snp

There are 3 repositories under snp topic.

ncbi / icn3d
web-based protein structure viewer and analysis tool interactively or in batch mode
icn3d webgl protein 3d-structure 3d-viewer structure-viewer nucleotide chemical protein-viewer jupyter-notebook snp delphi nodejs molecular-viewer ar vr
Language:JavaScript 151
zhengxwen / SNPRelate
R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
gds-format pca snp simd r bioinformatics
Language:C++ 98
ramiromagno / gwasrapidd
gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
gwas-catalog r rest-client snp trait trait-ontology human association-studies
Language:R 88
intel / MultiArchUefiPkg
Multi-Architecture UEFI Environment Driver
aarch64 driver emulation gop ihv isa multi-architecture multi-isa oprom riscv64 rise snp uefi x64 x86emulatorpkg
Language:C 48
zhengxwen / SeqArray
Data management of large-scale whole-genome sequence variant calls (Development version only)
gds-format wgs snv snp r bioinformatics wes
Language:C++ 43
gtonkinhill / pairsnp
A set of scripts for calculating pairwise SNP distance
snp genetic distance pairwise
37
CDCgov / mycosnp-nf
CDCgov/mycosnp-nf
myco snp nf-core nextflow
Language:Nextflow 36
mkpython3 / Mutation-Simulator
A tool for simulating random mutations in any genome
bioinformatics genome mutation simulation snp snps sv simulator svs
Language:Python 33
MichaelSebero / Genetic-Trait-Detector
This python script detects known traits in raw human genetic data.
23andme ancestrydna data detector disease dna gedmatch genetics snp tool snpedia traits genes genotype match allele rsid ncbi mutation offline
Language:Python 31
orangeSi / GSSplayground
Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature
genomes genecluster synteny crosslink bioinformatics svg vcf snp bam read-mapping depth visualization structure-variation genome-viewer sv transcriptomics igv-like comparative-genomics long-reads indel
Language:HTML 31
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 31
zhengxwen / HIBAG
R package – HLA Genotype Imputation with Attribute Bagging (development version only)
hla mhc imputation snp r bioinformatics gpu
Language:C++ 29
JiscaH / sequoia
R package for pedigree inference based on SNP data
pedigree pedigree-reconstruction pedigrees r-package rstats rstats-package sequoia snp snp-data
Language:Fortran 25
mltrev23 / snp500_stock_prediction
S&P 500 stock price prediction using Transformer model
ai lstm modeling snp stock-price-prediction transformer
Language:Python 24
USDA-VS / vSNP
vSNP -- validate SNPs
snp pipeline genomics tuberculosis brucella analysis-pipeline mycobacterium-tuberculosis-complex snps whole-genome-sequencing high high-throughput-sequencing bam-files vcf phylogenetics freebayes wgs
Language:Python 19
mbhall88 / psdm
Compute a pairwise SNP distance matrix from one or two alignment(s)
alignment bioinformatics distance fasta matrix pairwise rust snp
Language:Rust 17
oncogenetics / LocusExplorer
An interactive graphical illustration of genetic associations and their biological context
snp gwas prostate cancer plot manhattan-plot prostate-cancer r genetic-associations
Language:R 14
YaoLab-Bioinfo / MaizeSNPDB
A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines
snp database shiny shiny-apps maize
Language:R 12
alinja / snipsa
Tools for analyzing raw DNA test data files. Shows Y chromosome and mitochondrial mtDNA haplogroups. LGPLv3 - use freely but share improvements.
haplogroup mtdna mtdna-haplotypes snp-genotyping snp
Language:Python 10
ipw012 / RIVER
R package for RIVER (RNA-Informed Variant Effect on Regulation)
geneticvariability snp transcription functionalprediction generegulation genomicvariation biomedicalinformatics functionalgenomics genetics systemsbiology transcriptomics bayesian clustering transcriptomevariant variant functional-variants
Language:R 10
rojaff / LanGen_pipeline
Suit of R-scripts to perform landscape genomic analyses
r landscape-genetics landscape-genomics snp vcf rda pcadapt spca venn-diagram snmf lfmm2
Language:R 10
wshuai294 / PStrain
Pstrain profiles strains in metagenomics data. It infers strain abundance and genotype for each species. Also, it has a single species mode; where given a BAM and VCF, it can phase the variants for any species.
strain phase metagenomics-toolkit profile-strains metaphlan3 genotype-frequency marker-gene-analysis metagenotyping snp microbial-strain
Language:Shell 8
dhimmel / snplentiful
SNP abundance correlates with network degree
hetionet confounding network network-degree hetnet snp gene
Language:Jupyter Notebook 7
DKFZ-ODCF / SNVCallingWorkflow
The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow
snp workflow roddy variant-calling variant-annotation
Language:Python 7
roman-tremmel / ggfastman
Fast manhattenplots using ggplot2
gwas plot ggplot2 r fast manhattan manhattan-plot qqplot pvalues plotting-pvalues snp
Language:R 7
wacguy / Simple
mapping genetics snp ems
Language:C 7
waqasuddinkhan / MACARON-GenMed-LabEx
Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)
annotation-framework annotator codon gatk github macaron pcsnv python snp snpcluster snpeff snv snv-annotation variants vcf
Language:Python 7
Endika / genome_report
Your genome report
genome report snp genotype 23andme
Language:Python 6
hdg204 / Rdna-nexus
Functions to analyse UK Biobank genetic data directly from DNA Nexus' RStudio Workbench
biobank bioinformatics dna genetics nexus r risk scores snp uk
Language:R 6
AmirHoseinSafari / Genotype-collector-and-SNP-dataset-creator
Collecting Genotypes from ENA and make their SNPs
snp gatk samtools ena genotype tuberculosis bwa-mem fastq-files isolate snp-calling
Language:Python 5
deepgrace / snp
Structured Network Programming with Sender / Receiver in Modern C++♦️
netowrk programming receiver sender snp concurrency asynchronous c-plus-plus cpp asio header-only
Language:C++ 5
JingfangSI / SnpCountCU
Count common and unique SNPs among several populations from a VCF format file.
snp vcf snpcount population-specific population-shared
Language:Python 5
NCBI-Hackathons / ScrubSV
A QC pipeline for SVs calls based on coverage and SNP calls
ngs ngs-analysis structural-variation snps snp svs qc
Language:R 5
snaketron / genphen
Tool for genome wide association studies with Bayesian inference and statistical learning
gwas gwas-pipeline gwas-tools bayesian-inference snp genotype-phenotype-map random-forest machine-learning bioinformatics
Language:R 5
akiomiyao / ped
Polymorphic Edge Detection - An efficient polymorphism detector for NGS data
polymorphism inversion insertion ngs deletion snp k-mer ngstools somatic-mutations genotype sequence-alignments variant cnv copy-number-variation crispr-cas9
Language:Perl 4
salvadorlab / mbovpan
Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.
comparative-genomics nextflow-pipeline pangenome snp tuberculosis
Language:Nextflow 4

snp

ncbi / icn3d

zhengxwen / SNPRelate

ramiromagno / gwasrapidd

intel / MultiArchUefiPkg

zhengxwen / SeqArray

gtonkinhill / pairsnp

CDCgov / mycosnp-nf

mkpython3 / Mutation-Simulator

MichaelSebero / Genetic-Trait-Detector

orangeSi / GSSplayground

solgenomics / SNPbinner

zhengxwen / HIBAG

JiscaH / sequoia

mltrev23 / snp500_stock_prediction

USDA-VS / vSNP

mbhall88 / psdm

oncogenetics / LocusExplorer

YaoLab-Bioinfo / MaizeSNPDB

alinja / snipsa

ipw012 / RIVER

rojaff / LanGen_pipeline

wshuai294 / PStrain

dhimmel / snplentiful

DKFZ-ODCF / SNVCallingWorkflow

roman-tremmel / ggfastman

wacguy / Simple

waqasuddinkhan / MACARON-GenMed-LabEx

Endika / genome_report

hdg204 / Rdna-nexus

AmirHoseinSafari / Genotype-collector-and-SNP-dataset-creator

deepgrace / snp

JingfangSI / SnpCountCU

NCBI-Hackathons / ScrubSV

snaketron / genphen

akiomiyao / ped

salvadorlab / mbovpan