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Contents
- additive effect
- Rqtl
- analysis
- ANALYSIS
- analysis phase
- ANALYSIS PHASE
- automatic actions
- AUTOMATIC ACTIONS
- background parameter
- Zmapqtl Model Six
- beta distribution
- Rqtl
- bootstrap
- Log File
| Bootstrapping
| Permutations, Bootstraps and Jackknives
| Eqtl
- bootstraps, jackknives and permutations
- BOOTSTRAPS, JACKKNIVES AND PERMUTATIONS
- bug
- Bug Reports
- categorical trait
- Other Traits
| Simple Linear Regression
- caveats
- CAVEATS
| CAVEATS
| CAVEATS
- command line
- General Usage of the
- composite interval mapping
- Permutation Tests
| Zmapqtl
| JZmapqtl
| Benchmarks
- covariate
- Permutation Tests
| Eqtl
- cross
- advanced intercross
- Experimental Design
- backcross
- Experimental Design
| Output
- Design III
- Experimental Design
- doubled haploid
- Experimental Design
- intercross
- Experimental Design
| Output
- recombinant inbred line
- Experimental Design
| Experimental Design
- repeated backcross
- Experimental Design
- test cross
- Experimental Design
- crosses
- CROSSES
- dominance
- Rqtl
| Dominant Markers
- ECM algorithm
- Computational Methodology
- Eqtl
- Permutation Test output
| Eqtl
| EQTL
- options
- Which Results?
- output
- Eqtl
- experimentwise significance level
- Permutation Test output
- filename stem
- Simulating/Reformatting Data
| FILENAME STEM
- ftp server
- How to Get and
| General tactics and notes
| Using MAPMAKER/EXP
- gamma distribution
- Rqtl
- gamma function
- Rqtl
- genetic linkage map
- Definition of the Problem
| Genetic Linkage Maps
| Simulating a Map
| Simulating Data
- global behavior
- GLOBAL BEHAVIOR
- global command line options
- GLOBAL COMMAND LINE OPTIONS
- GNUPLOT
- Gnuplot Copyright Information
| Rmap
| Output Flags
| Printing Results
| GNUPLOT
- heritability
- Rcross
| Phenotypic Values
| Phenotypic Values
- hints
- HINTS
- inbred line
- Experimental Design
- information criteria
- INFORMATION CRITERIA
- input format
- INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
| INPUT FORMAT
- install
- Macintosh
- Macintosh
- MS-Windows
- MS-Windows
- UNIX
- UNIX
- interactive menu
- Automatic Mode
| Interactive Mode
| Prune
- interval mapping
- Permutation Tests
| Zmapqtl
| JZmapqtl
| Benchmarks
- jackknife
- Permutations, Bootstraps and Jackknives
| Eqtl
- JZmapqtl
- JZmapqtl
| JZMAPQTL
- option
- JZmapqtl Options
- least squares
- Output
- linear regression
- Simple Linear Regression
- LINPACK
- LINPACK Copyright Information
- LOD
- Other Options
| Preplot
- log file
- Log File
- LR
- Other Options
| Preplot
- LRmapqtl
- LRmapqtl
| LRMAPQTL
- options
- Simple Linear Regression
- output
- Output
- Macintosh
- Programming Philosophy
| How to Get and
| Working directory
| Bootstrapping
- binhex
- Macintosh
- install
- Macintosh
- StuffitExpander
- Macintosh
- mailing list
- Mailing List
- MAPMAKER
- Genetic Linkage Maps
| Filenaming Conventions
| Using MAPMAKER/EXP files
| Translating Data
| MAPMAKER output files
| MAPMAKER raw files
- mapping function
- Map Function
- Fixed
- Map Function
- Haldane
- Map Function
- Kosambi
- Map Function
- maximum likelihood
- Computational Methodology
- MImapqtl
- MImapqtl
| MIMAPQTL
- option
- MImapqtl Options
- missing data
- Command Line Options
- model
- MODEL
- models
- MODELS
| MODELS
- MS-Windows
- Programming Philosophy
| Working directory
| Bootstrapping
- GNUPLOT
- MS-Windows
- Windows Explorer
- MS-Windows
- multiple interval mapping
- MImapqtl
- MULTIREGRESS
- MULTIREGRESS
- Note
- Listing options
| Verbosity
| Resource File
| Simulating/Reformatting Data
| Rmap
| Using MAPMAKER/EXP files
| Input Files
| Translating Data
| Output
- options
- OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
| OPTIONS
- output
- OUTPUT
- permutation test
- Permutation Tests
| Permutation Tests
| Zmapqtl
| Permutations, Bootstraps and Jackknives
| Permutation Test output
| Eqtl
| Other Options
- permutation tests
- PERMUTATION TESTS
- phenotype
- Phenotypic Values
- Preplot
- PREPLOT
- automagic
- Preplot
- options
- Preplot
- printing
- Printing Results
| Basic GNUPLOT
- Prune
- Prune
| Permutations, Bootstraps and Jackknives
| PRUNE
- interactive menu
- Pruning Datasets Interactively
- Qstats
- Qstats
| QSTATS
- options
- Command Line Options
- QTL
- Definition of the Problem
| Rqtl
- QTLCART
- QTLCART
- Rcross
- Rcross
| RCROSS
- input
- Translating Data
| Rcross input files
- output
- Output
- references
- REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
| REFERENCES
- resource file
- Resource File
| General tactics and notes
| RESOURCE FILE
- Rmap
- Rmap
| RMAP
- input
- Rmap input files
- input format
- Rmap
| QTL Cartographer user input
- options
- Simulating a Map
| Command Line Options
- output
- Output Flags
| Rmap output files
- Rqtl
- Rqtl
| RQTL
- input
- Rqtl
| Rqtl
| Rqtl input files
- output
- Eqtl
| Rqtl output files
- sample
- average deviation
- Qstats
- kurtosis
- Qstats
- mean
- Qstats
- skewness
- Qstats
- standard deviation
- Qstats
- variance
- Qstats
- simulation
- cross
- Simulating Data
- gametes
- Generation of Individuals
- genetic linkage map
- Simulating a Map
- genetic model
- Rqtl
- missing data
- Resampling data
| Simulating Missing Data
- QTL
- Rqtl
- random number seed
- Random Number Seed
- recombination
- Generation of Individuals
- trait
- Phenotypic Values
- SRmapqtl
- Permutation Tests
| Zmapqtl Model Six
| SRMAPQTL
- output
- Output
- standard deviation
- Permutations, Bootstraps and Jackknives
- stepwise regression
- Permutation Tests
| SRmapqtl
- backward
- SRmapqtl
- forward
- SRmapqtl
- forward-backward
- SRmapqtl
- token
- Rmap input files
- UNIX
- Programming Philosophy
| How to Get and
| General Usage of the
- install
- UNIX
- using the individual programs
- USING THE INDIVIDUAL PROGRAMS
- variance
- environmental
- Simulating Data
| Phenotypic Values
- genetic
- Phenotypic Values
- verbosity
- Verbosity
- virtual marker
- Eqtl
- web site
- Getting Help
| General tactics and notes
- window size
- Zmapqtl Model Six
- work code
- WORK CODE
- working directory
- Working directory
| Resource File
| General tactics and notes
| WORKING DIRECTORY
- Zmapqtl
- Permutation Tests
| Zmapqtl
| ZMAPQTL
- model
- Models
- option
- Zmapqtl Options
- output
- Output
- virtual marker
- Models
Christopher Basten
2002-03-27