Principal Component Analysis, PCA, Gaussian Markov Random Fields, Graphical model,
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Updated
Mar 24, 2018 - R
Principal Component Analysis, PCA, Gaussian Markov Random Fields, Graphical model,
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
A fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data
SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.
Jupyter notebook with a multimodal DBM example on SNP and gene expression data
Swapping algorithm analysis to aid Ensemble Feature Selection
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.
Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)
An analysis of SNP data from many rice genome samples. Includes PCA, MDS plots, processing with fastStructure, visualizing results
This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data
Efficient compression and retrieve of genotype data with integer sparse matrices
Simulation of a pair of Single Nucleotide Polymorphisms (SNPs) and associated binary response (e.g., disease status) based on real SNP data in R.
Powerful CNV calls filtering pipeline. Focused on fixed loci calling, before visual inspection.
R package for pedigree inference based on SNP data
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
R package for the analysis of massive SNP arrays.
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