SNPassoc - SNPs-Based Whole Genome Association Studies

Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.

Last updated 4 months ago

9.14 score 16 stars 6 dependents 89 scripts 2.7k downloads

methylclock - Methylclock - DNA methylation-based clocks

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

Last updated 4 months ago

dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp

6.52 score 39 stars 28 scripts 351 downloads

tweeDEseq - RNA-seq data analysis using the Poisson-Tweedie family of distributions

Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.

Last updated 4 months ago

immunooncologystatisticalmethoddifferentialexpressionsequencingrnaseqdnaseq

4.91 score 1 dependents 45 scripts 403 downloads

epimutacions - Robust outlier identification for DNA methylation data

The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.

Last updated 4 months ago

dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp

4.23 score 28 scripts 190 downloads