Petra Bleeker laboratory
- 4 followers
- University of Amsterdam
- P.M.Bleeker@uva.nl
Pinned
Repositories
- 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)
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- genotype_by_sequencing Public
A pipeline to call SNPs from RNA-seq data and plot it along chromosomal coordinates
- 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).
- small-rna-seq-pipeline Public
A pipeline to annotate miRNAs, phased siRNAs and other types using a reference genome and experimental sRNA-Seq data
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- 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.
- freebayes_snp_calling Public
A Snakemake pipeline to call variants (SNPs, InDels) from DNA-seq Illumina fastq files.
- natural-insecticides-thrips-whiteflies Public archive
Data and figures for the natural insecticides paper
- snakemake_mummer Public
A Snakemake pipeline to align a set of fasta sequences (query) to another (subject) using MUMMER4
