Skip to content

@NIB-SI National Institute of Biology

Change the repository type filter

All

    Repositories list

    33 repositories

    • Potato-GEM

      Public
      Potato GEM
      MIT License
      •0•0•0•0•Updated Sep 13, 2024Sep 13, 2024

    • DiNAR

      Public
      Differential Network Analysis in R
      HTML
      •
      GNU Affero General Public License v3.0
      •1•1•5•0•Updated Sep 9, 2024Sep 9, 2024

    • skm-tools

      Public
      Scripts and utilities for leveraging SKM resources
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•1•1•Updated Sep 1, 2024Sep 1, 2024

    • pss_viz

      Public
      Interactive search and visualization of the PSS model.
      JavaScript
      •
      MIT License
      •1•0•0•1•Updated Aug 31, 2024Aug 31, 2024

    • BoolDog

      Public
      A Python package for analyses of Boolean and semi-quantitative Boolean networks.
      pythonsimulationsystems-biologyboolean-network
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Aug 29, 2024Aug 29, 2024

    • multiOmics-integration

      Public
      Potato ‘omics data analysis pipelines
      HTML
      •
      MIT License
      •1•0•0•1•Updated Aug 21, 2024Aug 21, 2024

    • UJI-Omics-phd

      Public
      Omics integration
      HTML
      •
      MIT License
      •1•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • ckn_viz

      Public
      CKN network visualization app
      JavaScript
      •
      MIT License
      •1•0•0•1•Updated Jul 29, 2024Jul 29, 2024

    • unitato

      Public
      UniTato: a web server for evidence and community based Unification of poTato gene models
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jun 19, 2024Jun 19, 2024

    • promoteR

      Public
      Large scale promotor sequence extraction​ ​in R
      HTML
      •
      MIT License
      •0•0•0•0•Updated May 26, 2024May 26, 2024

    • skm-ckn

      Public
      The Comprehensive Knowledge Network of SKM
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • PhasiHunter

      Public
      Python
      •
      MIT License
      •2•0•0•1•Updated Dec 5, 2023Dec 5, 2023

    • Liftoff

      Public
      An accurate GFF3/GTF lift over pipeline
      Python
      •
      GNU General Public License v3.0
      •53•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • ckn_netviz

      Public
      A visual browser of the CKN network
      JavaScript
      •
      MIT License
      •1•0•0•1•Updated Dec 5, 2023Dec 5, 2023

    • skm-neo4j

      Public
      Jupyter Notebook
      •0•0•0•1•Updated Dec 5, 2023Dec 5, 2023

    • _p_stRT

      Public
      Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
      R
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•1•Updated Dec 5, 2023Dec 5, 2023

    • Potato_sRNA_analysis

      Public
      small RNA analyses, S. tuberosum
      R
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•1•Updated Dec 5, 2023Dec 5, 2023

    • ARMOR

      Public
      Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
      R
      •
      MIT License
      •34•0•3•0•Updated Jan 27, 2023Jan 27, 2023

    • pISA-tree-assay-types

      Public
      Collection of pISA-tree assay types.
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Dec 30, 2022Dec 30, 2022

    • pISA-tree

      Public
      pISA-tree: Standard project directory tree (ISA framework compliant)
      windowsproject-managementisabatch-filedirectory-treefile-managementbatch-filespisa-tree
      Batchfile
      •
      MIT License
      •1•5•13•0•Updated Nov 11, 2022Nov 11, 2022

    • pisar

      Public
      R support for pISA-tree
      rpisa-tree
      TeX
      •
      MIT License
      •3•1•2•0•Updated Oct 24, 2022Oct 24, 2022

    • seekr

      Public
      R interface for SEEK API (connection to FAIRDOMHub)
      apirfairseekpisa-treefairdomhub
      HTML
      •
      MIT License
      •1•5•4•0•Updated Oct 24, 2022Oct 24, 2022

    • newt

      Public
      A web application to visualize and edit pathway models
      JavaScript
      •
      GNU Lesser General Public License v3.0
      •27•0•0•0•Updated Jul 13, 2022Jul 13, 2022

    • geneID

      Public
      geneID app
      Pep8
      •
      MIT License
      •0•0•0•0•Updated Jun 1, 2022Jun 1, 2022

    • pISA-tst

      Public
      dosreproducible-sciencedirectory-treeisa-tabbatch-filesfair-data
      HTML
      •1•0•0•0•Updated Mar 15, 2022Mar 15, 2022

    • test

      Public
      Testing github workflow
      0•0•1•0•Updated Jan 9, 2022Jan 9, 2022

    • SensorPlantAnalysis

      Public
      Package for analysis of sensor plant data, based on microscopic images
      MATLAB
      •
      Other
      •0•0•0•0•Updated Jun 2, 2021Jun 2, 2021

    • circadian-lesion

      Public
      C++
      •
      MIT License
      •0•0•0•0•Updated Jun 2, 2021Jun 2, 2021

    • PTDA

      Public
      Book chapter data: RNA sequencing for transcriptomic studies to identify important genes/pathways for potato’s response to pathogens
      HTML
      •0•0•1•0•Updated Jan 19, 2021Jan 19, 2021

    • VSToverlap

      Public
      HTML
      •0•0•0•0•Updated Oct 14, 2020Oct 14, 2020