yjchen1201

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

ATAC-seq_QC_analysis

Atac-seq QC matrix

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

awesome-single-cell

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

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

brainchromatin

Code used to analyze single cell RNA and ATAC sequencing in developing human brain

cell-div-fin-reg

Analysis code used in Cellular diversity of the regenerating caudal fin

CellOracle

This is the alpha version of the CellOracle package

ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

yjchen1201/FinRegen_scMultiome_pub

Analysis code used in manuscript "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single-Cell Resolution"

yjchen1201/Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

yjchen1201/gatk

Official code repository for GATK versions 4 and up

yjchen1201/zebrafish_pigment_cell_dev

Analysis code used in Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish

yjchen1201/ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

yjchen1201/awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

yjchen1201/scMTNI

yjchen1201/chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

yjchen1201/sradownloader

A script to make downloading of SRA/GEO data easier

yjchen1201/CellOracle

This is the alpha version of the CellOracle package

yjchen1201/scRNAseq-analysis-notes

scRNAseq analysis notes from Ming Tang

yjchen1201/awesome-single-cell

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

yjchen1201/scRNA-seq_online

yjchen1201/brainchromatin

Code used to analyze single cell RNA and ATAC sequencing in developing human brain

yjchen1201/Ligand-Receptor-Pairs

Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.

yjchen1201/URD

URD - Reconstruction of Branching Developmental Trajectories

yjchen1201/cell-div-fin-reg

Analysis code used in Cellular diversity of the regenerating caudal fin

yjchen1201/ATAC-seq_QC_analysis

Atac-seq QC matrix

yjchen1201/TE_expression_in_scRNAseq

yjchen1201/MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline

yjchen1201/ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

yjchen1201/SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

yjchen1201/PyHRM

High Resolution Melt Analysis in Python

yjchen1201/wustl-latex-dissertation-template

LaTeX disseration and thesis template for The Graduate School at Washington University in St. Louis.