Skip to content

@NAMlab NAMlab

Change the repository type filter

All

    Repositories list

    31 repositories

    • deepCRE_reimplemented

      Public
      This repo reimplements deepCRE using tensorflow 2.10.0 and SHAP. Thus replacing tensorflow 1.14.0 and DeepLIFT
      Python
      •
      GNU Affero General Public License v3.0
      •2•2•0•0•Updated Dec 17, 2025Dec 17, 2025

    • DeepCistrome

      Public
      This repository contains code and scripts to reproduce the work on multi-label classifiers for DNA-TF binding
      Python
      •1•1•1•0•Updated Dec 11, 2025Dec 11, 2025

    • Rna-seq-metadata-gap-filling

      Public
      0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • streamlit_deepcre_app

      Public
      This repository contains the code for the deepCRE web application
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•9•0•Updated Nov 17, 2025Nov 17, 2025

    • tomato-rna-meta

      Public
      Data, code, and results for our paper Identification of core, conditional and crosstalk components of tomato heat stress response using integrative transcriptomics and orthology (https://doi.org/10.21203/rs.3.rs-4337825/v1). If you use any of our code or results in a scientific publication, we would be grateful if you cite the paper.
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • rnaseq-mapper

      Public
      Nextflow
      •1•0•0•0•Updated Sep 30, 2025Sep 30, 2025

    • evo_result_analysis

      Public
      Repository for the analysis of the results from the Evolutionary Algorithm
      Python
      •1•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • 2025_Intro_RNAseq_Analysis_Course

      Public
      Intro to RNAseq
      HTML
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • 2025_UoC_ML

      Public
      Materials for the UoC course on ML in biology
      0•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • 2025_Plant2030

      Public
      Materials for the Plant2030 Intro to Bioinformatics Workshop at the IPK Gatersleben
      Shell
      •0•2•0•0•Updated May 14, 2025May 14, 2025

    • panomiX-tool

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Apr 11, 2025Apr 11, 2025

    • 2024_Intro_RNAseq_Analysis_Course

      Public
      Introduction to RNAseq Analysis Course Material
      HTML
      •
      MIT License
      •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • PlantEd-AI

      Public
      Reinforcement learning based bots playing the PlantEd game
      Python
      •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • PlantEd

      Public
      RTS Simulation, Plant Survival Game
      Python
      •
      GNU General Public License v3.0
      •1•5•0•0•Updated Sep 27, 2024Sep 27, 2024

    • moca_blue

      Public
      R
      •1•1•0•0•Updated Aug 27, 2024Aug 27, 2024

    • QBIO

      Public
      QBIO HHU course materials
      R
      •0•0•4•0•Updated May 17, 2024May 17, 2024

    • DeepCRE

      Public
      Deep learning the cis-regulatory code for gene expression in selected model plants
      deep-learninggenomicscis-regulatory-elements
      R
      •4•22•0•0•Updated Mar 15, 2024Mar 15, 2024

    • Aiyesa_Tomato_Differential_Gene_Expression_Analysis

      Public
      Internship project aimed at identifying and investigating deferentially expressed genes in tomato (S.lycopersicum) using available data on heat stress experiment from online database.
      R
      •0•0•0•0•Updated May 3, 2022May 3, 2022

    • OMA-plant-genomes-proj

      Public
      For updated plant genome data, and code for quality assesment of protein sequences and gene co-evolution analysis.
      0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • Abul-Master-Thesis

      Public
      Co-expression and Co-evolution profiles of heat responsive genes in Tomato
      R
      •1•0•0•0•Updated Dec 14, 2021Dec 14, 2021

    • HETCROP

      Public
      Prediction-based normalization for developmental heterochrony in parallel molecular-level and phenomic studies in plants
      0•0•0•0•Updated Dec 7, 2021Dec 7, 2021

    • variant-caller

      Public
      Variant Calling Pipeline Using GATK4 and Nextflow
      Nextflow
      •49•0•0•0•Updated Aug 9, 2021Aug 9, 2021

    • TomatoPhagy

      Public
      0•0•0•0•Updated Feb 28, 2021Feb 28, 2021

    • WheatSouSi

      Public
      WheatSouSi: Wheat source-sink relationships and limitations
      0•0•0•0•Updated Feb 25, 2021Feb 25, 2021

    • CHESSproject

      Public
      This is a public repository of CHESS project
      0•0•0•0•Updated Dec 6, 2020Dec 6, 2020

    • DL_Wheat

      Public
      R
      •1•0•0•0•Updated Nov 24, 2020Nov 24, 2020

    • kILBIL

      Public
      Custom code used in the manuscript:
      R
      •2•2•0•0•Updated Jul 28, 2020Jul 28, 2020

    • IPK_R_courses

      Public
      IPK R courses, tutorials etc.
      0•0•0•0•Updated Mar 19, 2020Mar 19, 2020

    • 19_mlcb

      Public
      Code for Tareen & Kinney (MLCB 2019) https://doi.org/10.1101/835942
      Jupyter Notebook
      •
      MIT License
      •4•0•0•0•Updated Feb 7, 2020Feb 7, 2020

    • inference-of-GRN-using-Fused-LASSO

      Public
      Gene regulatory network inference using fused LASSO on multiple data sets: application to Escherichia coli
      R
      •9•0•0•0•Updated Dec 4, 2017Dec 4, 2017