Inpactor2: LTR retrotransposon detector and classificator using Deep Learning

Python-first CLI pipeline for transposable element discovery and annotation, integrating family-specific methods with reproducible diagnostics and modernization from legacy workflows. Published in BMC Bioinformatics (2023).

A machine learning pipeline for comparative analysis of 45S rRNA genes from plant NOR regions

An R package to identify plant transcription factors from protein sequence data and classify them in families

Genome-mining workflows for natural products: search public genomes and transcriptomes, compare candidate clusters, and plan follow-up work.

"植物基因组"(plantgenomes)微信公众号

An R interface to the PLAZA database for plant comparative genomics

NLR-Assembler is a command line tool for improving RenSeq Assemblies using linked-read sequencing by 10x Genomics.

Comprehensive notes, workflows, and projects from 2025 research trainings on 16S rRNA, scRNA-seq, Nextflow, Galaxy, plant & marine genomics, and cancer bioinformatics, including hands-on Galaxy and reproducible pipeline .

Curated agricultural and plant AI models relevant to grass AI-genomics.

Data and code used in the Plant Genomes dashboard

Plant genomics MCP server — 32 tools across 11 backends (Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR) + cross-source synthesis. stdio + Streamable-HTTP transports.

Phylogeny and classification of Azolla filiculoides MYB genes

Hub for graduate research and collaboration under Prof. Mitch Cruzan.

Phylogenetic tree of LAR and other PIP family enzymes as shown in Güngör et al. 2020. This repository details all code and intermediate files used.

Interpretable machine learning for plant stress prediction using public transcriptomic data.

Scripts for assembling a linkage map and using QTL mapping to isolate loci underlying failed ovule development in Mimulus nudatus