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@BleekerLab

Petra Bleeker laboratory

Laboratory of Petra Bleeker at University of Amsterdam

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  1. snakemake_rnaseq 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)

    Python 18 9

  2. small-rna-seq-pipeline 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 8 2

  3. genotype_by_sequencing genotype_by_sequencing Public

    A pipeline to call SNPs from RNA-seq data and plot it along chromosomal coordinates

    Python

Repositories

Showing 10 of 17 repositories
  • PhD_Marlot_00_wft_functional_annotation Public

    of this chromosome level assembly, there remain questions about the (functional) annotation quality:

    BleekerLab/PhD_Marlot_00_wft_functional_annotation's past year of commit activity
    0 0 0 0 Updated Oct 8, 2026
  • Riboflavin Public
    BleekerLab/Riboflavin's past year of commit activity
    R 0 0 0 0 Updated Jul 20, 2025
  • PhenoFeatureFinder Public

    A Python package dedicated to identifying plant metabolite features related to insect resistance

    BleekerLab/PhenoFeatureFinder's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Nov 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)

    BleekerLab/snakemake_rnaseq's past year of commit activity
    Python 18 MIT 9 5 0 Updated Mar 3, 2023
  • genetic_requirements Public

    Codes and datasets for the figures of the "genetic requirement" paper

    BleekerLab/genetic_requirements's past year of commit activity
    HTML 0 0 1 0 Updated Feb 1, 2023
  • genotype_by_sequencing Public

    A pipeline to call SNPs from RNA-seq data and plot it along chromosomal coordinates

    BleekerLab/genotype_by_sequencing's past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 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).

    BleekerLab/shiny_rnaseq_app's past year of commit activity
    R 1 Apache-2.0 0 0 0 Updated Aug 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

    BleekerLab/small-rna-seq-pipeline's past year of commit activity
    Python 8 MIT 2 3 0 Updated Aug 1, 2022
  • random_forest_with_sklearn Public archive

    Random Forest implementation using sklearn

    BleekerLab/random_forest_with_sklearn's past year of commit activity
    Jupyter Notebook 0 Apache-2.0 0 0 0 Updated Oct 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.

    BleekerLab/random_forest_with_ranger's past year of commit activity
    R 0 Apache-2.0 0 2 0 Updated Sep 28, 2021
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