Repositories list

• 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 Nov 22, 2024Nov 22, 2024

• deepCRE_reimplemented

  Public
  This repo reimplements deepCRE using tensorflow 2.10.0 and SHAP. Thus replacing tensorflow 1.14.0 and DeepLIFT

  Python

  •2•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• streamlit_deepcre_app

  Public
  This repository contains the code for the deepCRE web application

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• PlantEd-AI

  Public
  Reinforcement learning based bots playing the PlantEd game

  Python

  •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

• rnaseq-mapper

  Public
  Nextflow

  •1•0•0•0•Updated Oct 2, 2024Oct 2, 2024

• PlantEd

  Public
  RTS Simulation, Plant Survival Game

  Python

  •

  GNU General Public License v3.0

  •1•4•0•0•Updated Sep 27, 2024Sep 27, 2024

• moca_blue

  Public
  R

  •0•0•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

• 2024_Intro_RNAseq_Analysis_Course

  Public
  Introduction to RNAseq Analysis Course Material

  MIT License

  •0•0•0•0•Updated May 8, 2024May 8, 2024

• DeepCRE

  Public
  Deep learning the cis-regulatory code for gene expression in selected model plants

  deep-learninggenomicscis-regulatory-elements

  R

  •1•9•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

  •47•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

• fastqc

  Public
  csf fork of fastqc for usage on selected reads of unaligned bam file

  Java

  •

  GNU General Public License v3.0

  •41•0•0•0•Updated Mar 7, 2013Mar 7, 2013