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1. 1000 Genomes Project Pilot 1 SNP Calling
2. 830 - BasicMapper::main()
3. 830 - BestAlignment::ClearPositions()
4. 830 - BestAlignment::EvaluateAlignment() (detailed comparison)
5. 830 - BestAlignment::EvaluateAlignment() (main loop)
6. 830 - BestAlignment::IterateCache()
7. 830 - BestAlignment::MaqAlignment()
8. 830 - BestAlignment::isNewPosition()
9. 830 - Haplotyper::ConditionOnData()
10. 830 - Haplotyper::ImputeGenotypes()
11. 830 - Haplotyper::ImputeGenotypes() (edge)
12. 830 - Haplotyper::ImputeGenotypes() (internal)
13. 830 - Haplotyper::RandomSetup()
14. 830 - Haplotyper::SampleChromosomes()
15. 830 - Haplotyper::SampleHaplotypes()
16. 830 - Haplotyper::SampleOneHaplotype()
17. 830 - Haplotyper::ScoreLeftConditional()
18. 830 - Haplotyper::ScoreLeftConditional() (smart, complicated)
19. 830 - Haplotyper::SetupPrior()
20. 830 - Haplotyper::SummarizeOptions()
21. 830 - Haplotyper::Transpose()
22. 830 - MINIMAC::main()
23. 830 - MaqIndex::BuildIndex()
24. 830 - MaqIndex::CompareToIndex()
25. 830 - MaqIndex::GetWord()
26. 830 - MaqIndex::LookupWord()
27. 830 - MarkovModel::Condition()
28. 830 - MarkovModel::CountErrors()
29. 830 - MarkovModel::CountErrorsAndRecombinants()
30. 830 - MarkovModel::CountRecombinants()
31. 830 - MarkovModel::Impute()
32. 830 - MarkovModel::Transpose()
33. 830 - MarkovModel::WalkLeft()
34. 830 - MarkovModel::WalkRight()
35. AWS Credentials
36. AWS Resources
37. Abecasis Group Awards
38. Abecasis Lab
39. Alan Kwong
40. Amazon Single Node
41. Amazon Snapshot
42. Amazon Storage
43. An example of using libcsg
44. Analyses of Indels
45. Ancestry
46. Ann Arbor Travel Basics
47. BAM
48. BAM to FASTQ
49. BamGenotypeCheck
50. BamPileup
51. BamUtil: FAQ
52. BamUtil: bam2FastQ
53. Bar Harbor Statistical Genetics Workshop
54. BaseQualityCheck
55. Base Caller Summaries
56. Basic Linux Intro
57. Bayesdenovo
58. Ben Lerch
59. Better X Sessions from Home (NX)
60. Biostatistics 501: Main Page
61. Biostatistics 602: Main Page
62. Biostatistics 615/815: Main Page
63. Biostatistics 615/815 Fall 2011
64. Biostatistics 615/815 Winter 2011
65. Biostatistics 666: Advanced Coalescent, Changing Population Size
66. Biostatistics 666: Advanced Coalescent, Computation with the Coalescent
67. Biostatistics 666: Advanced Haplotype Estimation
68. Biostatistics 666: Analysis of Copy Number Using Sequence Data
69. Biostatistics 666: Analysis of Low Pass Sequence Data
70. Biostatistics 666: Applications of the Lander-Green Algorithm
71. Biostatistics 666: Association Tests in Structured Populations
72. Biostatistics 666: Contemporary Human Genetics
73. Biostatistics 666: Copy Number Variation
74. Biostatistics 666: Core Competencies
75. Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium
76. Biostatistics 666: Genotype Imputation
77. Biostatistics 666: Haplotype Association Tests
78. Biostatistics 666: Haplotype Estimation
79. Biostatistics 666: Hardy-Weinberg Equilibrium
80. Biostatistics 666: Introduction to De Novo Assembly
81. Biostatistics 666: Introduction to the Coalescent
82. Biostatistics 666: Introduction to the E-M Algorithm
83. Biostatistics 666: Introductory Lecture
84. Biostatistics 666: Likelihood Calculations for Large Pedigrees
85. Biostatistics 666: Linkage Analysis in Sibling Pairs
86. Biostatistics 666: Linkage Disequilibrium
87. Biostatistics 666: Linkage Tests for Pairs of Individuals
88. Biostatistics 666: Main Page
89. Biostatistics 666: Maximum Likelihood Allele Frequency Estimation
90. Biostatistics 666: Modeling Recombination and Migration in the Coalescent
91. Biostatistics 666: Modeling Variation in the Coalescent
92. Biostatistics 666: Multipoint Analysis in Sibling Pairs
93. Biostatistics 666: Power of Genomewide Association Studies
94. Biostatistics 666: Rare Variant Burden Tests
95. Biostatistics 666: Relationship Checking
96. Biostatistics 666: The Lander-Green Algorithm
97. Biostatistics 666: The Possible Triangle Constraint
98. Biostatistics 666: Variance Component Analyses
99. Biostatistics 666: Whole Genome Sequencing
100. Biostatistics 815 Term Project
101. Biostatistics 830: Core Competencies
102. Biostatistics 830: Fall 2013 Edition
103. Biostatistics 830: Main Page
104. Biostatistics 830 - Code Snippets
105. Biostatistics 866: Core Competencies
106. Biostatistics 866: Main Page
107. C++ Class: Pedigree Example
108. C++ Class Averages
109. C++ Library: FASTQ Change Log
110. C++ Library: general Change Log
111. CHARGE
112. CSG Tech Talks
113. CalcMatch
114. CheckVCF.py
115. ChunkChromosome
116. CigarRoller Proposed Update
117. Class Notes
118. Computer How-Tos
119. Configure GotCloud
120. ContaminationDetection
121. Creating a Snapshot on EC2
122. Creating an AMI on EC2
123. Dajiang Liu
124. Debuggers
125. DosageConvertor
126. Dosage convertor
127. EMADS
128. EMADS Primary Analysis Plan
129. EMMAX
130. EPACTS
131. EPACTS for DIAGRAM
132. Editing Sequence Analysis Practice 2011/03/10
133. Evaluating a Read Mapper on Simulated Data
134. Example
135. Examples of Read Mapping with Karma and BWA
136. Exome Chip Design
137. FASTA
138. FTEC
139. FamLDCaller
140. FamRvTest command
141. FamRvTest tutorial
142. Famrvtest
143. FastQ Validation Criteria
144. Fst
145. GBR60vc.conf
146. GLF
147. GREGOR
148. GTDT
149. GWAS
150. Garlic
151. Gene Ontology
152. Generic Exome Analysis Plan
153. Genezoom
154. Genotype Likelihood Based Allele Balance
155. Genotype Likelihood based Allele Frequency
156. Genotype Likelihood based Hardy-Weinberg Test
157. Genotype Likelihood based Inbreeding Coefficient
158. Git Cheat Sheet
159. Git FAQs
160. GlfMerge
161. Goncalo Abecasis
162. Goncalo Abecasis: Interview with Christiana Fogg
163. GotCloud
164. GotCloud: AMIs
165. GotCloud: Alignment Pipeline
166. GotCloud: Alignment Sub-Pipelines
167. GotCloud: Amazon
168. GotCloud: Amazon Demo
169. GotCloud: Binary Releases
170. GotCloud: Configuration
171. GotCloud: Creating a New Pipeline
172. GotCloud: FAQs
173. GotCloud: Filters
174. GotCloud: Genetic Reference and Resource Files
175. GotCloud: GenomeSTRiP Pipeline
176. GotCloud: RedHat Package
177. GotCloud: Reference Files
178. GotCloud: Source Releases
179. GotCloud: Variant Calling Options
180. GotCloud: Variant Calling Pipeline
181. GotCloud: Versions
182. Gzip
183. Gzip File
184. HAPMIX
185. Haploxt
186. Hardy Weinberg equilibrium
187. How To Use Git
188. How to use aspera
189. IGFPipe
190. IMPUTE2
191. IMPUTE2: 1000 Genomes Imputation Cookbook
192. Idriver
193. Imputation Server: Example
194. Indel
195. Installing MinGW & MSYS on Windows
196. Introduction to new students
197. Jennifer Bragg-Gresham
198. Karma-colorspace
199. Kyoto Encyclopedia of Genes and Genomes
200. LASER
201. Lars Fritsche
202. LibStatGen Download
203. LibStatGen Repository
204. LibStatGen Troubleshooting
205. LiftMap.py
206. LiftOver
207. LiftRsNumber.py
208. Ligate Minimac
209. Links to Sequence Analysis Tools
210. M3VCF Files
211. M3vcftools
212. M3vcftools Usage
213. MEAGA
214. MERLIN format
215. METAL ADDFILTER
216. METAL COLUMNCOUNTING
217. METAL CUSTOMVARIABLE
218. METAL Command Reference
219. METAL Documentation
220. METAL EFFECTLABEL
221. METAL FAQ
222. METAL GENOMICCONTROL
223. METAL Glucose Example Script
224. METAL LOGPVALUE
225. METAL Quick Start
226. METAL SOURCE
227. METAL VERBOSE
228. MaCH: 1000 Genomes Imputation Cookbook
229. MaCH: Input Files
230. MaCH: Pedigree with Integer Allele Codes
231. MaCH: machX
232. MaCH FAQ
233. MaCH Options
234. Mach2dat: Association with MACH output
235. Mach DAC
236. Main Page
237. Make file tutorial
238. Makefile.tool
239. Mantra.cpp
240. MappabilityScores
241. Mapping Quality Scores
242. Mary Kate Wing
243. MetaMinimac
244. Meta Analysis of SNPxEnvironment Interaction
245. Minimac3 - Full List of Options
246. Minimac3 ChangeLog
247. Minimac3 Cookbook : Chromosome X Imputation
248. Minimac3 Cookbook : Converting Files to VCF
249. Minimac3 Cookbook : Pre-Phasing
250. Minimac3 Examples

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