KChen-lab

Monopogen

SNV calling from single cell sequencing

METAFlux

bindSC

Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data

SCMER

Marker Selection by matching manifolds and elastic net

Texomer

Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data

Cyclum

Identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations

MEDALT

Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile

SCMarker

Marker gene selection from scRNA-seq data

MonoVar

Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data

stratified-tests-for-seurat

Stratified statistic hypothesis tests for Seurat

bcd

Visualization and analysis of single-cell RNA-seq data by alternative clustering

gsdensity

CytoSpill

A statistical approach that reduces spillover noise in the mass cytometry (CyTOF) data

SiFit

Reconstructing phylogenetic tree from noisy mutation profile of single cells

transition-cells-identification

novoBreak

A de novo genome breakpoint sequence assembly algorithm

TransVar

A multi-way annotator for genetic elements and genetic variations

novoRNABreak

CCAdge

Detection of disease-associated genes from single cell data

Cyclum-Demo

A self-contained demo of Cyclum, ships with the mESC data

Cyclum-GP

A more flexible version of Cyclum, utilizing GPLVM with periodic kernel

Data-Analysis-of-Variant-Functional-Effects

Data analysis for manuscript submission

epiNB

Efficient and interpretable HLA-I binding peptide identification

human-cell-atlas

INVAX_manuscript

Scripts/Codes for INVAX project paper

lad

Visualization and analysis of single-cell RNA-seq data by alternative clustering

MCL_ML_Project

Code for models and visualizations for HHill's MCL ML project.

NK_CEBPD_manuscript

Scripts/Codes for NK CEBPD paper

sensei

Sample size estimation for single cell studies

tf-rna-atac

Clustering transcription factors based on expression and chromatin openness