wang3702

Xiao Wang's starred repositories

faiss

A library for efficient similarity search and clustering of dense vectors.

Language:C++MIT30234 482 2447

cuml

cuML - RAPIDS Machine Learning Library

Language:C++Apache-2.04129 71 2453

datashader

Quickly and accurately render even the largest data.

Language:PythonBSD-3-Clause3292 90 580

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

Language:CNOASSERTION1603 102 1259

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Language:CGPL-3.01506 108 304

conditional-flow-matching

TorchCFM: a Conditional Flow Matching library

Language:PythonMIT1023 14 47

cs249r_book

Collaborative book Machine Learning Systems

Language:TeXNOASSERTION777 11 133

Integrated-Gradients

Attributing predictions made by the Inception network using the Integrated Gradients method

Language:Jupyter Notebook593 11 16

atac-seq-pipeline

ENCODE ATAC-seq pipeline

Language:PythonMIT380 26 310

HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

Language:PythonNOASSERTION380 18 590

UpSetPlot

Draw UpSet plots with Matplotlib

Language:PythonNOASSERTION319 8 153

dask-cuda

Utilities for Dask and CUDA interactions

Language:PythonApache-2.0283 24 374

pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Language:CMIT257 7 70

Juicebox

Visualization and analysis software for Hi-C data -

Language:JavaMIT238 23 824

pysamstats

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

Language:Python189 12 100

tangermeme

Biological sequence analysis for the modern age.

Language:PythonMIT164 10 10

scHiC_notes

Notes on single-cell Hi-C technologies, tools, and data

MIT63 2 1

mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Language:PythonMIT59 5 62

docker-4dn-hic

Docker for 4DN Hi-C processing pipeline

Language:Common Workflow LanguageMIT55 8 4

LISI

Methods to compute Local Inverse Simpson's Index (LISI)

Language:RGPL-3.055 15 12

BamQC

Mapped QC analysis program

Language:JavaGPL-3.041 10 18

hic-pipeline

Language:CGPL-3.024 4 4

SWORD2

SWift and Optimized Recognition of protein Domains

Language:PerlNOASSERTION23 7 7

HiCDCPlus

Language:R13 1 25

hic-straw

Command line and web utilities for reading .hic contact matrix files

Language:JavaScriptMIT8 7 8

nuc_processing

Chromatin contact paired-read single-cell Hi-C processing module for Nuc3D and NucTools

Language:PythonLGPL-3.07 30

fuserescue

A CLI tool to recover only the parts of a disk accessed and not yet recovered. Compatible with ddrescue mapfiles.

Language:CGPL-3.03 50

ComplexModeler

Language:Python2 20

tgif

Tree-Guided Integrated Factorization (TGIF)

Language:C2 4 1

HiCKRy

HiCKRy is a tool developed by the Ay Lab to normalize HiC data using the Knight-Ruiz algorithm for matrix normalization.

Language:Python100