Repositories list

• 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 27, 2024Oct 27, 2024

• QTL-mapping-pipeline

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

  snakemakepipelineeqtl+ 1sqtl

  Python

  •0•4•4•0•Updated Oct 22, 2024Oct 22, 2024

• mmQTL-pipeline

  Public
  Python

  •

  MIT License

  •0•2•0•0•Updated Oct 1, 2024Oct 1, 2024

• isoseq-pipeline

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

  rna-seqpipelinelong-reads

  Python

  •4•4•2•0•Updated Oct 1, 2024Oct 1, 2024

• downstream-QTL

  Public
  set of scripts and pipelines to work with QTL results

  HTML

  •1•4•6•2•Updated Oct 1, 2024Oct 1, 2024

• Genotype_QC_Pipeline_2.0

  Public
  Python

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

• isoMiGA

  Public
  The isoform-centric microglia genomic atlas.

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

• RajLab_website

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

  CSS

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

• echoconda

  Public
  echoverse module: conda environment handling

  pythonanacondaconda-environment+ 2echoverser

  R

  •2•1•3•0•Updated Jun 4, 2024Jun 4, 2024

• echoLD

  Public
  echoverse module: LD downloading and processing

  linkage-disequilibriumgenomics1000genomes+ 2ukbiobankechoverse

  R

  •0•0•4•0•Updated May 10, 2024May 10, 2024

• downloadR

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

  download-managervcf-filesechoverse

  R

  •0•0•2•0•Updated May 10, 2024May 10, 2024

• devoptera

  Public
  ⏩ Practical tools for R developers ⏪ 🔧🦇 🔨🦇 🧰🦇

  developer-toolsr-packageechoverse

  R

  •0•1•0•0•Updated Apr 1, 2024Apr 1, 2024

• AR_Rotation

  Public
  HTML

  •0•0•0•0•Updated Feb 29, 2024Feb 29, 2024

• MBV_Pipeline

  Public
  Python

  •0•0•1•0•Updated Feb 20, 2024Feb 20, 2024

• snakeSV

  Public
  Snakemake pipeline for SV discovery and analysis

  snakemakesvstructural-variation

  Python

  •

  MIT License

  •1•6•2•0•Updated Dec 3, 2023Dec 3, 2023

• echodata

  Public
  echoverse module: Example data.

  datagwasgenomics+ 3qtlfine-mappingechoverse

  R

  •0•0•4•0•Updated Nov 17, 2023Nov 17, 2023

• echotabix

  Public
  echoverse module: Tabix indexing and querying.

  genomicstabixvcf-files+ 1echoverse

  R

  •0•0•3•0•Updated Nov 17, 2023Nov 17, 2023

• echodeps

  Public
  echoverse module: Create package dependency graphs

  networksdependenciesrpackages+ 1echoverse

  R

  •0•0•1•0•Updated Oct 27, 2023Oct 27, 2023

• echoplot

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

  gwasplottingqtl+ 4locuscolocalizationfine-mappingechoverse

  R

  •1•5•3•0•Updated Oct 21, 2023Oct 21, 2023

• echoverseTemplate

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

  templatesrpackageechoverse+ 1r

  R

  •0•0•0•0•Updated Oct 20, 2023Oct 20, 2023

• echoannot

  Public
  echoverse module: Annotate fine-mapping results

  genome-annotationepigenomicsfine-mapping+ 1echoverse

  R

  •0•2•8•0•Updated Oct 20, 2023Oct 20, 2023

• leafcutter-pipeline

  Public
  Differential splicing and visualisation pipeline for the Raj lab

  rna-seqpipelinesplicing

  Python

  •5•2•4•2•Updated Aug 28, 2023Aug 28, 2023

• MiGA_public_release

  Public
  HTML

  •

  MIT License

  •0•7•2•0•Updated Aug 1, 2023Aug 1, 2023

• ldsc

  Public
  LD Score Regression Pipeline

  Python

  •

  MIT License

  •1•1•0•0•Updated Jun 12, 2023Jun 12, 2023

• Monocytes_RNA_Editing_Analysis

  Public
  HTML

  •0•2•0•0•Updated Apr 24, 2023Apr 24, 2023

• echogithub

  Public
  echoverse module: Extract data and metadata from GitHub

  githubapir-packages+ 3package-repository-visualisationechoverser

  R

  •0•0•3•0•Updated Mar 19, 2023Mar 19, 2023

• ggLocusZoom

  Public archive
  Create LocusZoom-style plots in R.

  gwasplottingqtl+ 4locuszoomfine-mappingechoverser

  R

  •

  MIT License

  •4•20•0•0•Updated Mar 5, 2023Mar 5, 2023

• echolocatoR

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

  gwaslinkage-disequilibriumqtl+ 5variant-annotationcolocalizationfinemapechoversebioinformatics

  R

  •

  MIT License

  •12•36•16•0•Updated Jan 20, 2023Jan 20, 2023

• New_beginnings_2.0

  Public
  1•1•0•0•Updated Jan 17, 2023Jan 17, 2023

• catalogueR

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

  apigwasqtl+ 4colocalizationechoversebioinformaticsr

  R

  •

  MIT License

  •1•13•5•0•Updated Dec 23, 2022Dec 23, 2022