Cis-mQTL-mapping-protocol-for-methylome

Regional Association of Methylome variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify genome-wide Variable Methylated Loci (VML) from microarray DNA methylation data; then, using genomic and exposomic data, it can identify which model out of the following explains best the DNA methylation variability at each VML: genetic (G), environmental (E), additive (G+E) or interactive (GxE).

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

Py-HLA-Match is a Python library for standardised, rule-based HLA (Human Leukocyte Antigen) matching in retrospective analyses, method development, benchmarking, and in-silico studies in immunogenetics and related fields.

Evaluates Hardy-Weinberg equilibrium for diploid loci with two to six alleles using chi-square and Guo-Thompson exact tests, inbreeding coefficient F, and plain-language verdicts from observed genotype counts, allele frequencies, or biallelic disease incidence. A browser calculator provides De Finetti plots, export, and Wright-Fisher simulation under selection, drift, mutation, and migration; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits genotype or simulation inputs and returns structured results and shareable run identifiers.

Constructs Punnett squares and offspring genotype and phenotype ratios for complete, incomplete, codominant, ABO multiple-allele, and sex-linked Mendelian crosses from parent genotypes, with step-by-step walkthroughs and reduced ratio output. A browser calculator provides live grids, textbook presets, PNG and SVG export, and shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits cross inputs and returns structured grids, ratios, walkthroughs, and shareable run identifiers.

Interactive browser for the complete Human Phenotype Ontology (~19,800 terms), with a graph-based term explorer and a clinical profile analyzer for phenotype similarity, differential diagnosis, and gene prioritization.