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38 repositories

ABMACT
Public
ABMACT project code
Jupyter Notebook
•
MIT License
•1•0•0•0•Updated May 21, 2026May 21, 2026
Abema_fas_Ovarian
Public
This repository includes scripts to generate figures of the paper that are generated with GeoMx DSP WTA data.
R
•
GNU General Public License v3.0
•0•0•0•0•Updated Feb 2, 2026Feb 2, 2026
HPV-specific-TCR
Public
Code for the paper on HPV16-specific TCRs
GNU General Public License v3.0
•0•0•0•0•Updated Feb 2, 2026Feb 2, 2026
ICKG
Public
Jupyter Notebook
•1•6•1•0•Updated Nov 5, 2025Nov 5, 2025
ST_Comparison
Public
Codes of images in Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor s…
R
•
GNU General Public License v3.0
•0•2•0•0•Updated Oct 28, 2025Oct 28, 2025
immune-knowledgegraph.github.io
Public
HTML
•1•0•0•0•Updated Aug 15, 2025Aug 15, 2025
transition-cells-identification
Public
Jupyter Notebook
•
MIT License
•2•12•2•0•Updated Feb 11, 2025Feb 11, 2025
Monopogen
Public
SNV calling from single cell sequencing
somatic-variants single-cell snvs
somatic-variants single-cell snvs germline-variants
HTML
•
GNU General Public License v3.0
•24•119•52•1•Updated Nov 11, 2024Nov 11, 2024
SCMER
Public
Marker Selection by matching manifolds and elastic net
feature-selection single-cell-analysis
feature-selection single-cell-analysis
HTML
•
MIT License
•4•23•0•0•Updated Oct 22, 2024Oct 22, 2024
INVAX_manuscript
Public
Scripts/Codes for INVAX project paper
R
•
Apache License 2.0
•0•0•0•0•Updated Oct 19, 2024Oct 19, 2024
LSGI
Public
HTML
•3•1•0•0•Updated Sep 6, 2024Sep 6, 2024
METAFlux
Public
HTML
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Other
•15•89•25•0•Updated Jun 29, 2024Jun 29, 2024
lad
Public
Visualization and analysis of single-cell RNA-seq data by alternative clustering
Jupyter Notebook
•2•0•0•0•Updated Feb 11, 2024Feb 11, 2024
bcd
Public
Visualization and analysis of single-cell RNA-seq data by alternative clustering
statistical-methods single-cell batch-effects
statistical-methods single-cell batch-effects
HTML
•2•5•1•0•Updated Nov 23, 2023Nov 23, 2023
NK_CEBPD_manuscript
Public
Scripts/Codes for NK CEBPD paper
R
•0•1•0•0•Updated Nov 20, 2023Nov 20, 2023
MEDALT
Public
Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile
R
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MIT License
•5•21•8•0•Updated Sep 8, 2023Sep 8, 2023
bindSC
Public
Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data
integrative-analysis single-cell-analysis
integrative-analysis single-cell-analysis
R
•
GNU General Public License v3.0
•7•41•2•0•Updated Aug 23, 2023Aug 23, 2023
MCL_ML_Project
Public
Code for models and visualizations for HHill's MCL ML project.
Jupyter Notebook
•1•0•0•0•Updated May 10, 2023May 10, 2023
Data-Analysis-of-Variant-Functional-Effects
Public
Data analysis for manuscript submission
R
•
MIT License
•0•0•0•0•Updated Apr 25, 2023Apr 25, 2023
novoRNABreak
Public
Perl
•
MIT License
•0•0•0•0•Updated Mar 21, 2023Mar 21, 2023
gsdensity
Public
HTML
•2•10•2•0•Updated Mar 12, 2023Mar 12, 2023
CCAdge
Public
Detection of disease-associated genes from single cell data
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated Jan 4, 2023Jan 4, 2023
epiNB
Public
Efficient and interpretable HLA-I binding peptide identification
Pep8
•0•0•0•0•Updated Oct 18, 2022Oct 18, 2022
Cyclum
Public
Identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations
single-cell-rna-seq artifical-neural-network trajectory-inference-methods
single-cell-rna-seq artifical-neural-network trajectory-inference-methods latent-process-inference
Python
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MIT License
•5•24•2•0•Updated Dec 17, 2021Dec 17, 2021
sensei
Public
Sample size estimation for single cell studies
single-cell-analysis sample-size-calculation study-design
single-cell-analysis sample-size-calculation study-design beta-binomial
HTML
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MIT License
•0•0•0•0•Updated Nov 18, 2021Nov 18, 2021
stratified-tests-for-seurat
Public
Stratified statistic hypothesis tests for Seurat
HTML
•
GNU General Public License v3.0
•2•6•0•0•Updated Nov 8, 2021Nov 8, 2021
CytoSpill
Public
A statistical approach that reduces spillover noise in the mass cytometry (CyTOF) data
R
•6•2•7•2•Updated Apr 30, 2021Apr 30, 2021
Cyclum-GP
Public
A more flexible version of Cyclum, utilizing GPLVM with periodic kernel
Jupyter Notebook
•0•0•0•0•Updated Dec 27, 2020Dec 27, 2020
SCMarker
Public
Marker gene selection from scRNA-seq data
statistical-methods high-dimensional-data feature-selection
statistical-methods high-dimensional-data feature-selection single-cell-rna-seq
HTML
•2•16•2•0•Updated Sep 15, 2020Sep 15, 2020
Texomer
Public
Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data
statistical-inference functional-variants tcga-data
statistical-inference functional-variants tcga-data tumor-heterogeneity
R
•8•21•3•1•Updated Aug 19, 2020Aug 19, 2020

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KChen-lab

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All

38 repositories

ABMACT

Abema_fas_Ovarian

HPV-specific-TCR

ICKG

ST_Comparison

immune-knowledgegraph.github.io

transition-cells-identification

Monopogen

SCMER

INVAX_manuscript

LSGI

METAFlux

lad

bcd

NK_CEBPD_manuscript

MEDALT

bindSC

MCL_ML_Project

Data-Analysis-of-Variant-Functional-Effects

novoRNABreak

gsdensity

CCAdge

epiNB

Cyclum

sensei

stratified-tests-for-seurat

CytoSpill

Cyclum-GP

SCMarker

Texomer

All

All

Repositories list

38 repositories