ChaorongC's repositories
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
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.
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.
PORPOISE
Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell