Tag: Power

QUANTO 1.2.4 – Computes Sample Size or Power for Association Studies

QUANTO 1.2.4

:: DESCRIPTION

Quanto is a program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs.

::DEVELOPER

The Division of Biostatistics @ usc.edu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 QUANTO

:: MORE INFORMATION

Citation

Gauderman (2002),
“Sample size requirements for matched case-control studies of gene-environment interaction“,
Statistics in Medicine, 21:35-50.

GECOR – Power for Gene-Environment Interaction Tests in Matched Case-Control Association Studies

GECOR

:: DESCRIPTION

GECOR is a software for calculating sample sizes in matched case-control studies examining genetic and environmental factors,and/or gene-environment interaction. It allows for sample size calculations for the main effects of geneand/or environment, as well as gene-environment interaction.

::DEVELOPER

Peter Kraft

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX/ Windows
  • java
  • R package

:: DOWNLOAD

 GECOR

:: MORE INFORMATION

MULTIPOW 2.1 – Power for Multi-stage Genome-wide Association Studies

MULTIPOW 2.1

:: DESCRIPTION

MULTIPOW calculates the power for both joint and replication-based analysis of general multi-stage genetic association studies.

::DEVELOPER

Peter Kraft

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX/ Windowsjava
  • R package

:: DOWNLOAD

 MULTIPOW

:: MORE INFORMATION

Citation

Adv Genet. 2008;60:465-504. doi: 10.1016/S0065-2660(07)00417-8.
Study designs for genome-wide association studies.
Kraft P, Cox DG.

NGS-Motif-Power – Significance and Power of Pattern Occurrences in NGS reads

NGS-Motif-Power

:: DESCRIPTION

NGS-Motif-Power is intended to calculate the p-value for pattern occurrences and the power of detecting enriched patterns in NGS reads.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Matlab

:: DOWNLOAD

  NGS-Motif-Power

:: MORE INFORMATION

Citation

Zhiyuan Zhai, Gesine Reinert, Kai Song, Michael S. Waterman, Yihui Luan, and Fengzhu Sun (2012)
Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads.
Journal of Computational Biology.
In press.

micropower – Power Estimation for Microbiome Studies

micropower

:: DESCRIPTION

The micropower package is designed to facilitate power estimation for microbiome studies that will be analyzed with pairwise distances (beta diversity) and PERMANOVA (a non-parametric extension of multivariate analysis of variance to a matrix of pairwise distances).

::DEVELOPER

Bushman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 micropower

:: MORE INFORMATION

Citation

Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA.
Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H.
Bioinformatics. 2015 Mar 29. pii: btv183.

INPower 0.0.1 – Estimating the number of Susceptibility SNPs and Power of Future studies

INPower 0.0.1

:: DESCRIPTION

IN.power is an R package for estimating the number of susceptibility SNPs and power of future studies.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

 IN.power

:: MORE INFORMATION

Citation

Park J-H, Wacholder S, Gail M, Peters U, Jacobs K, Chanock S, Chatterjee N.
Estimation of effect size distribution from genome-wide association studies and implications for future discoveries.
Nature Genetics, 2010, 42, pp.570-575.

PGA – Power for Genetic Association Analysis

PGA

:: DESCRIPTION

PGA (Power for Genetic Association Analyses)is a package of algorithms and graphical user interfaces developed in Matlab for power and sample size calculation under various genetic models and statistical constraints. The software is designed to facilitate decision making for case-control association studies of candidate genes, fine-mapping studies, and whole-genome scans.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PGA

:: MORE INFORMATION

Citation

Menashe I., Rosenberg P.S., and Chen B.E. (2008)
PGA: Power calculator for case-control genetic association analyses.
BMC Genetics, 9:36.

POWER 3.0 – Computation of Sample Size and Power for Binary Outcome Studies

POWER 3.0

:: DESCRIPTION

POWER is a windows-based program for computation of sample size and power for binary outcome studies (case-control and cohort studies) based on a logistic-like regression model with one covariate or two covariates (e.g., gene X exposure interactions).

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  POWER

:: MORE INFORMATION

Citation

Garcia-Closas, Lubin (1999),
“Power and sample size calculations in case-control studies of gene-environmental interactions: Comments on different approaches“,
American Journal of Epidemiology, 149:689-693.

RNASeqPowerCalculator – Calculate the Power and Sample size for RNA-Seq Differential Expression

RNASeqPowerCalculator

:: DESCRIPTION

RNASeqPowerCalculator captures the dispersion in the data and can serve as a practical reference under the budget constraint of RNA-Seq experiments.

::DEVELOPER

Lana Garmire Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 RNASeqPowerCalculator

:: MORE INFORMATION

Citation

RNA. 2014 Nov;20(11):1684-96. doi: 10.1261/rna.046011.114. Epub 2014 Sep 22.
Power analysis and sample size estimation for RNA-Seq differential expression.
Ching T, Huang S, Garmire LX

power.HE 1.2 – Calculate Sample Size and Power for the Haseman-Elston method in Linkage Analysis

power.HE 1.2

:: DESCRIPTION

power.HE is designed to calculate sample size and power for the Haseman-Elston method in linkage analysis for a quantitative trait.

::DEVELOPER

Institute of Medical Biometry and Statistics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Window/ MacOsX
  • R package

:: DOWNLOAD

 power.HE

:: MORE INFORMATION

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