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Jump to navigationJump to search- 16:18, 23 March 2010 diff hist +133 N Merlin Created page with 'A program for linkage and association analysis in human pedigrees. See [http://www.sph.umich.edu/csg/abecasis/Merlin/ Merlin Website]'
- 16:17, 23 March 2010 diff hist +449 N Phred scale Created page with 'A scale commonly used to measure data quality and error rates in sequence analysis. It was popularized by Phil Green's PHRED base-calling software. It is defined as: <math> …' current
- 12:42, 23 March 2010 diff hist 0 MediaWiki:Sidebar
- 12:42, 23 March 2010 diff hist +11 MediaWiki:Sidebar
- 12:42, 23 March 2010 diff hist +2 MediaWiki:Sidebar
- 12:41, 23 March 2010 diff hist +30 MediaWiki:Sidebar
- 12:38, 23 March 2010 diff hist +17 Abecasis Lab →Staff
- 10:28, 23 March 2010 diff hist +122 Abecasis Lab →Former Research Fellows
- 10:25, 23 March 2010 diff hist +450 Abecasis Lab →Former Research Fellows
- 10:16, 23 March 2010 diff hist +698 Abecasis Lab →Former Doctoral Students
- 10:09, 23 March 2010 diff hist +188 Abecasis Lab →Former Doctoral Students
- 10:08, 23 March 2010 diff hist +27 Abecasis Lab →Former Doctoral Students
- 07:43, 23 March 2010 diff hist +382 N Biostatistics 666: The Possible Triangle Constraint Created page with '== Content == Show how simple genetic models can be used to predict similarity between relative pairs and IBD sharing among sibling pairs. Introduce the possible triangle constr…' current
- 07:15, 23 March 2010 diff hist +1 Biostatistics 666: Linkage Tests for Pairs of Individuals →Recommended Reading
- 07:15, 23 March 2010 diff hist -132 Biostatistics 666: Linkage Tests for Pairs of Individuals →Recommended Reading
- 07:15, 23 March 2010 diff hist +648 N Biostatistics 666: Linkage Tests for Pairs of Individuals Created page with '== Overview == This lecture introduces simple linkage tests in the context of affected sibling pairs. One test, originally described by Bishop and Williamson (1990) focuses on i…'
- 07:11, 23 March 2010 diff hist +172 Biostatistics 666: Main Page →Class Notes
- 07:09, 23 March 2010 diff hist +64 N File:666.16.pdf Introduces multipoint analysis, in the context of sibling pairs.
- 07:09, 23 March 2010 diff hist +135 N File:666.15.pdf Shows how a simple disease model can be used to predict IBD probabilities for relative pairs. Introduces possible triangle constraint. current
- 07:17, 18 March 2010 diff hist +31 N MapabilityScores moved MapabilityScores to MappabilityScores current
- 07:17, 18 March 2010 diff hist 0 m MappabilityScores moved MapabilityScores to MappabilityScores current
- 07:17, 18 March 2010 diff hist 0 N File:666.14.pdf current
- 07:17, 18 March 2010 diff hist +90 Biostatistics 666: Main Page →Class Notes
- 04:37, 11 March 2010 diff hist -7 LocusZoom →Generate single plots using our publicly-available lipids GWAS data
- 04:35, 11 March 2010 diff hist -66 LocusZoom
- 04:28, 11 March 2010 diff hist -13 LocusZoom →Upload your own meta-analysis file and generate single plots using a web-based form
- 05:39, 8 March 2010 diff hist 0 ExomePicks →Download
- 04:09, 4 March 2010 diff hist +96 ExomePicks
- 04:07, 4 March 2010 diff hist 0 ExomePicks →Download
- 09:45, 3 March 2010 diff hist -1 ExomePicks →Download
- 09:45, 3 March 2010 diff hist +1 ExomePicks →Download
- 09:44, 3 March 2010 diff hist +9 ExomePicks →Download
- 09:44, 3 March 2010 diff hist +3,009 ExomePicks
- 09:28, 3 March 2010 diff hist +11 ExomePicks →Input Files
- 09:28, 3 March 2010 diff hist +2,420 N ExomePicks Created page with ''''ExomePicks''' is a program that suggests individuals to be sequenced in a large pedigree. '''ExomePicks''' assumes that a genotyping chip or another cost effective means will …'
- 03:00, 22 February 2010 diff hist +913 N Biostatistics 666: Association Tests in Structured Populations Created page with ' == Overview == This lecture introduces the problem of population stratification in the context of genetic association studies. It also discusses three possible strategies for h…'
- 02:56, 22 February 2010 diff hist +234 N File:666.13.pdf Introduces the problem of population stratification in the context of an association study. Discusses three possible solutions: a) Family based association tests. b) The genomic control method. c) Genotype based matching approaches.
- 02:54, 22 February 2010 diff hist +95 Biostatistics 666: Main Page →Class Notes
- 16:52, 19 February 2010 diff hist +1,228 N Outcomes For Mapping A Paired End Created page with '== Basics == Paired end reads have an expected relative orientation (for example, FR are expected to map to opposite strands of the genome) and distance (for example, 500 bp +/-…' current
- 08:20, 18 February 2010 diff hist +12 Biostatistics 666: Main Page →Course History
- 08:19, 18 February 2010 diff hist +940 N Biostatistics 666: Haplotype Association Tests Created page with '== Objective == This page introduces the idea of haplotype association tests. It includes a discussion of when haplotype association tests might be preferable to single marker a…'
- 08:15, 18 February 2010 diff hist +39 N File:666.12.pdf Introduces Haplotype Association Tests.
- 08:15, 18 February 2010 diff hist +79 Biostatistics 666: Main Page →Class Notes
- 02:42, 17 February 2010 diff hist -738 1000 Genomes Project Pilot 1 SNP Calling
- 02:40, 17 February 2010 diff hist -191 1000 Genomes Project Pilot 1 SNP Calling
- 17:45, 16 February 2010 diff hist -3 1000 Genomes Project Pilot 1 SNP Calling
- 23:01, 15 February 2010 diff hist -1 Biostatistics 666: Advanced Coalescent, Computation with the Coalescent →Guest Lecturer current
- 23:00, 15 February 2010 diff hist -1 Biostatistics 666: Advanced Coalescent, Changing Population Size →Guest Lecturer current
- 22:59, 15 February 2010 diff hist 0 File:666.10.pdf uploaded a new version of "File:666.10.pdf": Introduction to E-M Algorithm in Genetics. This version fixes reference to Excoffier and Slatkin paper.
- 22:58, 15 February 2010 diff hist 0 File:666.09.pdf uploaded a new version of "File:666.09.pdf": Fixed reference to Excoffier paper.
- 22:53, 15 February 2010 diff hist +42 N File:666.11.pdf Haplotyping Algorithms. February 16, 2010
- 22:48, 15 February 2010 diff hist +754 N Biostatistics 666: Haplotype Estimation Created page with '== Objective == This lecture introduces several strategies for estimating individual haplotypes and their frequencies. At heart, all population-based haplotyping algorithms look…'
- 22:42, 15 February 2010 diff hist +221 Biostatistics 666: Introduction to the E-M Algorithm
- 22:40, 15 February 2010 diff hist +72 Biostatistics 666: Main Page →Class Notes
- 09:46, 11 February 2010 diff hist 0 N File:666.10.pdf
- 06:15, 11 February 2010 diff hist +283 N Biostatistics 666: Introduction to the E-M Algorithm Created page with '== Objective == Introduce the E-M algorithm in genetics == Slides == Slide in PDF Format == Recommended Reading == Slatkin M, Excoffier L (1996) �Test…'
- 01:26, 11 February 2010 diff hist +4 Biostatistics 666: Advanced Coalescent, Changing Population Size
- 01:26, 11 February 2010 diff hist -387 Biostatistics 666: Advanced Coalescent, Computation with the Coalescent →Recommended Reading
- 01:25, 11 February 2010 diff hist +317 Biostatistics 666: Advanced Coalescent, Computation with the Coalescent
- 01:24, 11 February 2010 diff hist +642 N Biostatistics 666: Advanced Coalescent, Computation with the Coalescent Created page with '== Objective == == Slides == Slides in PDF format == Recommended Reading == Richard R. Hudson (1990) Gene genealogies and the coalescent process ''in'' O…'
- 01:23, 11 February 2010 diff hist -4 Biostatistics 666: Advanced Coalescent, Changing Population Size →Objectives
- 01:22, 11 February 2010 diff hist +6 Biostatistics 666: Advanced Coalescent, Changing Population Size →Notes
- 01:22, 11 February 2010 diff hist -1 Biostatistics 666: Advanced Coalescent, Changing Population Size →Guest Lecturer =
- 01:21, 11 February 2010 diff hist +334 N Biostatistics 666: Advanced Coalescent, Changing Population Size Created page with '== Guest Lecturer === This will be a guest lecture by Sebastian Zoellner, who is our department's resident expert on the coalescent.s == Objectives == Provide an introduction …'
- 01:19, 11 February 2010 diff hist +286 Biostatistics 666: Main Page →Class Notes
- 01:17, 11 February 2010 diff hist +123 N File:666.08.pdf Advanced guest lecture by Sebastian Zoellner. Focused on computation methods related to the coalescent. February 4, 2010. current
- 01:16, 11 February 2010 diff hist +156 N File:666.07.pdf Advanced lecture on the coalescent by guest lecturer, Sebastian Zoellner. Focused on coalescent modeling with changing population sizes. February 2, 2009. current
- 12:01, 9 February 2010 diff hist 0 File:666.09.pdf uploaded a new version of "File:666.09.pdf": Fixed minor typos. February 9, 2010
- 04:59, 9 February 2010 diff hist +6 Biostatistics 666: Modeling Variation in the Coalescent →Slides
- 04:58, 9 February 2010 diff hist 0 Biostatistics 666: Modeling Variation in the Coalescent →Slides
- 04:58, 9 February 2010 diff hist +6 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Slides
- 04:57, 9 February 2010 diff hist +6 Biostatistics 666: Maximum Likelihood Allele Frequency Estimation →Slides
- 04:57, 9 February 2010 diff hist 0 Biostatistics 666: Maximum Likelihood Allele Frequency Estimation →Slides
- 04:57, 9 February 2010 diff hist +712 N Biostatistics 666: Maximum Likelihood Allele Frequency Estimation Created page with '== Objective == This lecture examines maximum likelihood based estimation of allele frequencies in several simple settings, such as estimation of allele frequencies from samples…'
- 04:49, 9 February 2010 diff hist +189 N File:666.09.pdf This lecture reviews maximum likelihood estimation and applies maximum likelihood concepts to derive estimates of allele frequency in several simple settings. Last update February 9, 2010.
- 04:48, 9 February 2010 diff hist +1 Biostatistics 666: Main Page →Class Notes
- 04:48, 9 February 2010 diff hist +97 Biostatistics 666: Main Page →Class Notes
- 15:53, 2 February 2010 diff hist -60 MediaWiki:Sidebar
- 15:52, 2 February 2010 diff hist +31 MediaWiki:Sidebar
- 15:51, 2 February 2010 diff hist 0 MediaWiki:Sidebar
- 15:50, 2 February 2010 diff hist +242 N MediaWiki:Sidebar Created page with '* navigation ** mainpage|mainpage-description ** portal-url|portal ** currentevents-url|currentevents ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|…'
- 15:28, 2 February 2010 diff hist +31 Evaluating a Read Mapper on Simulated Data
- 15:17, 2 February 2010 diff hist +128 Evaluating a Read Mapper on Simulated Data →Grouping
- 15:05, 2 February 2010 diff hist +1,393 N Evaluating a Read Mapper on Simulated Data Created page with '== Grouping == When evaluating read mappers, we should always focus on well defined sets of reads: * Reads with no polymorphisms. * Reads with 1, 2, 3 or more SNPs. * Reads wit…'
- 13:06, 28 January 2010 diff hist 0 Links to Sequence Analysis Tools →Base Calling Tools
- 13:06, 28 January 2010 diff hist +796 Links to Sequence Analysis Tools
- 04:23, 28 January 2010 diff hist +60 N File:666.06.pdf Coalescent with Recombination or Migration January 26, 2010
- 03:05, 28 January 2010 diff hist -1 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Recommended Reading
- 02:46, 28 January 2010 diff hist +11 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Objective
- 02:45, 28 January 2010 diff hist +227 Biostatistics 666: Modeling Recombination and Migration in the Coalescent
- 02:44, 28 January 2010 diff hist +1 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Recommended Reading
- 02:43, 28 January 2010 diff hist +543 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Recommended Reading
- 02:37, 28 January 2010 diff hist +56 N Biostatistics 666: Modeling Recombination and Migration in the Coalescent Created page with '== Objective == == Slides == == Recommended Reading =='
- 02:36, 28 January 2010 diff hist +106 Biostatistics 666: Main Page →Class Notes
- 02:21, 26 January 2010 diff hist +215 Biostatistics 666: Modeling Variation in the Coalescent →Recommended Reading
- 02:20, 26 January 2010 diff hist +407 N Biostatistics 666: Modeling Variation in the Coalescent Created page with '== Objective == This class builds on previous descriptions of the coalescent. In the class we model the impact of mutations on the coalescent and use it to study: * What is the…'
- 02:15, 26 January 2010 diff hist +214 N File:666.05.pdf This lecture covers three concepts: * Estimating theta using sequence data as input. * Modeling frequency spectra using simulations * Analytically modeling the distribution of total variant count January 26, 2010
- 02:12, 26 January 2010 diff hist +88 Biostatistics 666: Main Page →Class Notes
- 11:36, 21 January 2010 diff hist +141 N Links to Sequence Analysis Tools Created page with ' http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration Quality Score Calibration Tool at the Broad Institute.'
- 11:35, 21 January 2010 diff hist +65 Main Page →Sequence Analysis Tools