skelviper

HiRES

Scripts for HiRES analysis

bulkHiCprocess

Skelviper's version of bulk Hi-C data process pipeline in Xing Lab

CHARMtools

Scripts for CHARM data analysis

BubbleCluster

Cluster single cell Hi-C data

clipmath

Dip_C_snakemake

Skelviper's version of Dip-C pipeline using snakemake in Xing Lab.

Higashi

Forked from ma-compbio. Learn the higashi algorithm and add my own notes to it.

awesome-single-cell

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

BandNorm

Simple Normalization Method for single-cell Hi-C

bulk4Cprocess

Process 4C-seq data

bulkATACprocess

Preprocess bulk cut&tag or atac seq data with double insertion, adapt from JWY

C.Origami

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

chromoskein

CTG

EagleC

A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps

GGL

hic_basic

hires_utils

scripts for hires pipline

HMM-GMM-Timing-Strategy

HMMs_Stock_Market

Contains all code related to using HMMs to predict stock market prices.

loopNet

A toy-program for learning deep learning. Call loop from Hi-C data.

OmicsIn3D

OT2

OT-2 setup, code, 3D printing supplies warehouse for my own use

Paired-Tag

Analysis of Paired-Tag datasets

R2D2

RNA with 2nd seq demultiplex 2 single cell pipeline

scHiCanalysis

sinto

Tools for single-cell data processing

SnapHiC

SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data

Snifter

Have a closer look at your 3dg file, it's like tasting a double IPA.

torch_examples

A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.