All

51 repositories

skm-tools
Public
Scripts and utilities for leveraging SKM resources
Jupyter Notebook
•
GNU General Public License v3.0
•0•3•0•1•Updated Apr 21, 2026Apr 21, 2026
promoteR
Public
Large scale promotor sequence extraction in R
HTML
•
MIT License
•0•1•0•0•Updated Apr 13, 2026Apr 13, 2026
BoolDog
Public
A Python package for analyses of Boolean and semi-quantitative Boolean networks.
python simulation systems-biology
python simulation systems-biology boolean-network
Jupyter Notebook
•
GNU General Public License v3.0
•0•0•4•0•Updated Mar 5, 2026Mar 5, 2026
Adapt_field_ML
Public
Potato yield can be predicted by using drone-captured and environmental measurements early in the growing season
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Mar 4, 2026Mar 4, 2026
FaDSeqSes
Public
Factorial design of RNA-seq analyses
integration metabolomics transcriptomics
integration metabolomics transcriptomics factorial-design
Other
•0•0•0•0•Updated Mar 2, 2026Mar 2, 2026
polyase
Public
A package for analyzing allele-specific expression in polyploid organisms
plants long-read rna-seq-analysis
plants long-read rna-seq-analysis polyploidy allele-specific-expression bioninformatics
Python
•
MIT License
•0•0•0•0•Updated Feb 27, 2026Feb 27, 2026
syntelogfinder
Public
Nextflow pipeline to find syntelogous genes in phased genome assemblies of polyploid plants
genome plants polyploid
genome plants polyploid
Nextflow
•0•3•0•0•Updated Feb 18, 2026Feb 18, 2026
longrnaseq
Public
Long-read RNA-seq nextflow pipeline for quantification, novel isoform discovery and quality control
rna-seq long-read transcriptomics
rna-seq long-read transcriptomics
HTML
•
MIT License
•1•3•1•0•Updated Feb 13, 2026Feb 13, 2026
HCS-proc
Public
Data processing pipeline for High-Content Screening using CellProfiler data.
Python
•
MIT License
•0•0•0•0•Updated Jan 13, 2026Jan 13, 2026
pss_viz
Public
Interactive search and visualization of the PSS model.
JavaScript
•
MIT License
•1•0•1•1•Updated Jan 10, 2026Jan 10, 2026
AlKoSol
Public
repository for code and supplementary material of the AlKoSol project
HTML
•0•0•0•0•Updated Dec 23, 2025Dec 23, 2025
Bacillus-Pti5
Public
understanding endophyte/plant relationships
statistical-analysis rna-seq-analysis gsea
statistical-analysis rna-seq-analysis gsea qpcr-analysis
HTML
•
MIT License
•0•0•0•0•Updated Dec 23, 2025Dec 23, 2025
SPOZNAJ
Public
SPOZNAJ materials
HTML
•
Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Dec 10, 2025Dec 10, 2025
unitato
Public
UniTato: a web server for evidence and community based Unification of poTato gene models
gff3 genome-browser solanum-tuberosum
gff3 genome-browser solanum-tuberosum
HTML
•
MIT License
•0•1•0•0•Updated Dec 1, 2025Dec 1, 2025
skm-pss-adapters
Public
Export adapters from PSS neo4j db to other formats
Python
•
MIT License
•0•0•0•0•Updated Nov 19, 2025Nov 19, 2025
Nuclei-segmentation
Public
Segmentation of nuclei, chloroplasts or both, and remaining regions. Area, mean intensity, histograms export.
image-analysis-and-processing
image-analysis-and-processing
MATLAB
•0•0•0•0•Updated Nov 17, 2025Nov 17, 2025
pISA-tree
Public
pISA-tree: Standard project directory tree ( ISA framework compliant )
windows project-management isa
windows project-management isa batch-file directory-tree file-management batch-files pisa-tree
Batchfile
•
MIT License
•3•7•6•0•Updated Nov 10, 2025Nov 10, 2025
Hyphae_segmentation
Public
Image quality feature extraction, using them for shallow learning to train 2 different classifiers (good vs. bad images; semi-good vs. good image) to separate i…
Python
•
MIT License
•0•0•0•0•Updated Nov 3, 2025Nov 3, 2025
multiOmics-integration
Public
Potato ‘omics data analysis pipelines
feature-selection statistical-analysis phenotyping
feature-selection statistical-analysis phenotyping omics network-analysis omics-data-integration proteomics-data-analysis
HTML
•
MIT License
•3•4•0•0•Updated Oct 13, 2025Oct 13, 2025
skm-translate
Public
Translation pipeline from SKM to crop and crop wild relatives
translation orthologs arabidopsis-thaliana
translation orthologs arabidopsis-thaliana
HTML
•
MIT License
•1•0•0•0•Updated Sep 26, 2025Sep 26, 2025
pymapman
Public
Python tool to help create MapMan diagrams
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Aug 26, 2025Aug 26, 2025
Potato-GEM
Public
Potato GEM
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Aug 20, 2025Aug 20, 2025
ckn_viz
Public
CKN network visualization app
JavaScript
•
MIT License
•1•0•1•1•Updated Jul 25, 2025Jul 25, 2025
skm-ckn
Public
The Comprehensive Knowledge Network of SKM
Jupyter Notebook
•
Other
•0•0•0•0•Updated Jul 7, 2025Jul 7, 2025
desiree-genome
Public
Scripts and supplementary information on potato cv. Desiree genome assembly
0•4•0•0•Updated Jun 30, 2025Jun 30, 2025
skm-neo4j
Public
Cypher
•0•0•0•0•Updated Mar 19, 2025Mar 19, 2025
skm-biocypher
Public
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Mar 5, 2025Mar 5, 2025
CampyDEA
Public
Campylobacter jejuni biofilm differential expression analysis (DEA)
data-science data-analysis bacteria
data-science data-analysis bacteria transcriptomics differential-expression
R
•
MIT License
•0•0•0•0•Updated Feb 11, 2025Feb 11, 2025
pISA-tree-assay-types
Public
Collection of pISA-tree assay types.
Jupyter Notebook
•
MIT License
•0•0•1•0•Updated Nov 28, 2024Nov 28, 2024
DE_analysis_limma
Public
Script for DE analysis with limma-voom protocol
R
•0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

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National Institute of Biology

All

All

51 repositories

skm-tools

promoteR

BoolDog

Adapt_field_ML

FaDSeqSes

polyase

syntelogfinder

longrnaseq

HCS-proc

pss_viz

AlKoSol

Bacillus-Pti5

SPOZNAJ

unitato

skm-pss-adapters

Nuclei-segmentation

pISA-tree

Hyphae_segmentation

multiOmics-integration

skm-translate

pymapman

Potato-GEM

ckn_viz

skm-ckn

desiree-genome

skm-neo4j

skm-biocypher

CampyDEA

pISA-tree-assay-types

DE_analysis_limma

All

All

Repositories list

51 repositories