zhuochenbioinfo

Zhuo CHEN's starred repositories

resistify

Language:PythonMIT2000

HiTE

High-precision TE Annotator

Language:PythonGPL-3.02900

tracy

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Language:C++BSD-3-Clause9700

allo

Allo: a multi-mapped read rescue strategy for gene regulatory analyses

Language:PythonMIT1800

CART

Chromatin accessibility in multiple tissues throughout the entire cycle of rice.

Language:Jupyter Notebook100

GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

Language:RNOASSERTION10300

gReLU

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

Language:PythonMIT16000

cutevariant

A standalone and free application to explore genetics variations from VCF file

Language:PythonGPL-3.010200

public_kssd

K-mer substring space decomposition

Language:CNOASSERTION3700

GPSite

Geometry-aware protein binding site predictor

Language:PythonMIT1300

evo

Biological foundation modeling from molecular to genome scale

Language:Jupyter NotebookApache-2.089700

gem3-mapper

GEM-Mapper v3

Language:CGPL-3.05500

SpeciesLM

Language:Jupyter NotebookMIT1200

minipileup

Simple pileup-based variant caller

Language:C7900

NGG_python

Language:Python700

wfmash

base-accurate DNA sequence alignments using WFA and mashmap2

Language:C++MIT17200

MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

Language:CAP CDS21200

gatk

Official code repository for GATK versions 4 and up

Language:JavaNOASSERTION165500

bioawk-tutorial

4100

leviosam2

Fast and accurate coordinate conversion between assemblies

Language:C++MIT10100

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

Language:Shell112700

oneliners.txt

7500

Qwen

The official repo of Qwen (通义千问) chat & pretrained large language model proposed by Alibaba Cloud.

Language:PythonApache-2.01288600

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Language:PerlNOASSERTION34000