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allelic_epigenome

biomarker-survival

Utilities for performing biomarker survival analyses (e.g. cox proportional hazards, kaplan-meier, etc) from TCGA, CBioPortal, and other datasets

celfie

cfDNA cell type of origin estimation

cfdnapipe

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

comprehensive-tcga-survival

Comprehensive survival analyses on the TCGA data.

cpg_me

A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)

ctdnatools

R package to work with ctDNA sequencing data

delfi_scripts

egtex_mqtls_eqtls_gwas

epidish

This package contains a reference-based function to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.

ewas_mine

feat_imp_gwas

ggplot_theme_publication

This repo consists of three themes for the ggplot2 and new colour palettes. Enjoy the new themes!

glue

Graph-linked unified embedding for single-cell multi-omics data integration

ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

mesa

meth_atlas

porpoise

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

tca

uxm_deconv