===== Documentation =====
==== Data Input and Output ====
	*  SEQPower [[http://bioinformatics.org/spower/input|input]] data
	*  SEQPower simulation of [[http://bioinformatics.org/spower/write|association data]]
	*  SEQPower power analysis [[http://bioinformatics.org/spower/output|results]]
	*  [[http://bioinformatics.org/spower/benchmark#usage|Graphic representation]] of power calculation results

==== Complete List of Command Options ====
[[http://bioinformatics.org/spower/allargs|Argument list]]

==== Guide to Command Usage ====
=== Common options ===
	*  Genotype simulation options
	*  Phenotype simulation options
	*  Analysis options
	*  Association tests options
	*  <color blue>Read more</color> [[http://bioinformatics.org/spower/options|>>]]

=== Model specific options ===
	*  [[http://bioinformatics.org/spower/mlogit|LOGIT]] model
	*  [[http://bioinformatics.org/spower/mpar|PAR]] model
	*  [[http://bioinformatics.org/spower/mlnr|LNR]] model
	*  [[http://bioinformatics.org/spower/melnr|ELNR]] model
	*  [[http://bioinformatics.org/spower/mblnr|BLNR]] model

==== Genetic Sequences ====
	*  Population genetics model based simulation
		*  ''spower simulate'' command for forward time simulation of DNA sequences
	*  Data based simulation
	*  Direct sampling from real world data-set
	*  <color blue>Read more</color> [[http://bioinformatics.org/spower/simseq|>>]]

==== Disease Associations ====
=== Effects of variants ===
	*  Fixed effect vs. variable effects
	*  Protective, deleterious and neutral variants
	*  <color blue>Read more</color> [[http://bioinformatics.org/spower/simtraits|>>]]

=== Phenotype simulations ===
	*  Linear mean-shift model
	*  Extreme quantitative trait model
	*  Logit model of odds ratios
	*  Population attributable risk model
	*  Linear model with qualitative outcome
	*  Phenotype simulation for sequences drawn from haplotype pools
	*  <color blue>Read more</color> [[http://bioinformatics.org/spower/simtraits|>>]]

==== Power of Association Tests ====
	*  [[http://bioinformatics.org/spower/cc|Analytic power and sample size calculation for case control design]]
	*  [[http://bioinformatics.org/spower/qt|Analytic power and sample size calculation for quantitative traits design]]
	*  [[http://bioinformatics.org/spower/empirical|Empirical power and sample size calculations]]

==== Rare Variants Association Methods (RVAM) ====
	*  [[http://bioinformatics.org/spower/vat-methods|RVAM]] catalog
	*  [[http://bioinformatics.org/spower/benchmark|Power comparison for RVAM]]

==== Evaluating Novel Statistical Tests ====
	*  Writing [[http://bioinformatics.org/spower/vat-r|R extensions]]