PCSCS – Power Calculator of Sequence Comparison Statistic

PCSCS

:: DESCRIPTION

PCSCS is the theoretical power calculator for D2 and D2*. The sofware facilitates the use of D2 or D2* for sequence or genome comparison and for evaluation of statistical power for detecting the relationship between the sequences.

::DEVELOPER

PCSCS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R package

:: DOWNLOAD

 PCSCS

:: MORE INFORMATION

Citation:

Alignment-free sequence comparison (II): theoretical power of comparison statistics.
Wan L, Reinert G, Sun F, Waterman MS.
J Comput Biol. 2010 Nov;17(11):1467-90. doi: 10.1089/cmb.2010.0056.

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

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.

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.

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

W. James Gauderman

:: 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.

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.

PIAGE 1.0 – Power of Indirect Association Studies of Gene-Environment Interactions

PIAGE 1.0

:: DESCRIPTION

PIAGE (Power of Indirect Association Studies of Gene-Environment Interactions) performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects

::DEVELOPER

Division of Cancer Epidemiology, German Cancer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PIAGE

:: MORE INFORMATION

Citation

Genet Epidemiol. 2008 Apr;32(3):235-45.
Sample size requirements for indirect association studies of gene-environment interactions (G x E).
Hein R, Beckmann L, Chang-Claude J.

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

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.

PopCycle 1.0 – Explore the Power of Combining Mendelian Genetics with Darwinian Selection

PopCycle 1.0

:: DESCRIPTION

PopCycle lets the user explore the power of combining Mendelian genetics with Darwinian selection.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

PopCycle

:: REQUIREMENTS

  • MacOsX / Windows

:: DOWNLOAD

 PopCycle

:: MORE INFORMATION