snps

There are 8 repositories under snps topic.

tseemann / snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
variant-calling haploid bacteria fastq-analysis snps vcf indel-discovery bioinformatics genomics
Language:Perl 436
Illumina / strelka
Strelka2 germline and somatic small variant caller
bioinformatics indels snps snvs
Language:C++ 347
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical medicine cancer cancer-genomics cancer-genomes ensembl gtf vcf snps csv-parser bed
Language:Python 307
edgardomortiz / vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
vcf snps phylip alignment phylogenetics nexus binary snapp fasta outgroup convert-snps vcf-files phylogenetic-analysis vcf-format phylip-matrix haploid diploid polyploid
Language:Python 249
apriha / lineage
tools for genetic genealogy and the analysis of consumer DNA test results
dna genes genetics genealogy snps chromosomes genotype bioinformatics ancestry
Language:Python 140
cslarsen / arv
A fast 23andMe DNA parser and inferrer for Python
23andme dna python genome bioinformatics snpedia snps
Language:C++ 114
mentatpsi / OSGenome
An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies
23andme snps genome data-crawling python genetic-data kendo flask genetics snpedia raw-data
Language:Python 107
apriha / snps
tools for reading, writing, merging, and remapping SNPs
snps dna chromosomes bioinformatics vcf
Language:Python 88
cslarsen / dna-traits
A fast 23andMe genome text file parser, now superseded by arv
23andme python snps health-report snpedia dna genomics bioinformatics
Language:Python 65
MAGMA_Celltyping
neurogenomics / MAGMA_Celltyping
Find causal cell-types underlying complex trait genetics
gwas genomics single-cell-omics magma single-cell snps statistical-genetics
Language:R 65
ropensci / rsnps
Wrapper to a number of SNP web APIs
data r r-package rstats snps web-api
Language:R 51
PopGen.jl
BioJulia / PopGen.jl
Population Genetics in Julia
genetics genomics snps microsatellites fst structure popgen
Language:Julia 43
chadlaing / Panseq
Pan-genomic sequence analysis
pan-genome genome-sequencing snps accessory-genome core-genome comparative-genomics
Language:HTML 43
OpenMendel / SnpArrays.jl
Compressed storage for SNP data
snps openmendel plink julia
Language:Julia 41
BioJulia / GeneticVariation.jl
Datastructures and algorithms for working with genetic variation
bioinformatics biology julia variation mutation snps polymorphism
Language:Julia 38
huwenboshi / hess
Estimate local SNP heritability and genetic covariance from GWAS summary association statistics.
reference-panel snps summary-statistics
Language:HTML 33
kaustubhad / fastman
An R package for fast and efficient visualizing of GWAS results using Q-Q and Manhattan plots directly from PLINK output files.
manhattan-plot snps chromosome chromosome-positions
Language:HTML 33
mkpython3 / Mutation-Simulator
A tool for simulating random mutations in any genome
bioinformatics genome mutation simulation snp snps sv simulator svs
Language:Python 33
ilarsf / gwasTools
Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)
gwas rscript qq manhattan-plot genome-analysis snps power plotting optparse
Language:R 28
slowkow / proxysnps
:bookmark: Get SNP proxies from the 1000 Genomes Project.
bioinformatics linkage-disequilibrium snps statistics rstats
Language:R 28
aquaskyline / 16GT
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
call-variants genome vcf indels snps bioinformatics computational-biology
Language:Perl 27
EricArcher / strataG
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
population-structure locus-summaries population-genetics population-genomics genetics snps snp-data dna-sequences microsatellites
Language:HTML 25
pievos101 / PopGenome
An Efficient Swiss Army Knife for Population Genomic Analyses in R
population-genomics snps genome-analysis
Language:R 24
CandiHap
xukaili / CandiHap
A haplotype analysis toolkit for natural variation study.
haplotype-analysis gwas sanger natural-variation snps candidate-genes target-traits
Language:Perl 24
medvedevgroup / vargeno
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
algorithms bioinformatics computational-biology data-structures genotyping snps
Language:C++ 19
pimbongaerts / radseq
Collection of Python scripts for parsing/analyses of RAD-seq data
python radseq vcf pyrad snps
Language:Python 19
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 18
chgibb / PHAT
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
ngs alignment visualization analysis pathogen host next-generation-sequencing circos circos-graphs circos-plot snps quality-control bioinformatics bioinformatics-analysis bioinformatics-tool dna phat bam bam-files electron
Language:TypeScript 17
glasgowm148 / Phenotype
An Open Source Web Application for Genetic Data (SNPs) Data Crawling
snps genome genetic-tests os-genome snpedia dbsnp 23andme ancestrydna clinvar omni rsid genetic-data genetic-algorithm phenotype data-crawling
Language:JavaScript 14
YTLogos / BnaSNPDB
An interactive web portal for exploring SNPs among 1,007 rapeseed germplasm accessions
rapeseed shiny-apps snps snp-database shiny-server shiny
Language:R 12
justincbagley / piranha
Scripts for file processing and analysis in phylogenetics and phylogeography
phylogeny phylogeography shell r bayesian-inference maximum-likelihood snps population-structure supercomputer ssh
Language:Shell 11
Sydney-Informatics-Hub / Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-analysis sydney-informatics-hub research-computing germline-variants somatic-variants cancer genomics indels metagenomics ngs rnaseq snps transcriptomics variant-calling nextflow nextflow-pipelines
11
esteinig / brick
BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons :microbe:
blast brig cds d3 genomics html mge snps svg bakta genomad
Language:Svelte 10
jonas-fuchs / virHEAT
Visualize microbial evolution at the SNP level!
genome-visualization heatmap pypi-package snps variant-analysis vcf-files viral-genomics
Language:Python 10
tbrunetti / QuaCK
Quality Control Summary Pipeline for Array-based Genome Studio Projects (idats, raw genotype quality)
gwas illumina-bead-chip plink-files quality-assurance quality-control snps
Language:Python 10
alexcoppe / iWhale
:whale: Dockerized WES pipeline for variants identification in mathced tumor-normal samples
bioinformatics biology docker genomics indels scons snps tumor whole-exome-sequencing
Language:Python 9