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    • MINI-EX

      Public
      Motif-Informed Network Inference of cell type-specific gene regulatory networks in plants
      Python
      Other
      81500Updated Dec 19, 2024Dec 19, 2024
    • Framework for transferring single-cell cluster annotations cross-species
      Python
      0000Updated Dec 19, 2024Dec 19, 2024
    • Jupyter Notebook
      0000Updated Dec 19, 2024Dec 19, 2024
    • 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 experiments with transcription factor binding site enrichment to learn gene regulatory networks in plants
      Python
      Other
      0651Updated Jul 31, 2024Jul 31, 2024
    • ksrates

      Public
      ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
      Python
      GNU General Public License v3.0
      91612Updated Jun 28, 2024Jun 28, 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
      41780Updated Jun 28, 2024Jun 28, 2024
    • 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 protein sequences.
      Perl
      GNU General Public License v3.0
      0000Updated Apr 19, 2024Apr 19, 2024
    • trapid

      Public
      TRAPID is a web application for the analysis of de novo transcriptomes
      PHP
      2300Updated Oct 30, 2023Oct 30, 2023
    • vHRR

      Public
      vHRR: co-expression based gene function prediction
      Python
      GNU General Public License v3.0
      0110Updated Apr 28, 2023Apr 28, 2023
    • Python
      0100Updated Sep 23, 2022Sep 23, 2022
    • iGRN

      Public
      iGRN data and code repository
      Perl
      1210Updated Feb 19, 2021Feb 19, 2021
    • Reciprocally retained genes in the angiosperm lineage show the hallmarks of dosage balance sensitivity
      Java
      GNU General Public License v3.0
      0000Updated Aug 3, 2017Aug 3, 2017
    • PlantRRBS

      Public
      Code base for RRBS and WGBS analyzes in Plants
      Shell
      GNU General Public License v3.0
      1200Updated Nov 25, 2016Nov 25, 2016