XiaoTaoWang

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Fudan University

Shanghai

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YueLab3D

Xiaotao Wang's repositories

HiCLift

A fast and efficient tool for converting chromatin interaction data between genome assemblies

Language:PythonNOASSERTION59 2 17

NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

Language:PythonNOASSERTION52 2 65

EagleC

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

NOASSERTION50 3 36

HiC_pipeline

An easy-to-use Hi-C data processing software supporting distributed computation.

Language:PythonGPL-3.048 5 15

HiCPeaks

A Python implementation for BH-FDR and HiCCUPS

Language:PythonGPL-3.039 2 9

TADLib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Language:PythonGPL-3.039 3 25

StripeCaller

A toolkit for analyzing architectural stripes

Language:PythonGPL-3.016 2 1

Best-Labs-of-3D-Genome

Data and the co-authored network I extracted for lab selection in 3D genome research field

Language:Python13 20

domaincaller

A Python implementation of the original DI domain caller

Language:PythonGPL-3.013 1 2

Project-Euler

Python solutions for Project Euler

Language:Python6 20

calTADs

A hierarchical domain caller for Hi-C data based on a modified version of Directionality Index

Language:PythonGPL-3.05 1 3

Think-Complexity-Notes

Jupyter notebooks I created during reading Allen Downey's book Think Complexity

Language:Jupyter Notebook3 20

peakachu

Genome-wide contact analysis using sklearn

Language:PythonMIT2 10

GradeSudoku

Python library for generating Sudoku puzzles of different grades

Language:Python100

Python

All Algorithms implemented in Python

Language:PythonMIT1 20

awesome-public-datasets

A topic-centric list of high-quality open datasets in public domains. Propose NEW data ☛☛☛PR☛☛☛

MIT020

bioconda-recipes

Conda recipes for the bioconda channel.

MIT000

cooler

A cool place to store your Hi-C

Language:PythonNOASSERTION020

cs-video-courses

List of Computer Science courses with video lectures.

000

free-programming-books

:books: Freely available programming books

NOASSERTION020

gimmemotifs

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.

MIT000

GSEApy

Gene Set Enrichment Analysis in Python

Language:PythonBSD-3-Clause010

imbalanced-learn

Python module to perform under sampling and over sampling with various techniques.

Language:PythonNOASSERTION000

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Language:CMIT000

negspy

Python NGS Repository

Language:Python010

pomegranate

Fast, flexible and easy to use probabilistic modelling in Python.

Language:Jupyter NotebookMIT020

pyensembl

Python interface to ensembl reference genome metadata (exons, transcripts, etc...)

Language:PythonApache-2.0000

smoove

structural variant calling and genotyping with existing tools, but, smoothly.

Language:GoApache-2.0010

speedseq

A flexible framework for rapid genome analysis and interpretation

Language:CMIT010

Valentine-gift

For my girlfriend

Language:Jupyter Notebook020