snp-data

R package for the analysis of massive SNP arrays.

SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

Efficient compression and retrieve of genotype data with integer sparse matrices

R package for pedigree inference based on SNP data

A fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data

Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)

Package to work with single nucleotide polymorpishms (SNPs)

This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data

Various python programs I use for the manipulation of SNP genotype datasets and other bioinformatics tasks. This repository features miscellaneous scripts to help work efficiently in common bioinformatics tasks I encounter. Use at own risk

The sourcecode of DeepSNP

Jupyter notebook with a multimodal DBM example on SNP and gene expression data

Principal Component Analysis, PCA, Gaussian Markov Random Fields, Graphical model,

Simulation of a pair of Single Nucleotide Polymorphisms (SNPs) and associated binary response (e.g., disease status) based on real SNP data in R.

SNPware is a family of short bash scripts that allows to translate genotypes coded as GCTA or Illuimina Top Strand to AB coding using standard Illumina FinalReport files to create a library of genotype equivalences at each locus.

An analysis of SNP data from many rice genome samples. Includes PCA, MDS plots, processing with fastStructure, visualizing results

Powerful CNV calls filtering pipeline. Focused on fixed loci calling, before visual inspection.

Swapping algorithm analysis to aid Ensemble Feature Selection