haplotype
There are 18 repositories under haplotype topic.
zengxiaofei/HapHiC
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
odelaneau/shapeit5
Segmented HAPlotype Estimation and Imputation Tool
deepomicslab/SpecHLA
SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.
SAMtoBAM/PhasedDiploidGenomeAssemblyPipeline
Using de-novo assembly and read-phasing to assemble reference-free diploid genomes
cannin/snp_plotter
snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data.
fengcong3/HAPPE
A tool to visualize the haplotype pattern and various information in excel.
Chenglin20170390/Haplotype-diversity
This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato breeding“
pdimens/harpy
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
alethere/mpQTL
github repository for R package mpQTL
GeneMAP-Research/genemapgwas
gwas workflow from raw intensity data to in-silico functional mapping
daissi/thesias
THESIAS: Testing Haplotype Effects In Association Studies
GeneMAP-Research/genemapimputationservice
haplotype estimation, custom panel creation, and genotype imputation
qj009/GWAS2
GWAS2: 2nd generation GWAS tool
bmds-lab/Crackling-phased
*HaploCrackling* -- The Crackling-based method for variant-aware, whole-genome CRISPR-Cas9 target detection
DanielRCA/NCR-mtDNA_ampliconbasedngs
A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods
roncuevas/Polymorphism
Programa Delfin 2022
zjwinn/Profiling-of-FHB-Resistance-QTL-Haplotypes-Through-MM-GBG-and-ML
This is the data repository for the publication of the same name.
colbyford/SeekDeep-Docker
Repository for running SeekDeep in a Docker Container