KChen-lab

Pinned Repositories

bindSC
Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data
Language:R31 5 67
Cyclum
Identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations
Language:Python19 2 44
MEDALT
Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile
Language:R15 2 112
METAFlux
Language:HTML34 1 126
Monopogen
SNV calling from single cell sequencing
Language:HTML63 3 5716
MonoVar
Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data
Language:Python11 1 46
SCMarker
Marker gene selection from scRNA-seq data
Language:HTML15 4 52
SCMER
Marker Selection by matching manifolds and elastic net
Language:HTML22 2 44
stratified-tests-for-seurat
Stratified statistic hypothesis tests for Seurat
Language:HTML7 2 02
Texomer
Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data
Language:R20 3 68

KChen-lab's Repositories

KChen-lab/Monopogen
SNV calling from single cell sequencing
Language:HTML63 3 5716
KChen-lab/METAFlux
Language:HTML34 1 126
KChen-lab/bindSC
Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data
Language:R31 5 67
KChen-lab/SCMER
Marker Selection by matching manifolds and elastic net
Language:HTML22 2 44
KChen-lab/Texomer
Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data
Language:R20 3 68
KChen-lab/Cyclum
Identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations
Language:Python19 2 44
KChen-lab/MEDALT
Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile
Language:R15 2 112
KChen-lab/SCMarker
Marker gene selection from scRNA-seq data
Language:HTML15 4 52
KChen-lab/MonoVar
Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data
Language:Python11 1 46
KChen-lab/stratified-tests-for-seurat
Stratified statistic hypothesis tests for Seurat
Language:HTML7 2 02
KChen-lab/bcd
Visualization and analysis of single-cell RNA-seq data by alternative clustering
Language:HTML4 1 12
KChen-lab/gsdensity
Language:HTML3 1 22
KChen-lab/CytoSpill
A statistical approach that reduces spillover noise in the mass cytometry (CyTOF) data
Language:R2 2 46
KChen-lab/SiFit
Reconstructing phylogenetic tree from noisy mutation profile of single cells
2 1 42
KChen-lab/transition-cells-identification
Language:R2 1 01
KChen-lab/novoBreak
A de novo genome breakpoint sequence assembly algorithm
Language:C1 2 1
KChen-lab/TransVar
A multi-way annotator for genetic elements and genetic variations
Language:Python1 2 1
KChen-lab/novoRNABreak
Language:Perl0 1 00
KChen-lab/CCAdge
Detection of disease-associated genes from single cell data
Language:HTML2 0
KChen-lab/Cyclum-Demo
A self-contained demo of Cyclum, ships with the mESC data
Language:Python2 02
KChen-lab/Cyclum-GP
A more flexible version of Cyclum, utilizing GPLVM with periodic kernel
Language:Jupyter Notebook2 0
KChen-lab/Data-Analysis-of-Variant-Functional-Effects
Data analysis for manuscript submission
Language:R1 0
KChen-lab/epiNB
Efficient and interpretable HLA-I binding peptide identification
Language:Pep81 0
KChen-lab/human-cell-atlas
2 0
KChen-lab/INVAX_manuscript
Scripts/Codes for INVAX project paper
Language:R1 0
KChen-lab/lad
Visualization and analysis of single-cell RNA-seq data by alternative clustering
Language:Jupyter Notebook
KChen-lab/MCL_ML_Project
Code for models and visualizations for HHill's MCL ML project.
Language:Jupyter Notebook1 01
KChen-lab/NK_CEBPD_manuscript
Scripts/Codes for NK CEBPD paper
Language:R1 0
KChen-lab/sensei
Sample size estimation for single cell studies
Language:HTML2 0
KChen-lab/tf-rna-atac
Clustering transcription factors based on expression and chromatin openness
Language:HTML2 01