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2019-puzi-multi-gut-disease-classifier

machine learning models capable of distinguishing multiple intestinal diseases, including CRC, CD and UC

2020_mayr

This repo contains the analysis code describing the findings of Mayr_et_al

acs_polyp_study

auto_workflow_scrnaseq

Simple automated workflow for scRNAseq analysis

beautiful-visualization-with-python

python数据可视化之美

beautiful-visualization-with-r

《R语言数据可视化之美》配套代码

bioinfo_course_python

bioinformatics_pipeline

Bioinformatics Pipeline

biologicalprocessactivity

bravo_et_al_eyeantennaldisc

Code for reproducing the figures presented in the manuscript 'Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics' (Bravo et al., 2020)

cag

CAG means Chronic Atrophic Gastritis. This project used CNN to dectect CAG .

calculate_mutational_burden

A lightweight python script to calculate mutational burden.

cancer_notes

A continually expanding collection of cancer genomics notes and data

cancervar

Clinical interpretation of somatic mutations in cancer

cdips_tutorial_2017

Tutorial on Data Manipulation in Python

compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes

covid_balf

R script for the covid balf data analysis

crassphage_project

Source code for the crAssphage project

crc_bmi_meta_analysis

A meta-analysis of the 16S rRNA and WGS studies looking for biomarkers of obesity-associated colon cancer

csf_aging

Single cell transcriptomics reveals cerebrospinal fluid immune dysregulation during healthy brain aging and cognitive impairment

cytosponge-triage

This repository contains the source code for the manuscript titles 'Triage-driven diagnosis for early detection of esophageal cancer using deep learning' by Gehrung et al.

degradability2021

Protein-intrinsic features predict tractability of targeted protein degradation

dietary_methionine_restriction

Code and scripts for analyzing metabolomics datasets for mice and human subjects undergoing dietary methionine restriction.

easymetagenome

Easy Metagenome Pipeline 2019 (1.0)

easymicrobiome

gatk_mutation_analysis

Mutation calling code for the paper: Radiation Therapy Enhances Immunotherapy Response in Microsatellite-stable Colorectal and Pancreatic Adenocarcinoma in a Phase II Trial

gb_code

source codes for HIPO-016

gbm_immune_validation

Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors

gwas-scrnaseq-integration

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

heuristics2012

Projects for Heuristic Problem Solving class at NYU, Fall 2012