lhqing

ALLCools

Toolkit for single-cell DNA methylation analysis.

cemba_data

Mapping pipeline for snmC-seq based technologies.

mouse_brain_2020

Jupyter notebook repository for reproducing analysis in "DNA Methylation Landscape of the Mouse Brain at Single-Cell Resolution"

wmb2023

Code and data sharing of Liu et al. 2023 manuscript

gliderport

Launch jobs on sky

merfishing

Code for MERFISH analysis

omb

Oh Mouse Brain

cemba_browser

CEMBA browser: mongoDB + flask + Vue + echarts

wmb-browser

py_genome_sci_book

Repo for the "Essential Python For Genome Science" book

brain

Deal with Allen Brain Atlas API and non-sequencing data

scmallet

snmCAT-seq_integration

allcools_doc

documentation backup for allcools and yap

allen_ccf

cemba_dissection

CEMBA dissction segmentation based on Allen CCFv3

clustering_example

Example pipeline of using ALLCools and other packages to do clustering on snmC-seq2 dataset.

commons

Code deck for daily works

dash-sample-apps

Apps hosted in the Dash Gallery

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

flagship_tf_figure

JCCCHH

Journal Club

lhqing

lhqing.github.io

Personal website

meta

A community dedicated to supporting tools for technical and scientific communication and interactive computing

paperpile

My paperpile library

py_genome_sci_book_backup

pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks

vector-quantize-pytorch

Vector (and Scalar) Quantization, in Pytorch

velocyto.py

RNA velocity estimation in Python