Repositories list

• AD_MPRA

  Public
  AD Fine-mapping and MPRA

  HTML

  •1•1•0•0•Updated Mar 21, 2026Mar 21, 2026

• SingleBrain

  Public
  R

  •0•7•0•0•Updated Mar 21, 2026Mar 21, 2026

• echolocatoR

  Public
  Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

  bioinformaticsgwaslinkage-disequilibrium+ 5

  bioinformaticsgwaslinkage-disequilibriumqtlvariant-annotationcolocalizationfinemapechoverse

  R

  •

  MIT License

  •14•46•10•0•Updated Mar 16, 2026Mar 16, 2026

• echoannot

  Public
  echoverse module: Annotate fine-mapping results

  genome-annotationepigenomicsfine-mapping+ 1

  genome-annotationepigenomicsfine-mappingechoverse

  R

  •0•2•0•0•Updated Mar 16, 2026Mar 16, 2026

• echotabix

  Public
  echoverse module: Tabix indexing and querying.

  genomicstabixvcf-files+ 1

  genomicstabixvcf-filesechoverse

  R

  •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

• echoLD

  Public
  echoverse module: LD downloading and processing

  linkage-disequilibriumgenomics1000genomes+ 2

  linkage-disequilibriumgenomics1000genomesukbiobankechoverse

  R

  •0•1•0•0•Updated Mar 16, 2026Mar 16, 2026

• echoconda

  Public
  echoverse module: conda environment handling

  pythonranaconda+ 2

  pythonranacondaconda-environmentechoverse

  R

  •3•1•0•0•Updated Mar 16, 2026Mar 16, 2026

• catalogueR

  Public
  Easy-to-use R wrappers for the eQTL Catalogue's API (both with tabix and the REST API).

  apibioinformaticsgwas+ 4

  apibioinformaticsgwasrqtlcolocalizationechoverse

  R

  •

  MIT License

  •2•14•0•0•Updated Mar 16, 2026Mar 16, 2026

• echoAI

  Public
  Echoverse Module: AI/ML Variant-Level Predictions

  R

  •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

• echodata

  Public
  echoverse module: Example data.

  datagwasgenomics+ 3

  datagwasgenomicsqtlfine-mappingechoverse

  R

  •1•0•0•0•Updated Mar 16, 2026Mar 16, 2026

• echodeps

  Public
  echoverse module: Create package dependency graphs

  networksdependenciesrpackages+ 1

  networksdependenciesrpackagesechoverse

  R

  •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

• echoplot

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

  gwasplottingqtl+ 4

  gwasplottingqtllocuscolocalizationfine-mappingechoverse

  R

  •1•6•0•0•Updated Mar 16, 2026Mar 16, 2026

• devoptera

  Public
  ⏩ Practical tools for R developers :rewind: :wrench::bat: :hammer::bat: :toolbox::bat:

  developer-toolsr-packageechoverse

  developer-toolsr-packageechoverse

  R

  •0•1•0•0•Updated Mar 16, 2026Mar 16, 2026

• echogithub

  Public
  echoverse module: Extract data and metadata from GitHub

  githubapir+ 3

  githubapirr-packagespackage-repository-visualisationechoverse

  R

  •1•0•0•0•Updated Mar 16, 2026Mar 16, 2026

• downloadR

  Public
  echoverse module: Single- and multi-threaded downloading functions.

  download-managervcf-filesechoverse

  download-managervcf-filesechoverse

  R

  •0•1•0•0•Updated Mar 16, 2026Mar 16, 2026

• echoverseTemplate

  Public template
  Self-updating template for creating echoverse R packages.

  rtemplatesrpackage+ 1

  rtemplatesrpackageechoverse

  R

  •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

• echofinemap

  Public
  echoverse module: Statistical and functional fine-mapping functions.

  gwasstatisticsgenomics+ 3

  gwasstatisticsgenomicsqtlfinemapechoverse

  R

  •1•2•1•0•Updated Mar 16, 2026Mar 16, 2026

• RajLab_website

  Public
  Official website for the Raj Lab detailing personnel, updates, current projects and opportunities.

  CSS

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Mar 10, 2026Mar 10, 2026

• mmQTL-pipeline

  Public
  Python

  •

  MIT License

  •1•7•0•0•Updated Jan 22, 2026Jan 22, 2026

• downstream-QTL

  Public
  set of scripts and pipelines to work with QTL results

  HTML

  •2•10•7•2•Updated Jan 21, 2026Jan 21, 2026

• editing-pipeline

  Public
  A set of snakemake pipelines for doing RNA editing

  R

  •3•4•0•0•Updated Jan 20, 2026Jan 20, 2026

• SAIGEQTL-pipeline

  Public
  R

  •

  MIT License

  •0•1•0•0•Updated Jan 14, 2026Jan 14, 2026

• ldsc

  Public
  LD Score Regression Pipeline

  Python

  •

  MIT License

  •1•1•0•0•Updated Nov 22, 2025Nov 22, 2025

• RNA-pipelines

  Public
  A repo to contain various RNA-seq processing pipelines, to cut down how many different repos I have.

  Python

  •3•3•4•0•Updated Oct 6, 2025Oct 6, 2025

• GBA-LRRK2-monocytes

  Public
  0•0•0•0•Updated Oct 2, 2025Oct 2, 2025

• QTL-mapping-pipeline

  Public
  A snakemake pipeline for QTL mapping. Based on the GTEX pipeline

  snakemakepipelineeqtl+ 1

  snakemakepipelineeqtlsqtl

  Python

  •0•6•4•0•Updated May 19, 2025May 19, 2025

• isoseq-pipeline

  Public
  pipeline for working with PacBio long read RNA data using the outputs of isoseq3

  rna-seqpipelinelong-reads

  rna-seqpipelinelong-reads

  Python

  •4•9•2•0•Updated Apr 8, 2025Apr 8, 2025

• leafcutter-pipeline

  Public
  Differential splicing and visualisation pipeline for the Raj lab

  rna-seqpipelinesplicing

  rna-seqpipelinesplicing

  Python

  •5•3•4•2•Updated Mar 25, 2025Mar 25, 2025

• MBV_Pipeline

  Public
  Python

  •0•0•1•0•Updated Nov 26, 2024Nov 26, 2024

• Genotype_QC_Pipeline_2.0

  Public
  Python

  •0•1•1•0•Updated Oct 1, 2024Oct 1, 2024