teng-gao

hahmmr

Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq

numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

scistreer

R/Rcpp implementation of the ScisTree algorithm

Gao_NC_CH

Code and Data for Gao et al., Nature Communications 2021

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

BayesCF

Bayesian inference of mutational cell fractions

BreaKmer_analysis

ockerized BreaKmer algorithm by Ryan Abo: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330340/

BreaKmer_backup

A method to identify structural variation from sequencing data in target regions (Abo et al.)

facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing. Package created to test FACETS with both matched and unmatched normal.

genomics_utils

Utilities for genomics and NGS data analysis

teng-gao/genomics_utils

Utilities for genomics and NGS data analysis

teng-gao/facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing. Package created to test FACETS with both matched and unmatched normal.

teng-gao/awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

teng-gao/BayesCF

Bayesian inference of mutational cell fractions

teng-gao/BreaKmer_analysis

ockerized BreaKmer algorithm by Ryan Abo: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330340/

teng-gao/BreaKmer_backup

A method to identify structural variation from sequencing data in target regions (Abo et al.)

teng-gao/clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing

teng-gao/kmeans

Implementation of K-means clustering algorithm with Spark and application on earthquake data

teng-gao/DALEX

Descriptive mAchine Learning EXplanations

teng-gao/docker-cnacs

🐳 A python 2.7 container with CNACs requirements and db.

teng-gao/fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

teng-gao/genomics

2017 AI & Genomics Hackathon in San Francisco

teng-gao/hiraksarkar.github.io

teng-gao/INTEGRATE-Vis

Tool for comprehensive gene fusion visualization

teng-gao/minimal-mistakes

:triangular_ruler: Jekyll theme for building a personal site, blog, project documentation, or portfolio.

teng-gao/numbat

Haplotype-aware CNV analysis from scRNA-Seq

teng-gao/phangorn

Phylogenetic analysis in R

teng-gao/redefining_cancer_treatment

Applying Bayesian methods to Kaggle competition "Personalized Medicine: Redefining Cancer Treatment"

teng-gao/rTensor

rTensor v1.2

teng-gao/sciclone

An R package for inferring the subclonal architecture of tumors

teng-gao/scRNA-seq_notes

A list of scRNA-seq analysis tools

teng-gao/teng-gao.github.io

teng-gao/teng-gao.github.io_MM

https://teng-gao.github.io/

teng-gao/teng-gao.github.io_old

Website

teng-gao/treehmm

Implementation of treeHMM for CNV detection

teng-gao/website

Personal website

teng-gao/website-new