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fine-mapping

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polyfun

omerwe /polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)

gwas statistical-genetics fine-mapping

UpdatedDec 9, 2024
Python

mmkim1210 /GeneticsMakie.jl

🧬High-performance genetics- and genomics-related data visualization using Makie.jl

visualization data-science bioinformatics gwas genomics genetics julia julia-language multivariate qtl linkage openmendel phewas colocalization locuszoom fine-mapping makie v2f cairomakie multi-ethnic

UpdatedMar 14, 2025
Julia

sankaranlab /SCAVENGE

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

single-cell network-propagation random-walk complex-traits single-cell-analysis fine-mapping scatac-seq disease-mechanisms cell-heterogeneity cell-state cell-trajectory causal-celltype gwas-tool disease-celltype

UpdatedSep 1, 2023
R

variani /finemapr

Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF

rstats rpackage fine-mapping caviar finemap paintor

UpdatedJan 16, 2024
R

WansonChoi /HATK

A collection of modules to process and analyze IMGT-HLA sequences.

hla imgt fine-mapping

UpdatedDec 18, 2022
Parrot

caulilin /QTG_Seq

bsa ngs-pipeline qtl-analyses fine-mapping

UpdatedJan 11, 2019
R

RajLabMSSM /ggLocusZoom

Create LocusZoom-style plots in R.

gwas r plotting qtl locuszoom fine-mapping echoverse

UpdatedMar 5, 2023
R

mancusolab /sushie

Software to perform multi-ancestry SNP fine-mapping on molecular data

python gwas genetics bayesian-inference variational-inference eqtl susie jax fine-mapping pqtl

UpdatedOct 27, 2024
Python

Jianhua-Wang /easyfinemap

user-friendly pipeline for GWAS fine-mapping

python gwas conditional ld gcta fine-mapping paintor clumping caviarbf

UpdatedMar 9, 2025
Python

naim-panjwani /LocusFocus

Application of the Simple Sum method for testing co-localization of GWAS with any other SNP-level data (e.g. eQTL data)

gwas eqtl phewas locuszoom fine-mapping gwas-tools mechanism-of-action cis-regulation eqtl-mapping gwas-summary-statistics gtex-eqtl-association

UpdatedDec 23, 2024
JavaScript

czheluo /MBSA

Multple methods for BSA Pipeline

stats rnaseq bsa ngs-analysis qtl-analyses bsr fine-mapping

UpdatedDec 22, 2019
R

GangLiTarheel /DeepGWAS

DeepGWAS: Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network

gwas deeplearning fine-mapping

UpdatedDec 22, 2024
R

RajLabMSSM /echoplot

echoverse module: Locus plot creation for fine-mapping and colocalization studies.

gwas plotting qtl locus colocalization fine-mapping echoverse

UpdatedOct 21, 2023
R

RajLabMSSM /Fine_Mapping_Shiny

Shiny app for plotting and sharing fine-mapping results from echolocatoR

r shiny fine-mapping echoverse

UpdatedApr 10, 2021
R

wugene /RADAR_SNP

Find risk snp in the LD region of GWAS snps by convolutional neural network

gwas snps deep-neural-networks imputation convolutional-neural-networks epigenomics 1000genomes fine-mapping

UpdatedFeb 28, 2019
Python

jennasimit /MGflashfm

MGflashfm: joint fine-mapping of genetic association signals in several traits amongst multiple population groups.

gwas fine-mapping gwas-tools multi-trait multi-ancestry

UpdatedJan 21, 2024
R

esohkevin /ei-gwas

gwas workflow from raw intensity data to in-silico functional mapping

gwas plink imputation meta-analysis illumina phasing emmax heritability fine-mapping saige haplotype genotype-imputation plink2 gencall idat-to-vcf idat2vcf functional-gwas bolt-lmm

UpdatedJan 7, 2025
Shell

jennasimit /flashfm

Flashfm: multi-trait fine-mapping that uses GWAS summary statistics from several traits. Updated and more flexible wrapper functions available at jennasimit.github.io/flashfmZero/

gwas fine-mapping gwas-tools multi-trait

UpdatedJul 25, 2022
R

RajLabMSSM /echoannot

echoverse module: Annotate fine-mapping results

genome-annotation epigenomics fine-mapping echoverse

UpdatedOct 20, 2023
R

Pintaius /LDmergeFM

Generating a weighed average of LDSTORE matrices for locus-based fine-mapping.

linkage-disequilibrium genomic-data-analysis fine-mapping

UpdatedMar 19, 2021
R

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