Alternatives and similar repositories for STAARpipeline

Users that are interested in STAARpipeline are comparing it to the libraries listed below

• xihaoli / STAARpipeline-Tutorial

  View on GitHub
  The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVOR…
  ☆35Dec 3, 2024Updated last year
• xihaoli / STAARpipelineSummary

  View on GitHub
  An R package for summarizing and visualizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies genera…
  ☆12Oct 16, 2024Updated last year
• xihaoli / STAAR

  View on GitHub
  An R package for performing STAAR procedure in whole-genome sequencing studies
  ☆97Feb 9, 2025Updated last year
• zhouhufeng / FAVORannotator

  View on GitHub
  ☆23Mar 7, 2023Updated 2 years ago
• xihaoli / MetaSTAAR

  View on GitHub
  An R package for performing MetaSTAAR procedure in whole-genome sequencing studies
  ☆27Nov 9, 2024Updated last year
• xihaoli / MultiSTAAR

  View on GitHub
  An R package for performing MultiSTAAR procedure in whole-genome sequencing studies
  ☆11Nov 14, 2024Updated last year
• CCICB / introme

  View on GitHub
  Introme prioritises coding and noncoding splice-altering variants for clinical variant interpretation
  ☆22Dec 18, 2025Updated last month
• fmicompbio / mutscan

  View on GitHub
  Software to process, statistically analyse and visualise deep mutational scanning data
  ☆14Oct 29, 2025Updated 3 months ago
• PalamaraLab / ASMC

  View on GitHub
  Ascertained Sequentially Markovian Coalescent
  ☆16Oct 22, 2025Updated 3 months ago
• ICGC-TCGA-PanCancer / Seqware-BWA-Workflow

  View on GitHub
  This is the BWA workflow used in the PanCancer project used to allign all the BAM files.
  ☆11Dec 27, 2022Updated 3 years ago
• ShujiaHuang / basevar

  View on GitHub
  This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially …
  ☆27Jul 28, 2025Updated 6 months ago
• FINNGEN / saige-pipelines

  View on GitHub
  ☆16Sep 14, 2023Updated 2 years ago
• HTGenomeAnalysisUnit / nf-pipeline-regenie

  View on GitHub
  GWAS and rare variants tests at high speed using regenie
  ☆16Jan 9, 2026Updated last month
• ding-lab / BICSEQ2

  View on GitHub
  BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA
  ☆16Apr 13, 2021Updated 4 years ago
• rgcgithub / regenie

  View on GitHub
  regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
  ☆249Nov 13, 2025Updated 3 months ago
• bdaisley / isolateR

  View on GitHub
  Automated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries
  ☆12Jan 4, 2026Updated last month
• UW-GAC / analysis_pipeline

  View on GitHub
  TOPMed analysis pipeline
  ☆52Oct 10, 2023Updated 2 years ago
• Illumina / PrimateAI-3D

  View on GitHub
  ☆72Nov 14, 2025Updated 3 months ago
• broadinstitute / str-analysis

  View on GitHub
  Scripts and utilities for analyzing tandem repeats (TRs).
  ☆42Updated this week
• similab / FSTest

  View on GitHub
  An efficient tool for cross-population fixation index estimation on variant call format files
  ☆11Jan 12, 2024Updated 2 years ago
• getian107 / PRScsx

  View on GitHub
  Cross-population polygenic prediction
  ☆98Nov 13, 2025Updated 3 months ago
• kage-genotyper / kage

  View on GitHub
  Alignment-free genotyper for SNPs and short indels, implemented in Python.
  ☆54Mar 7, 2025Updated 11 months ago
• tf2 / CNest

  View on GitHub
  Copy Number Methods for Detection and Genome Wide Association Tests
  ☆22Nov 4, 2024Updated last year
• nf-cmgg / structural

  View on GitHub
  A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region exp…
  ☆27Jan 15, 2026Updated last month
• edg1983 / GREEN-VARAN

  View on GitHub
  Annotate non-coding regulatory vars using our GREEN-DB, prediction scores, conservation and pop AF
  ☆20Jun 13, 2025Updated 8 months ago
• ventolab / Human-Endometrial-Cell-Atlas_HECA

  View on GitHub
  Human Endometrial Cell Atlas (HECA). An integrated single-cell reference atlas of the human endometrium.
  ☆30Jun 19, 2024Updated last year
• kurtsemih / copyVAE

  View on GitHub
  A variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics
  ☆10Mar 11, 2024Updated last year
• ZhiGroup / Syllable-PBWT

  View on GitHub
  ☆12Aug 23, 2023Updated 2 years ago
• jfnavarro / hla_pipeline

  View on GitHub
  DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions
  ☆11Jul 8, 2021Updated 4 years ago
• ProGenNo / ProHap

  View on GitHub
  Proteogenomics database-generation tool for protein haplotypes and variants
  ☆11Jun 19, 2025Updated 7 months ago
• broadinstitute / gnomad_qc

  View on GitHub
  ☆69Updated this week
• Illumina / PromoterAI

  View on GitHub
  ☆89Nov 19, 2025Updated 2 months ago
• statgen / topmed_variant_calling

  View on GitHub
  ☆24Nov 27, 2024Updated last year
• rivasiker / trails

  View on GitHub
  Tree reconstruction of ancestry using incomplete lineage sorting
  ☆11Jan 9, 2026Updated last month
• xiaoming-liu / stairway-plot-v2

  View on GitHub
  The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequ…
  ☆61Sep 19, 2025Updated 4 months ago
• jeongdo801 / scNOVA

  View on GitHub
  scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
  ☆11Jul 29, 2023Updated 2 years ago
• ding-lab / morph

  View on GitHub
  ☆14Oct 24, 2025Updated 3 months ago
• casanova-lab / NHC

  View on GitHub
  NHC: A computational approach to detect physiological homogeneity in the midst of genetic heterogeneity
  ☆12Feb 4, 2024Updated 2 years ago
• nf-cmgg / exomecnv

  View on GitHub
  A nextflow pipeline for calling exome CNVs
  ☆13Feb 9, 2026Updated last week