snp-data

There are 5 repositories under snp-data topic.

privefl / bigsnpr
R package for the analysis of massive SNP arrays.
big-data parallel-computing r r-package statistical-methods polygenic-scores bioinformatics population-structure-inference snp-data memory-mapped-file
Language:R 180
solgenomics / SNPbinner
SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.
bioinformatics analysis snp snp-data recombination genotype hmm
Language:Python 29
EricArcher / strataG
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
dna-sequences genetics locus-summaries microsatellites population-genetics population-genomics population-structure snp-data snps
Language:HTML 24
JiscaH / sequoia
R package for pedigree inference based on SNP data
sequoia snp snp-data pedigree pedigrees pedigree-reconstruction rstats-package rstats r-package
Language:Fortran 24
YaoLab-Bioinfo / ECOGEMS
Efficient compression and retrieve of genotype data with integer sparse matrices
shiny shiny-apps snp-data genotype sparse-matrices
Language:R 15
justincbagley / MAGNET
Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)
phylogeny gene-trees maximum-likelihood snp-data raxml inferring-species-trees pipeline
Language:Shell 6
rtahmasbi / GeneEvolve
A fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data
simulator snp-data bioinformatics statistics cpp sequencing genomics
Language:C++ 5
igsr / igsr_analysis
This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data
python jupyter-notebook perl snp-genotyping snp-data pipelines rna-seq nextflow-pipelines
Language:Jupyter Notebook 4
daormar / snptools
Package to work with single nucleotide polymorpishms (SNPs)
snpedia snp-data snp
Language:M4 3
CNuge / miscellaneous_scripts
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
snp-data snp-genotype-datasets bioinformatics-tasks miscellaneous-scripts microarray-data snp-file affymetrix microarray-design
Language:Python 1
SCCH-KVS / deepsnp
The sourcecode of DeepSNP
deep-learning bioinformatics snp-data
Language:Python 1
stefan-m-lenz / BMs4BInf2019
Jupyter notebook with a multimodal DBM example on SNP and gene expression data
bioinformatics deep-boltzmann-machine dimensionality-reduction gene-expression snp-data unsupervised-learning
Language:Jupyter Notebook 1
Rice-PCA-SNPs
aangush / Rice-PCA-SNPs
An analysis of SNP data from many rice genome samples. Includes PCA, MDS plots, processing with fastStructure, visualizing results
bioinformatics faststructure genomics pca-analysis population-structure-inference snp-data
Language:HTML 0
Simulate_a_SNP_Pair
hrmazumder / Simulate_a_SNP_Pair
Simulation of a pair of Single Nucleotide Polymorphisms (SNPs) and associated binary response (e.g., disease status) based on real SNP data in R.
single-nucleotide-polymorphisms simulation bioinformatics snp-data
Language:R 0
josuechinchilla / SNPware
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.
genomics-data-sets genomics snp-data snp-genotyping bioinformatics-tool
Language:Shell 0
RaulCoroban / EnsembleFeatureSelector_MinorThesis
Swapping algorithm analysis to aid Ensemble Feature Selection
feature-selection ensemble-model machine-learning-algorithms diabetes-prediction snp-data
Language:TeX 0
SinomeM / QCtreeCNV
Powerful CNV calls filtering pipeline. Focused on fixed loci calling, before visual inspection.
cnv-analysis snp-data cnv r
Language:R 0
dabne003 / Unsupervised-Machine-Learning
Principal Component Analysis, PCA, Gaussian Markov Random Fields, Graphical model,
principal-component-analysis pca unsupervised-machine-learning guassian-markov-random-fields graphical-models clustering-hierarchy snp-data snps phenotypes plant-breeding
Language:R

snp-data

privefl / bigsnpr

solgenomics / SNPbinner

EricArcher / strataG

JiscaH / sequoia

YaoLab-Bioinfo / ECOGEMS

justincbagley / MAGNET

rtahmasbi / GeneEvolve

igsr / igsr_analysis

daormar / snptools

CNuge / miscellaneous_scripts

SCCH-KVS / deepsnp

stefan-m-lenz / BMs4BInf2019

aangush / Rice-PCA-SNPs

hrmazumder / Simulate_a_SNP_Pair

josuechinchilla / SNPware

RaulCoroban / EnsembleFeatureSelector_MinorThesis

SinomeM / QCtreeCNV

dabne003 / Unsupervised-Machine-Learning