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    16 repositories

    • MINI-AC

      Public
      Motif-Informed Network Inference based on Accessible Chromatin (MINI-AC) is a method that combines accessible chromatin data from bulk or single-cell experiment…
      Python
      •
      Other
      •1•7•5•2•Updated Apr 10, 2026Apr 10, 2026

    • EPAN-QC

      Public
      QC of genomes and genome annotations, as part of a pangenome. Code was developed within the context of the ELIXIR EPAN project.
      Nextflow
      •0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

    • MINI-EX

      Public
      Motif-Informed Network Inference of cell type-specific gene regulatory networks in plants
      Python
      •
      Other
      •10•23•0•0•Updated Mar 16, 2026Mar 16, 2026

    • ksrates

      Public
      ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
      evolutionsubstitution-ratewgd
      evolutionsubstitution-ratewgdwgmwhole-genome-duplicationks-distributions
      Python
      •
      GNU General Public License v3.0
      •9•23•3•0•Updated Jan 21, 2026Jan 21, 2026

    • TripleXtract

      Public
      Pipeline for automated extraction of species–gene–trait triples in plants from scientific literature
      text-mining
      text-mining
      Python
      •
      Other
      •0•0•0•0•Updated Jul 14, 2025Jul 14, 2025

    • DeepDifE

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 23, 2025May 23, 2025

    • wheat_root_atlas

      Public
      Jupyter Notebook
      •0•2•0•0•Updated May 12, 2025May 12, 2025

    • BirthDeathModel

      Public
      Reciprocally retained genes in the angiosperm lineage show the hallmarks of dosage balance sensitivity
      Java
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • cross_species_annotation_transfer

      Public
      Framework for transferring single-cell cluster annotations cross-species
      Python
      •1•2•0•0•Updated Dec 19, 2024Dec 19, 2024

    • i-ADHoRe

      Public
      i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.
      C++
      •
      GNU Affero General Public License v3.0
      •5•17•10•1•Updated Jun 28, 2024Jun 28, 2024

    • OrthoMCLight

      Public
      OrthoMCLight is an edited version of OrthoMCL v1.4 that requires less memory and has a faster runtime. It is a genome-scale algorithm for grouping orthologous p…
      Perl
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 19, 2024Apr 19, 2024

    • trapid

      Public
      TRAPID is a web application for the analysis of de novo transcriptomes
      bioinformaticsdatabaseannotation
      bioinformaticsdatabaseannotationtranscriptomes
      PHP
      •2•3•0•0•Updated Oct 30, 2023Oct 30, 2023

    • vHRR

      Public
      vHRR: co-expression based gene function prediction
      Python
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Apr 28, 2023Apr 28, 2023

    • tomato_motif_enrichment

      Public
      Python
      •0•1•0•0•Updated Sep 23, 2022Sep 23, 2022

    • iGRN

      Public
      iGRN data and code repository
      Perl
      •1•3•1•0•Updated Feb 19, 2021Feb 19, 2021

    • PlantRRBS

      Public
      Code base for RRBS and WGBS analyzes in Plants
      Shell
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Nov 25, 2016Nov 25, 2016
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