Repositories list

• lab_scripts

  Public
  Common scripts for the Goate and Marcora labs

  R

  •0•1•0•0•Updated Jun 6, 2025Jun 6, 2025

• GWASampleFiltering

  Public
  Post imputation QC and processing of Michigan Imputation Server Jobs

  Python

  •1•1•1•0•Updated Jun 6, 2025Jun 6, 2025

• vcf_liftover

  Public
  Pipeline for lifting over vcf files and filesets

  Python

  •0•0•0•1•Updated Jun 6, 2025Jun 6, 2025

• qc-ancestry-impute-qc

  Public
  An integrated pipeline to do initial genotype QC, impute by ancestry, combine results and do remaining QC on microarray genotypes

  Python

  •2•1•0•1•Updated Jun 6, 2025Jun 6, 2025

• imputePipeline

  Public
  A Snakemake pipeline to prepare binary PLINK files for the Michigan Imputation Server.

  Python

  •3•1•0•2•Updated Jun 6, 2025Jun 6, 2025

• postImpute

  Public
  Post imputation QC and processing of Michigan Imputation Server Jobs

  Python

  •3•4•0•2•Updated Jun 6, 2025Jun 6, 2025

• lab_operations

  Public
  Guides, scripts and config files for everyday operations, onboarding and offboarding

  Shell

  •

  Creative Commons Zero v1.0 Universal

  •0•1•0•0•Updated Jun 3, 2025Jun 3, 2025

• sra_downloader

  Public
  Download and extract files from Sequence Read Archive (SRA)

  Python

  •1•0•0•0•Updated Feb 19, 2025Feb 19, 2025

• admixture_pipeline

  Public
  Pipeline to run unsupervised ADMIXTURE with a gnomAD reference

  Python

  •1•1•0•1•Updated Feb 11, 2025Feb 11, 2025

• garref01.2024-11-11.B2_B3_KD_apoepop_iMGL_bulkRNAseqDream

  Public
  HTML

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• shapeit5_pipeline

  Public
  Pipeline to phase genotypes using ShapeIt5

  Python

  •1•1•0•1•Updated Dec 5, 2024Dec 5, 2024

• gvc_agora_opentargets_ora

  Public
  0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• RAREMETAL

  Public
  RAREMETAL pipeline

  0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

• snakemake_7vs8_primer

  Public
  Primer on differences between Snakemake 7 and 8 for Mount Sinai

  Python

  •0•0•0•0•Updated May 17, 2024May 17, 2024

• msigdb

  Public
  Create Molecular Signatures Database (MSigDB) GMT files for Gene Set Enrichment Analysis (GSEA) using Ensembl gene IDs

  R

  •

  The Unlicense

  •0•0•0•0•Updated Mar 11, 2024Mar 11, 2024

• bhlhe_manuscript

  Public
  R

  •0•0•0•0•Updated Jan 16, 2024Jan 16, 2024

• adsp_gvc_paper

  Public
  0•0•0•0•Updated Oct 5, 2023Oct 5, 2023

• lsf

  Public
  Snakemake profile for running jobs on an LSF cluster

  Python

  •

  MIT License

  •22•0•0•0•Updated Oct 13, 2022Oct 13, 2022

• MRcovid

  Public
  HTML

  •

  MIT License

  •5•11•0•0•Updated Jun 15, 2022Jun 15, 2022

• multivariate_MR

  Public
  0•1•0•0•Updated May 9, 2022May 9, 2022

• daniele_myelin_phagocytosis

  Public
  HTML

  •0•0•0•0•Updated Mar 16, 2022Mar 16, 2022

• GEO_Submission

  Public
  0•0•0•0•Updated Feb 18, 2022Feb 18, 2022

• docker_bcftools_gtc2vcf

  Public
  Docker for Ruth HWE

  Dockerfile

  •3•0•0•0•Updated Nov 17, 2021Nov 17, 2021

• dedup_plink

  Public
  Python

  •0•0•0•0•Updated Sep 21, 2021Sep 21, 2021

• singularity-rstudio-r4

  Public
  Python

  •3•0•0•0•Updated Aug 18, 2021Aug 18, 2021

• gatk-mitochondria-pipeline

  Public
  Snakemake workflow for GATK SNP and INDEL variant calling on mitochondria DNA

  Python

  •

  MIT License

  •1•2•0•0•Updated Aug 18, 2021Aug 18, 2021

• looping_rmd

  Public
  An example Rmd with a looping included sub-document

  HTML

  •0•0•0•0•Updated Aug 17, 2021Aug 17, 2021

• mtDNAcn

  Public
  Association of mitochondrial DNA CN with Alzheimer's disease

  HTML

  •0•0•0•0•Updated Aug 17, 2021Aug 17, 2021

• datahub

  Public
  Clojure

  •1•0•0•0•Updated Apr 25, 2020Apr 25, 2020

• SumHer_pipeline

  Public
  Python

  •0•0•0•0•Updated Apr 1, 2020Apr 1, 2020