Inpactor2: LTR retrotransposon detector and classificator using Deep Learning
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Jun 17, 2025 - Jupyter Notebook
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plant-genomics
Here are 33 public repositories matching this topic...
Plant genomics MCP server — 50+ tools across 23 backends (Ensembl Plants, Phytozome, UniProt, AlphaFold DB, PDBe, InterPro, JASPAR, PANTHER, OrthoDB, AraGWAS, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR, …) + cross-source synthesis. stdio + Streamable-HTTP.
python bioinformatics genomics mcp uniprot kegg plant-genomics ensembl-plants llm-tools model-context-protocol
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Oct 1, 2026 - Python
Python CLI for discovering and classifying transposable elements, with adapter-based methods and smoke-test diagnostics. Published in BMC Bioinformatics (2023).
bioinformatics pipeline genomics transposable-elements plant-genomics repeatmodeler repeat-annotation te-detection
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Sep 29, 2026 - Python
Genome-mining workflows for natural products: search public genomes and transcriptomes, compare candidate clusters, and plan follow-up work.
bioinformatics computational-biology microbial-genomics comparative-genomics transcriptomics genome-mining ai-agents natural-products research-software plant-genomics biological-research pathway-discovery
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Sep 22, 2026 - Python
A method for predicting chromatin features and prioritizing non-coding rice variants using DNA language models.
deep-learning rice histone-modifications chromatin-accessibiity plant-genomics non-coding-variants post-gwas variant-prioritization
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Aug 8, 2026 - Python
A machine learning pipeline for comparative analysis of 45S rRNA genes from plant NOR regions
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Mar 23, 2026 - Python
Primary gene structure (GFF/proteins) + TE soft-mask floor — not functional annotation
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Sep 17, 2026 - Python
Labels after proteins (GO/domains/names); upstream gene-structure-annotation
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Sep 17, 2026 - Python
De novo genome assembly (MaSuRCA), reference-guided scaffolding (RagTag), and QC (QUAST, BUSCO, synteny analysis) for Humulus lupulus cv. Julian Gold
bioinformatics hpc scaffolding synteny genome-assembly pbs masurca quast plant-genomics ragtag humulus-lupulus
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Aug 18, 2026 - Shell
An R package to identify plant transcription factors from protein sequence data and classify them in families
transcription-factors plants rstats gene-families hidden-markov-models protein-domains functional-genomics plant-genomics
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Mar 14, 2023 - R
"植物基因组"(plantgenomes)微信公众号
bioinformatics genomics plant weixin wechat genomes plantgenomes plantgenomics plant-genomics plant-genomes
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Jul 19, 2022
An R interface to the PLAZA database for plant comparative genomics
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Jul 28, 2025 - R
NLR-Assembler is a command line tool for improving RenSeq Assemblies using linked-read sequencing by 10x Genomics.
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Aug 2, 2023 - Python
Repository of all files and code needed to develop a GRN of Arabidopsis thaliana by incorporating novel PDIs and PPIs from the dDAP-seq technique in the AIV2/ePlant database.
data-visualization bioinformatics-pipeline protein-dna-interactions protein-protein-interactions plant-genomics gene-regulatory-networks
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May 14, 2026 - JavaScript
Reference-guided reanalysis of published finger millet (Eleusine coracana) drought RNA-seq against the chromosome-scale KNE 796-S assembly, with a documented audit of four analytical defects found and corrected.
snakemake deseq2 reproducibility transcriptomics rna-seq-analysis bioinformatics-analysis snakemake-workflow plant-genomics snakemake-pipeline deseq2-analysis finger-millet drought-stress eleusine-coracana
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Sep 6, 2026 - Python
Fail-closed plant benchmark intake, blinding, provenance, and leakage auditor
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Sep 27, 2026 - Python
Chloroplast genome structural region extractor (LSC/IRa/SSC/IRb) — published in PeerJ 2020
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Jul 30, 2026 - Perl
Fail-closed source, identity, and record-to-publication provenance for plant receptor studies
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Aug 13, 2026 - Python
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 .
bash bioinformatics genomics reproducible-research scrna-seq galaxy quarto 16s-rrna nextflow-workflow plant-genomics marine-genomics training-notes cancer-bioinformatics
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Mar 16, 2026 - Nextflow
Data and code used in the Plant Genomes dashboard
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Mar 13, 2022 - R
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