Zhiyuan Liu's repositories
Evaluate-scHi-C-imputation-methods
Evaluate scHi-C imputation methods
Dip_C_snakemake
Skelviper's version of Dip-C pipeline using snakemake in Xing Lab.
bulkHiCprocess
Skelviper's version of bulk Hi-C data process pipeline in Xing Lab
OT2
OT-2 setup, code, 3D printing supplies warehouse for my own use
SnapHiC
SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data
bulk4Cprocess
Process 4C-seq data
GraphMAE
GraphMAE: Self-Supervised Masked Graph Autoencoders in KDD'22
bulkATACprocess
Preprocess bulk cut&tag or atac seq data with double insertion, adapt from JWY
loopNet
A toy-program for learning deep learning. Call loop from Hi-C data.
Snifter
Have a closer look at your 3dg file, it's like tasting a double IPA.
C.Origami
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
torch_examples
A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
R2D2
RNA with 2nd seq demultiplex 2 single cell pipeline
sinto
Tools for single-cell data processing
EagleC
A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
HMMs_Stock_Market
Contains all code related to using HMMs to predict stock market prices.
BandNorm
Simple Normalization Method for single-cell Hi-C
hires_utils
scripts for hires pipline
Paired-Tag
Analysis of Paired-Tag datasets