siggenes - Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

Last updated 5 months ago

multiplecomparisonmicroarraygeneexpressionsnpexonarraydifferentialexpression

7.86 score 33 dependents 74 scripts 4.9k downloads

scrime - Analysis of High-Dimensional Categorical Data Such as SNP Data

Tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). Main focus is on SNP data. But most of the functions can also be applied to other types of categorical data.

Last updated 6 years ago

4.98 score 34 dependents 53 scripts 2.5k downloads

trio - Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

Last updated 3 months ago

snpgeneticvariabilitymicroarraygenetics

4.36 score 19 scripts 324 downloads

logicFS - Identification of SNP Interactions

Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.

Last updated 5 months ago

snpclassificationgenetics

3.60 score 8 scripts 356 downloads

mcbiopi - Matrix Computation Based Identification of Prime Implicants

Computes the prime implicants or a minimal disjunctive normal form for a logic expression presented by a truth table or a logic tree. Has been particularly developed for logic expressions resulting from a logic regression analysis, i.e. logic expressions typically consisting of up to 16 literals, where the prime implicants are typically composed of a maximum of 4 or 5 literals.

Last updated 6 years ago

1.48 score 1 dependents 2 scripts 261 downloads