0. Quasi-likelihood parameter estimation- The package provides methods for parameter estimation for statistical models that can be simulated. We follow a quasi-likelihood approach to estimate the unknown parameter by the root of the so-called quasi-score estimating function.
1. Monte Carlo IBD Matrix Estimation- Flexible Monte Carlo Identity-By-Descent (IBD) Matrix Estimation with Within-Line Segregation for Use of Quantitative Trait Loci (QTL) Detection in F2 Intercross Designs.
2. cRacker- cRacker automates standard normalization strategies of quantitative proteomic experiments. It simplifies the analysis of quantified peptide lists coming from various proteomic quantitation softwares.
3. Bayesian Biclustering- This package uses a Bayesian spike-and-slab model to construct bidendrograms using log posterior as the natural distance defined by the model and calculates importance using log Bayes factor.
5. Testing HWE for Multiallelic Genes- This package calculates plain and fully conditional P-values for the root-mean-square statistic, chi-square statistic, and log likelihood-ratio statistic for the user-provided genotype counts to be consistent with the Hardy-Weinberg equilibrium model.
8. RMacoqui- RMacoqui develops a probability procedure for the identification of chorotypes, i.e. distribution patterns shared by a group of species, which can be operatively identified within an area (Baroni-Urbani et al., 1978).
9. Evolution simulation and classification- After measuring gene frequencies of modern populations that have a common ancestor, we estimate ancestral allele frequency and selection state for each gene. A bayesian model is used and verified using the included simulator.