Repositories list

• SpaSimulator

  Public
  SRT data simulator

  Python

  •0•1•0•0•Updated Sep 11, 2024Sep 11, 2024

• GOMC

  Public
  R

  •0•8•1•0•Updated Sep 10, 2024Sep 10, 2024

• TGS-GapCloser

  Public
  A gap-closing software tool that uses long reads to enhance genome assembly.

  C++

  •

  GNU General Public License v3.0

  •12•173•9•0•Updated Sep 6, 2024Sep 6, 2024

• SpaGRN

  Public
  A comprehensive tool to infer TF-centred, spatial gene regulatory networks for the spatially resolved transcriptomic data.

  Python

  •

  GNU General Public License v3.0

  •2•5•0•0•Updated Aug 30, 2024Aug 30, 2024

• 4D-BioReconX

  Public
  a bioinformatic framework for reconstructing 4D spatial transcriptomics atlas and spatiotemporal analyses+

  Jupyter Notebook

  •

  MIT License

  •0•5•0•0•Updated Aug 23, 2024Aug 23, 2024

• ZebrafishHeartRegeneration_project

  Public
  All scripts for project: zebrafish heart regeneneration

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

• Circle-Map

  Public
  A method for circular DNA detection based on probabilistic mapping of ultrashort reads

  Python

  •

  MIT License

  •20•2•0•0•Updated Jul 17, 2024Jul 17, 2024

• Burnett

  Public
  evolution

  Python

  •0•0•0•0•Updated Jul 10, 2024Jul 10, 2024

• scMultimodal

  Public
  Multimodal integration of various types of sequencing data

  Python

  •0•1•0•0•Updated Jun 13, 2024Jun 13, 2024

• stacpro

  Public
  STructure based Alignment and Clustering of PROteins

  Python

  •

  MIT License

  •0•2•0•0•Updated May 30, 2024May 30, 2024

• TGS-GapCloser2

  Public
  A gap-closing software tool that uses long reads to enhance genome assembly.

  C++

  •

  GNU General Public License v3.0

  •12•8•0•0•Updated Apr 25, 2024Apr 25, 2024

• strobeQV

  Public
  This script calculates the quality value (QV) based on strobemers.

  C++

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Apr 16, 2024Apr 16, 2024

• VT3D

  Public
  VT3D: a versatile Visualization Toolbox for 3D spatial transcriptomics atlas

  JavaScript

  •

  GNU General Public License v3.0

  •0•13•0•0•Updated Feb 7, 2024Feb 7, 2024

• VT3D_Browser

  Public
  Vue

  •0•3•0•0•Updated Feb 7, 2024Feb 7, 2024

• stLFR_reads_sim

  Public
  [Develeping] Reads Simulator of stLFR

  C++

  •0•5•0•0•Updated Jan 29, 2024Jan 29, 2024

• Module_completeness

  Public
  Checks if the given module is complete

  Perl

  •1•0•0•0•Updated Dec 18, 2023Dec 18, 2023

• GEM3D_toolkit

  Public
  A tool to use stereo-seq GEM and ssDNA to generate single-cell and 3D spatial resolved transtriptomics data

  Python

  •1•11•1•0•Updated Oct 12, 2023Oct 12, 2023

• Lungfish_scRNA_data_analysis

  Public
  Analysis code for lungfish single cell RNA-seq data

  R

  •2•3•0•0•Updated Jul 25, 2023Jul 25, 2023

• Planarian4D

  Public
  Python

  •0•2•0•0•Updated Jul 12, 2023Jul 12, 2023

• fish10k

  Public
  Scripts for fish10k project

  Perl

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jul 8, 2023Jul 8, 2023

• MetaTrass

  Public
  Metagenomics Taxonomic Reads Assembly Single-Species

  Rebol

  •

  GNU General Public License v3.0

  •4•16•1•0•Updated May 25, 2023May 25, 2023

• Circle-Map-cpp

  Public
  rewirte part of Realign module in Circle-Map by c++

  C++

  •0•6•0•0•Updated Apr 25, 2023Apr 25, 2023

• HAST

  Public
  HAST: Haplotype-Resolved Assembly for Synthetic Long Reads Using A Trio-Binning Strategy

  C++

  •

  GNU General Public License v3.0

  •1•18•0•0•Updated Apr 20, 2023Apr 20, 2023

• SpaGRN_HomePage

  Public
  The homepage of SpaGRN project

  Vue

  •2•0•0•0•Updated Apr 19, 2023Apr 19, 2023

• ProcessGroupMonitor

  Public
  A simple tool to monitor a process group and record its CPU, MEM and time cost.

  C++

  •1•16•0•0•Updated Mar 21, 2023Mar 21, 2023

• EMA_SF

  Public
  C++

  •0•2•0•0•Updated Mar 17, 2023Mar 17, 2023

• stlfr2supernova_pipeline

  Public
  A pipeline to de novo assemble the stLFR reads using Supernova Assembler

  Shell

  •5•21•0•0•Updated Feb 22, 2023Feb 22, 2023

• stereopy

  Public
  A toolkit of spatial transcriptomic analysis.

  Jupyter Notebook

  •

  MIT License

  •65•0•0•0•Updated Feb 13, 2023Feb 13, 2023

• Symbiont-Screener

  Public
  a reference-free tool to separate host sequences from symbionts for error-prone long reads

  C++

  •

  GNU General Public License v3.0

  •2•8•0•0•Updated Jan 30, 2023Jan 30, 2023

• HicTrioBinning

  Public
  Shell

  •0•11•2•0•Updated Nov 29, 2022Nov 29, 2022