Repositories list

• BCH709

  Public
  Introduction to Bioinformatics

  Python

  •

  Other

  •44 forks•22 stars•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• PGRP_Snakemake

  Public
  PGRP_Snakemake

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• Sylvan

  Public

  plantgenomicslab/Sylvan’s past year of commit activity
  Comprehensive genome annotation pipeline for plant combining EVM/PASA, GETA, AUGUSTUS and Helixer with semi-supervised filtering for high-quality gene models.

  bioinformaticsgenomebioinformatics-pipeline+ 4

  bioinformaticsgenomebioinformatics-pipelinegenome-annotationgenome-analysisgene-predictionsigularity

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 2, 2026Apr 2, 2026

• BCH709_midterm

  Public
  Python

  •1212 forks•00 stars•00 issues•1111 pull requests•Updated Mar 10, 2026Mar 10, 2026

• chimera_scan

  Public
  chimera_scan from genome annotation

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 13, 2026Feb 13, 2026

• Helixer

  Public
  Using Deep Learning to predict gene annotations

  Python

  •

  GNU General Public License v3.0

  •3535 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2025Apr 8, 2025

• HelixerPost

  Public
  Rust

  •

  GNU General Public License v3.0

  •55 forks•00 stars•00 issues•00 pull requests•Updated Nov 26, 2024Nov 26, 2024

• Hyper-editing

  Public
  Hyper-editing

  Perl

  •

  MIT License

  •44 forks•00 stars•00 issues•00 pull requests•Updated Sep 18, 2024Sep 18, 2024

• hisat2

  Public
  Graph-based alignment (Hierarchical Graph FM index)

  C++

  •

  GNU General Public License v3.0

  •130130 forks•00 stars•00 issues•00 pull requests•Updated Aug 7, 2024Aug 7, 2024

• PsiCLASS

  Public
  Simultaneous multi-sample transcript assembler for RNA-seq data

  C

  •66 forks•00 stars•00 issues•00 pull requests•Updated May 2, 2024May 2, 2024

• HMMerMe

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 11, 2024Apr 11, 2024

• geta

  Public
  Perl

  •

  GNU General Public License v3.0

  •2828 forks•00 stars•00 issues•00 pull requests•Updated Feb 20, 2024Feb 20, 2024

• SbicolorProject

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 6, 2023Nov 6, 2023

• RNASeq_CSSI

  Public
  RNASeq_CSSI

  Python

  •44 forks•00 stars•00 issues•00 pull requests•Updated Feb 25, 2023Feb 25, 2023

• ALLHiC_Pipeline

  Public
  Pipeline for Straightforward Usage of ALLHic

  Python

  •00 forks•55 stars•00 issues•00 pull requests•Updated Feb 24, 2023Feb 24, 2023

• Ice-plant-transcriptome-profiling

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 13, 2022Dec 13, 2022

• plantgenomicslab.github.io

  Public
  SCSS

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 13, 2022Sep 13, 2022

• lab

  Public
  labwebsite

  00 forks•00 stars•00 issues•00 pull requests•Updated Sep 13, 2022Sep 13, 2022

• MutFinder_EMS

  Public
  A pipeline to identify causal mutations in EMS mutant

  HTML

  •44 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2022Jul 22, 2022

• jcvi

  Public
  Python library to facilitate genome assembly, annotation, and comparative genomics

  Python

  •

  BSD 2-Clause "Simplified" License

  •199199 forks•00 stars•00 issues•00 pull requests•Updated Jun 10, 2022Jun 10, 2022

• Scripts_for_GB

  Public
  The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".

  Perl

  •2323 forks•00 stars•00 issues•00 pull requests•Updated Jun 9, 2022Jun 9, 2022

• plantTF_identifier

  Public
  Perl

  •33 forks•00 stars•00 issues•00 pull requests•Updated Feb 18, 2022Feb 18, 2022

• CLASS_2021

  Public template
  Statistical and computational analysis of the human genome

  R

  •77 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2021Mar 7, 2021

• awesome-CRISPR

  Public
  List of software/websites/databases/other stuff for genome engineering

  MIT License

  •122122 forks•11 star•00 issues•00 pull requests•Updated Dec 16, 2020Dec 16, 2020

• allhic

  Public
  Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1313 forks•00 stars•00 issues•00 pull requests•Updated Dec 8, 2020Dec 8, 2020

• DEG_analysis

  Public
  Flexible Gene Differential Expression Analysis

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 20, 2020Nov 20, 2020

• workflow-pipeline-scripts

  Public
  Various scripts for running different bioinformatics workflow pipelines

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 27, 2020Oct 27, 2020

• statements

  Public
  Successful Job Applications and Grants

  Other

  •150150 forks•00 stars•00 issues•00 pull requests•Updated Oct 22, 2020Oct 22, 2020

• GeneLab-sampleProcessing

  Public
  1414 forks•00 stars•00 issues•00 pull requests•Updated Oct 9, 2020Oct 9, 2020

• biotools

  Public
  A list of useful bioinformatics resources

  168168 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2020Jun 18, 2020