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@BleekerLab Petra Bleeker laboratory

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    15 repositories

    • PhenoFeatureFinder

      Public
      A Python package dedicated to identifying plant metabolite features related to insect resistance
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • snakemake_rnaseq

      Public
      A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)
      dockerbioinformaticssnakemakegenomicscondarna-seq-analysisrna-seq-pipeline
      Python
      •
      MIT License
      •7•13•5•0•Updated Mar 3, 2023Mar 3, 2023

    • genetic_requirements

      Public
      Codes and datasets for the figures of the "genetic requirement" paper
      HTML
      •0•0•1•0•Updated Feb 1, 2023Feb 1, 2023

    • genotype_by_sequencing

      Public
      A pipeline to call SNPs from RNA-seq data and plot it along chromosomal coordinates
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 10, 2022Oct 10, 2022

    • shiny_rnaseq_app

      Public
      An Shiny application to explore RNA-seq results produced from the laboratory on tomato. Web application is private under password protection (please request access).
      rna-seqshinytomatotrichome
      R
      •
      Apache License 2.0
      •0•1•0•0•Updated Aug 25, 2022Aug 25, 2022

    • small-rna-seq-pipeline

      Public
      A pipeline to annotate miRNAs, phased siRNAs and other types using a reference genome and experimental sRNA-Seq data
      Python
      •
      MIT License
      •2•6•3•0•Updated Aug 1, 2022Aug 1, 2022

    • random_forest_with_sklearn

      Public archive
      Random Forest implementation using sklearn
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 18, 2021Oct 18, 2021

    • random_forest_with_ranger

      Public archive
      An Rscript wrapper around the MUVR package of R. Contains a Docker image to ensure portability of the R script.
      R
      •
      Apache License 2.0
      •0•0•2•0•Updated Sep 28, 2021Sep 28, 2021

    • freebayes_snp_calling

      Public
      A Snakemake pipeline to call variants (SNPs, InDels) from DNA-seq Illumina fastq files.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 21, 2021Jul 21, 2021

    • natural-insecticides-thrips-whiteflies

      Public archive
      Data and figures for the natural insecticides paper
      Jupyter Notebook
      •
      Other
      •0•0•3•0•Updated Jul 12, 2021Jul 12, 2021

    • snakemake_mummer

      Public
      A Snakemake pipeline to align a set of fasta sequences (query) to another (subject) using MUMMER4
      R
      •
      GNU General Public License v3.0
      •1•0•2•1•Updated Nov 29, 2020Nov 29, 2020

    • protocols

      Public
      Protocols for molecular biology, bioassays, metabolite analysis, etc.
      molecular-biologyinsectbioassayprotocol
      MIT License
      •2•1•0•0•Updated Nov 3, 2020Nov 3, 2020

    • rnaseq-analysis-kallisto-sleuth

      Public
      mRNA-Seq analysis using Kallisto and Sleuth
      Python
      •
      MIT License
      •0•0•3•0•Updated Oct 15, 2020Oct 15, 2020

    • paper_Alain_Zabel2020

      Public archive
      R
      •0•0•0•0•Updated Sep 17, 2020Sep 17, 2020

    • project20accessions

      Public archive
      STW-VIDI project "tomato rearm themselves"
      rna-seqgenomicsmetabolismtomato
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jun 1, 2018Jun 1, 2018