fine-mapping

There are 3 repositories under fine-mapping topic.

• polyfun

  omerwe / polyfun

  PolyFun (POLYgenic FUNctionally-informed fine-mapping)

  statistical-geneticsgwasfine-mapping
  Language:Python 79

• mmkim1210 / GeneticsMakie.jl

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

  geneticsgenomicsjuliavisualizationmakiebioinformaticscairomakiegwasphewaslocuszoomcolocalizationfine-mappingqtllinkagejulia-languagedata-sciencemulti-ethnicv2fmultivariateopenmendel
  Language:Julia 74

• sankaranlab / SCAVENGE

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

  cell-heterogeneitycell-statecell-trajectorycomplex-traitsdisease-mechanismsfine-mappingnetwork-propagationrandom-walkscatac-seqsingle-cell-analysiscausal-celltypegwas-toolsingle-celldisease-celltype
  Language:R 73

• variani / finemapr

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

  fine-mappingrpackagerstatscaviarfinemappaintor
  Language:R 27

• WansonChoi / HATK

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

  hlafine-mappingimgt
  Language:Parrot 26

• caulilin / QTG_Seq

  qtl-analysesfine-mappingbsangs-pipeline
  Language:R 20

• RajLabMSSM / ggLocusZoom

  Create LocusZoom-style plots in R.

  rechoversegwasqtlplottinglocuszoomfine-mapping
  Language:R 20

• mancusolab / sushie

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

  bayesian-inferenceeqtlfine-mappinggeneticsgwasjaxpqtlpythonsusievariational-inference
  Language:Python 13

• 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)

  gwasgwas-toolsgwas-summary-statisticseqtleqtl-mappinggtex-eqtl-associationmechanism-of-actioncis-regulationlocuszoomphewasfine-mapping
  Language:JavaScript 8

• czheluo / MBSA

  Multple methods for BSA Pipeline

  bsaqtl-analysesfine-mappingstatsngs-analysisrnaseqbsr
  Language:R 7

• Jianhua-Wang / easyfinemap

  user-friendly pipeline for GWAS fine-mapping

  fine-mappinggwaspythonconditionalgctaldpaintorcaviarbfclumping
  Language:Python 5

• RajLabMSSM / Fine_Mapping_Shiny

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

  echoversershinyfine-mapping
  Language:R 4

• wugene / RADAR_SNP

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

  gwasimputationsnpsfine-mappingdeep-neural-networksconvolutional-neural-networksepigenomics1000genomes
  Language:Python 4

• GeneMAP-Research / genemapgwas

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

  emmaxfine-mappinggencallgenotype-imputationgwashaplotypeheritabilityidat-to-vcfilluminaimputationmeta-analysisphasingplinkplink2saigebolt-lmmfunctional-gwasidat2vcf
  Language:Nextflow 3

• gymrek-lab / happler

  A haplotype-based fine-mapping method

  fine-mapping
  Language:Jupyter Notebook 2

• jennasimit / flashfm

  Flashfm: multi-trait fine-mapping that uses GWAS summary statistics from several traits

  fine-mappinggwas-toolsmulti-traitgwas
  Language:R 2

• jennasimit / MGflashfm

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

  fine-mappinggwas-toolsmulti-traitgwas
  Language:R 2

• Pintaius / LDmergeFM

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

  genomic-data-analysisfine-mappinglinkage-disequilibrium
  Language:R 2

• RajLabMSSM / echoannot

  echoverse module: Annotate fine-mapping results

  echoversefine-mappingepigenomicsgenome-annotation
  Language:R 2

• RajLabMSSM / echoplot

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

  locusgwasqtlplottingechoversefine-mappingcolocalization
  Language:R 2

• cmomo / LocNet

  This method incorporates dense linkage disequilibrium block structure of SNPs for prioritizing a set of genetic variants using GWAS summary statisticis before performing fine-mapping.

  fine-mappinggwaslinkage-disequilibriumcausal-variantsdense-graphhaplotype-blocks
  Language:HTML 0

• gil2rok / fine-mapping

  Knowles Lab Research: determine which genetic variants cause a phenotype with non-binary functional annotations

  computational-biologyfine-mappingfunctional-annotationgradient-descentvariational-inference
  Language:Python 0

• jennasimit / flashfm-ivis

  flashfm-ivis: interactive visualisation for fine-mapping of multiple quantitative traits

  fine-mappingfinemapinteractive-visualizationsmulti-traitrshinyvisualisationgwas
  0

• RajLabMSSM / echodata

  echoverse module: Example data.

  echoversedatafine-mappinggenomicsgwasqtl
  Language:R