Gant61

irGSEA

The integration of single cell rank-based gene set enrichment analysis

Single-nuclei-epigenomic-and-transcriptomic-landscape-in-Alzheimer-disease

Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease

eQTpLot

Visualization of Colocalization Between eQTL and GWAS Data

TRAPD

Burden testing against public controls

epigraphdb-pqtl

This is the github repository to provide the R scripts been used in the phenome-wide Mendelian randomization study of plasma proteome.

RNA-seq_notes

A continually expanding collection of RNA-seq tools

mr_druggable_genome_pd

createUKBphenome

Create a PheWAS code based phenome using ICD9 and ICD10 data from baskets of the UK biobank

HumanKidney_eQTL_and_snATAC-seq

codes used in the human kidney eQTL(cf) and eQTL(ci) and snATAC-seq data

AnnotateVariants

This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.

rpkm_rnaseq_count

RPKM for RNASeq counts

obesity_femrepr_MR

Code for analyses in "Obesity and risk of female reproductive disorders: A Mendelian Randomisation Study"

Kidney_Epi_Pri

Kidney Epigenome and Transcriptome-based multi-stage Prioritization

wgs_sample_preparation

Trim, Align to genome, Deduplicate, Realign WGS sequencing samples

hawe2021_meQTL_analyses

Code for the meQTL analyses presented in Hawe et al. 2021 Nature Genetics

RBD_SMR

Using SMR for eQTL mendelian randomization.

JM-GWAS

GWAS pipeline: Vitamin-D in the UKB including SMR analysis

somatico

GATK 4 Mutect2 Somático

CKD_cancer_MR

The impact of kidney function and albuminuria on risk of 19 site-specific cancers: A Mendelian randomization study

moloco

A tool for performing multiple-trait colocalization test using GWAS summary statistics

DNA

DNA_mutation_analysis_Fastqc_trim_bwa_gatk4_mutect2_HC_freebayes_annovar_pipeline

compute-grs

A small Perl script for computing genetic risk scores for obesity from a VCF file

PleiotropyGeneticRiskScores

Mendelian-randomization-OSA-AF

TVMR

Time-varying Mendelian randomization

mutect2_CHIP

gene-targeted-drugs

Finding gene targeted drugs for various diseases through ML methods

CAMERA

Mendelian Randomization approach using Cross Ancestral Model

GWAS-scRNAseq-Integration

A Shiny tool to define the cell-type of action by integrating single cell expression data with GWAS

CVDMVMR

Additional materials for CVD MVMR paper