WANGDI0212

BE-GIM_Comparison

Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia

ACC_Project

Intratumor microbes in adrenocortical carcinoma

Benchmarking-of-Phenotype-driven-Gene-Prioritization-Methods

cancer-proteomics-compendium-n2002

We assembled a compendium dataset of mass-spectrometry-based proteomics data of 2002 primary tumors from 14 cancer types and 17 studies

Code_for_circSC

Analysis pipeline for our circSC manuscript

COPD_multiomics

This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interaction in Chronic Obstructive Pulmonary Disease'.

CRDscore

ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

gastric-cancer

host_gene_microbiome_interactions

Analysis framework for integrating gut microbiome and host gene expression data

iPMIC

IRLS

Machine learning-based integrative analysis develops an immune-derived lncRNA signature for improving clinical outcomes in colorectal cancer

ISLR-Exercises

Exercises of 'An Introduction to Statistical Learning with Applications in R (V1)'

MFP

Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

MIAS

Codes for the manuscript: Prediction of biomarkers and therapeutic combinations for anti-PD-1 immunotherapy using the global gene network association

MIMESIS

A package to identify type/subtype of tumor samples and estimate tumor content using minimal DNA-methylation signatures

ml4calibrated450k

This is a companion repository for the article "Comparative analysis of machine learning classifiers and calibration algorithms for estimating class probabilities for personalized cancer diagnostics on DNA methylation microarray data"

neoantigen-specific-T-cells-NSCLC

organ-site-mapping

Mapping ICD billing codes and terms to a standard ontology

pan-cancer-host-microbiome-associations

Manuscript for pan-cancer-host-microbiome-associations

Pancan-ICI

pancancer_prot_act

Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival

PASS-ON-codes

PEACE_melanoma_14_paper

Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways

Precily

pytorch-tutorial

PyTorch Tutorial for Deep Learning Researchers

sygnal

SYstems Genetic Network AnaLysis (SYGNAL) pipeline

tcga-microbiome-prediction

Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-seq sequencing data for 32 TCGA cancers (Poore et al. Nature 2020), including equivalent models using TCGA RNA-seq gene expression and combined microbial abundance and gene expression for comparison.

TMEscore

Calculating Tumor microenvironment score

Tumor-cellular-states-and-ecosystems-in-CRC

Deep immunophenotyping reveals clinically distinct cellular states and ecosystems in large-scale colorectal cancer