3 October 2011 diff hist -4 Abecasis Lab →Graduate Students
- 06:58, 3 October 2011 diff hist -14 Abecasis Lab →Research Fellows
- 06:57, 3 October 2011 diff hist +260 Abecasis Lab →Former Research Fellows
- 06:05, 3 October 2011 diff hist 0 File:666.06.pdf uploaded a new version of "File:666.06.pdf": Minor updates to the lecture, including: * Explicit formulae for Tajima's D (very complicated!) * More extended discussion of the impact of population size on the coalescent
- 09:37, 30 September 2011 diff hist +9 Exome Chip Design →Content Contributors
- 22:43, 29 September 2011 diff hist +11 Exome Chip Design →Assay Design Rates
- 22:20, 29 September 2011 diff hist +43 Exome Chip Design →Content Contributors
- 22:16, 29 September 2011 diff hist +28 Exome Chip Design →Content Contributors
- 22:12, 29 September 2011 diff hist +31 Exome Chip Design →Content Contributors
- 22:10, 29 September 2011 diff hist +1,486 Exome Chip Design →Grunt Work
- 19:19, 29 September 2011 diff hist +104 METAL Documentation →Specifying Weights in P-value Based Analysis
- 19:13, 29 September 2011 diff hist +163 Exome Chip Design →Coding Variants
- 19:11, 29 September 2011 diff hist +33 Exome Chip Design →Grunt Work
- 19:11, 29 September 2011 diff hist 0 Exome Chip Design →Assay Design Rates
- 19:10, 29 September 2011 diff hist +7 Exome Chip Design →Assay Design Rates
- 19:09, 29 September 2011 diff hist -13 Exome Chip Design →Assay Design Rates
- 19:09, 29 September 2011 diff hist +90 Exome Chip Design →Assay Design Rates
- 19:08, 29 September 2011 diff hist +387 Exome Chip Design →Assay Design Rates
- 19:04, 29 September 2011 diff hist +5 Exome Chip Design →Assay Design Rates
- 19:04, 29 September 2011 diff hist +485 Exome Chip Design
- 18:58, 29 September 2011 diff hist +1,429 Exome Chip Design →Coding Variants
- 18:46, 29 September 2011 diff hist -60 Exome Chip Design →HLA tag SNPs
- 18:45, 29 September 2011 diff hist +7 Exome Chip Design →Chromosome Y SNPs
- 18:45, 29 September 2011 diff hist -1 Exome Chip Design →Mitochondrial SNPs
- 18:44, 29 September 2011 diff hist +65 Exome Chip Design →Functionally interesting variants
- 18:44, 29 September 2011 diff hist -62 Exome Chip Design →Fingerprint SNPs
- 18:44, 29 September 2011 diff hist +127 Exome Chip Design →Random set of synonymous variants (as comparator)
- 18:43, 29 September 2011 diff hist -54 Exome Chip Design →Scaffold for Identity by Descent
- 18:42, 29 September 2011 diff hist -17 Exome Chip Design →Native American vs European Ancestry
- 18:39, 29 September 2011 diff hist 0 Exome Chip Design →African American vs European Ancestry
- 18:39, 29 September 2011 diff hist -59 Exome Chip Design →African American vs European Ancestry
- 18:38, 29 September 2011 diff hist -574 Exome Chip Design →Tags for Previously Described GWAS Hits
- 12:59, 29 September 2011 diff hist +77 Exome Chip Design →Additional Content
- 12:58, 29 September 2011 diff hist +432 Exome Chip Design →Variants that Alter Protein Function
- 12:52, 29 September 2011 diff hist +116 Exome Chip Design →Splice Variants
- 12:48, 29 September 2011 diff hist +612 Exome Chip Design →HLA tag SNPs
- 12:42, 29 September 2011 diff hist -358 Exome Chip Design →Variants that Alter Protein Function
- 11:55, 29 September 2011 diff hist +523 Exome Chip Design
- 08:39, 28 September 2011 diff hist +89 Biostatistics 666: Main Page →Scheduling
- 08:35, 28 September 2011 diff hist 0 File:666.04.pdf uploaded a new version of "File:666.04.pdf": Minor typo corrections. current
- 08:34, 28 September 2011 diff hist 0 File:666.05.pdf uploaded a new version of "File:666.05.pdf": Added frequency spectrum from 12,000 individuals. current
- 09:54, 27 September 2011 diff hist -32 Exome Chip Design →Coordination
- 11:24, 22 September 2011 diff hist +113 Abecasis Group Awards →American Society of Human Genetics
- 11:15, 22 September 2011 diff hist +110 Abecasis Group Awards →American Society of Human Genetics
- 00:05, 22 September 2011 diff hist +132 Abecasis Group Awards →American Society of Human Genetics
- 23:47, 21 September 2011 diff hist +344 Minimac Command Reference →Output Parameters
- 23:39, 21 September 2011 diff hist 0 Minimac →Download
- 02:31, 21 September 2011 diff hist +23 Polymutt: a tool for calling polymorphism and de novo mutations in families for sequencing data
- 08:12, 19 September 2011 diff hist +10 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 08:11, 19 September 2011 diff hist +215 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 08:10, 19 September 2011 diff hist +37 Minimac: 1000 Genomes Imputation Cookbook →Further Time Savings
- 08:09, 19 September 2011 diff hist -1 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 08:08, 19 September 2011 diff hist +133 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 07:50, 19 September 2011 diff hist +289 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 07:49, 19 September 2011 diff hist +543 Minimac Command Reference →Reference Haplotype Set
- 07:48, 19 September 2011 diff hist -543 Minimac Command Reference →Target Haplotype Set
- 07:44, 19 September 2011 diff hist +5 Minimac Command Reference →Target Haplotype Set
- 07:44, 19 September 2011 diff hist +6 Minimac Command Reference →Target Haplotype Set
- 07:43, 19 September 2011 diff hist +532 Minimac Command Reference →Target Haplotype Set
- 04:27, 19 September 2011 diff hist -2 Minimac: 1000 Genomes Imputation Cookbook →Questions and Comments
- 04:13, 19 September 2011 diff hist -31 File:666.03.pdf
- 04:12, 19 September 2011 diff hist 0 File:666.03.pdf uploaded a new version of "File:666.03.pdf": →Minor updates to the lecture - added recommended reading list, synchronized content with 2011 lecture series
- 07:33, 12 September 2011 diff hist +348 Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium →Slides current
- 07:32, 12 September 2011 diff hist +48 Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium →Slides
- 07:31, 12 September 2011 diff hist +216 Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium →Objective
- 07:29, 12 September 2011 diff hist +289 N Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium Created page with '== Objective == This lecture does double duty, introducing course objectives and the concept of Hardy Weinberg Equilibrium. It combines topics previously covered in two separat…'
- 07:27, 12 September 2011 diff hist +150 Biostatistics 666: Main Page →Older Lectures
- 07:27, 12 September 2011 diff hist -43 Biostatistics 666: Main Page →Class Notes
- 07:26, 12 September 2011 diff hist +75 N File:2011.666.01.pdf Course Introduction and Hardy Weinberg Lecture Combined into A Single Class
- 05:48, 12 September 2011 diff hist -167 Biostatistics 666: Main Page →Problem Set Solutions
- 05:45, 12 September 2011 diff hist +12 Biostatistics 666: Main Page →Course History
- 05:44, 12 September 2011 diff hist -24 Biostatistics 666: Main Page →Office Hours
- 05:42, 12 September 2011 diff hist -1 Biostatistics 666: Main Page →Scheduling
- 05:42, 12 September 2011 diff hist +65 Biostatistics 666: Main Page →Scheduling
- 05:41, 12 September 2011 diff hist +61 Biostatistics 666: Main Page →Target Audience
- 06:50, 7 September 2011 diff hist -6 Tutorial: Low Pass Sequence Analysis →Converting Alignments to BAM format
- 06:42, 7 September 2011 diff hist -4 Tutorial: Low Pass Sequence Analysis →Browsing Alignment Results
- 06:42, 7 September 2011 diff hist -4 Tutorial: Low Pass Sequence Analysis →Indexing the BAM file
- 06:41, 7 September 2011 diff hist +5 Tutorial: Low Pass Sequence Analysis →Converting Alignments to BAM format
- 06:38, 7 September 2011 diff hist -4 Tutorial: Low Pass Sequence Analysis →Converting Alignments to BAM format
- 06:36, 7 September 2011 diff hist +27 Tutorial: Low Pass Sequence Analysis →Browsing Alignment Results
- 06:29, 7 September 2011 diff hist +5 Tutorial: Low Pass Sequence Analysis →Browsing Alignment Results
- 06:28, 7 September 2011 diff hist -1 Tutorial: Low Pass Sequence Analysis →Mapping Reads to The Genome
- 05:47, 7 September 2011 diff hist -1 Tutorial: Low Pass Sequence Analysis →Initial set of variant calls
- 05:36, 7 September 2011 diff hist +7 Tutorial: Low Pass Sequence Analysis →Initial set of variant calls
- 05:35, 7 September 2011 diff hist -5 Tutorial: Low Pass Sequence Analysis →Converting Alignments to BAM format
- 05:35, 7 September 2011 diff hist -4 Tutorial: Low Pass Sequence Analysis →Indexing and Annotating the BAM file
- 05:18, 7 September 2011 diff hist +1,593 Tutorial: Low Pass Sequence Analysis →Mapping Reads to The Genome
- 04:55, 7 September 2011 diff hist +1,940 Tutorial: Low Pass Sequence Analysis →Initial set of variant calls
- 04:37, 7 September 2011 diff hist +1 Tutorial: Low Pass Sequence Analysis →Mapping Reads to The Genome
- 04:35, 7 September 2011 diff hist -3 Tutorial: Low Pass Sequence Analysis →Sequence Analysis Workshop
- 04:32, 7 September 2011 diff hist +4,561 N Tutorial: Low Pass Sequence Analysis Created page with '= Sequence Analysis Workshop = In this workshop, we will illustrate some of the essential steps in the analysis of next generation sequence data. As part of the process, you wil…'
- 04:27, 7 September 2011 diff hist +42 Short Workshops
- 06:14, 2 September 2011 diff hist 0 Minimac →Download
- 11:19, 23 August 2011 diff hist +47 Exome Chip Design →Ancestry Informative Markers
- 11:18, 23 August 2011 diff hist +54 Exome Chip Design →Scaffold for Identity by Descent
- 11:16, 23 August 2011 diff hist +50 Exome Chip Design →Random set of synonymous variants (as comparator)
- 11:06, 23 August 2011 diff hist +59 Exome Chip Design →Ancestry Informative Markers
- 10:01, 23 August 2011 diff hist +154 Exome Chip Design →Tags for Previously Described GWAS Hits
- 09:56, 23 August 2011 diff hist -3 Exome Chip Design →Variants that Alter Protein Function
- 09:56, 23 August 2011 diff hist +2 Exome Chip Design →Variants that Alter Protein Function
- 09:55, 23 August 2011 diff hist +217 Exome Chip Design →Ancestry Informative Markers
- 09:46, 23 August 2011 diff hist 0 Exome Chip Design →Fingerprint SNPs
- 09:44, 23 August 2011 diff hist +143 Exome Chip Design →HLA tag SNPs
- 09:42, 23 August 2011 diff hist +57 Exome Chip Design →Fingerprint SNPs
- 22:09, 18 August 2011 diff hist 0 Minimac →Download
- 23:07, 16 August 2011 diff hist +8,205 N Exome Chip Design Created page with 'This page describes characteristics of the Illumina Exome Chip. The plan is that this page will be publicly visible. = Key Credit = We thank all the individuals who generously …'
- 06:47, 12 August 2011 diff hist -1 Minimac →Additional Sources of Information
- 06:46, 12 August 2011 diff hist 0 Minimac →Download
- 16:24, 10 August 2011 diff hist +336 IMPUTE2: 1000 Genomes Imputation Cookbook →Association Analysis
- 16:19, 10 August 2011 diff hist +138 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing using IMPUTE2
- 16:17, 10 August 2011 diff hist +76 IMPUTE2 current
- 15:13, 5 August 2011 diff hist +1 Minimac →Additional Sources of Information
- 11:15, 5 August 2011 diff hist +504 Minimac →Getting Started
- 11:10, 5 August 2011 diff hist +48 Minimac →Download
- 11:09, 5 August 2011 diff hist -2 Minimac →X Chromosome Imputation
- 10:12, 5 August 2011 diff hist -222 Minimac →NCBI build 36 / NCBI build 37
- 10:12, 5 August 2011 diff hist +748 Minimac: 1000 Genomes Imputation Cookbook →Further Time Savings
- 10:06, 5 August 2011 diff hist +43 Minimac: 1000 Genomes Imputation Cookbook →Further Time Savings
- 10:05, 5 August 2011 diff hist +1,596 Minimac: 1000 Genomes Imputation Cookbook →Further Time Savings
- 10:05, 5 August 2011 diff hist -16 ChunkChromosome →Usage
- 09:14, 5 August 2011 diff hist +359 Minimac: 1000 Genomes Imputation Cookbook
- 09:02, 5 August 2011 diff hist +287 Minimac: 1000 Genomes Imputation Cookbook →Your Own Data
- 08:55, 5 August 2011 diff hist +42 ChunkChromosome →Download
- 08:55, 5 August 2011 diff hist +102 ChunkChromosome →Download
- 08:52, 5 August 2011 diff hist +114 Minimac →Download
- 08:40, 5 August 2011 diff hist +150 ChunkChromosome →Download
- 08:06, 5 August 2011 diff hist +5 ChunkChromosome →Usage
- 08:05, 5 August 2011 diff hist +376 ChunkChromosome →Usage
- 07:55, 5 August 2011 diff hist +439 ChunkChromosome →Usage
- 07:43, 5 August 2011 diff hist +393 ChunkChromosome →Usage
- 07:26, 5 August 2011 diff hist +23 ChunkChromosome →Usage
- 07:23, 5 August 2011 diff hist 0 ChunkChromosome →Usage
- 07:22, 5 August 2011 diff hist +1,171 N ChunkChromosome Created page with '''ChunkChromosome'' is a helper utility for minimac and MaCH. It can be used to facilitate analyses of very large datasets in overlapping slices. == Parameters == ''Chu…'
- 07:12, 5 August 2011 diff hist +841 N Hardy Weinberg equilibrium Created page with 'In the absence of migration, mutation, natural selection, and assortative mating, genotype frequencies at any locus are a simple function of allele frequencies. This phenomenon, …' current
- 07:07, 5 August 2011 diff hist +1 Minimac: 1000 Genomes Imputation Cookbook →Shoud I use MaCH or minimac?
- 07:02, 5 August 2011 diff hist +44 Minimac: 1000 Genomes Imputation Cookbook →X Chromosome Imputation
- 07:00, 5 August 2011 diff hist +14 Minimac: 1000 Genomes Imputation Cookbook →Imputation quality evaluation
- 06:59, 5 August 2011 diff hist -3 Minimac: 1000 Genomes Imputation Cookbook →X Chromosome Imputation
- 06:57, 5 August 2011 diff hist +269 Minimac: 1000 Genomes Imputation Cookbook →Reference Haplotypes
- 06:54, 5 August 2011 diff hist +591 Minimac: 1000 Genomes Imputation Cookbook →Your Own Data
- 06:49, 5 August 2011 diff hist +69 N IMPUTE2 Created page with 'An imputation package developed by Bryan Howie and Jonathan Marchini.'
- 06:48, 5 August 2011 diff hist +189 IMPUTE2: 1000 Genomes Imputation Cookbook →Content
- 06:47, 5 August 2011 diff hist +127 Minimac: 1000 Genomes Imputation Cookbook
- 06:43, 5 August 2011 diff hist +391 IMPUTE2: 1000 Genomes Imputation Cookbook →Content