marcoralab Goto Github PK

admixture_pipeline

Pipeline to run unsupervised ADMIXTURE with a gnomAD reference

adsp_gvc_paper

bhlhe_manuscript

bsub_jupyter

Connect to a LSF main node directly or trough a ssh jump node, launch a jupyter notebook via bsub and open automatically a tunnel. The name of the connection can be used to reestablish the connection later or to terminate it.

daniele_myelin_phagocytosis

datahub

dedup_plink

docker_bcftools_gtc2vcf

Docker for Ruth HWE

gatk-mitochondria-pipeline

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

geo_submission

gwasamplefiltering

Post imputation QC and processing of Michigan Imputation Server Jobs

imputepipeline

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

lab_operations

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

lab_scripts

Common scripts for the Goate and Marcora labs

looping_rmd

An example Rmd with a looping included sub-document

lsf

Snakemake profile for running jobs on an LSF cluster

mr_tnf

Causal Association of TNF on AD

mrcovid

mrpipeline

Investigating the causal relationship between exposures and Alzheimer's endophenotypes

msigdb

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

multivariate_mr

postimpute

Post imputation QC and processing of Michigan Imputation Server Jobs

qc-ancestry-impute-qc

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

shapeit5_pipeline

Pipeline to phase genotypes using ShapeIt5

singularity-rstudio-r4

snakemake_7vs8_primer

Primer on differences between Snakemake 7 and 8 for Mount Sinai

sumher_pipeline

vcf_liftover

Pipeline for lifting over vcf files and filesets

washu