makrez
Bioinformatician and Data Scientist. Expertise in omics applications (e.g. metagenomics, RNA-Seq, scRNA-Seq) using CLI, R, Python, Snakemake, Bash etc.
Interfaculty Bioinformatics Unit, University of BernBern
Pinned Repositories
BioinformaticsTools
A collection of bioinformatics tools using python, R and bash.
cardio_train
Short machine learning project
CNN_16S_classification
ETL
genome_assembly_pipeline
Snakemake pipeline for assembling and annotating bacterial genomes from NGS paired-end data.
Hypericum_analysis
This analysis is published in: Howard C, Hill E, Kreuzer M, Mali P, Masiero E, Slater A, Sgamma T (2019) DNA Authentication of St John’s Wort (Hypericum perforatum L.) Commercial Products Targeting the ITS Region; Genes 10(4), 286 This file consists of the metabarcoding analysis after the querying the reads to the NCBI database. The blast output was parsed with MEGAN. The starting data is the file __specieslist.ncbi.txt__.
meta-genomisc-snakemake
microbial-assembly-exercises
BC2Bio assembly exercise
MLCV
Machine Learning for Computer Vision course
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
makrez's Repositories
makrez/BioinformaticsTools
A collection of bioinformatics tools using python, R and bash.
makrez/cardio_train
Short machine learning project
makrez/CNN_16S_classification
makrez/ETL
makrez/genome_assembly_pipeline
Snakemake pipeline for assembling and annotating bacterial genomes from NGS paired-end data.
makrez/Hypericum_analysis
This analysis is published in: Howard C, Hill E, Kreuzer M, Mali P, Masiero E, Slater A, Sgamma T (2019) DNA Authentication of St John’s Wort (Hypericum perforatum L.) Commercial Products Targeting the ITS Region; Genes 10(4), 286 This file consists of the metabarcoding analysis after the querying the reads to the NCBI database. The blast output was parsed with MEGAN. The starting data is the file __specieslist.ncbi.txt__.
makrez/meta-genomisc-snakemake
makrez/microbial-assembly-exercises
BC2Bio assembly exercise
makrez/MLCV
Machine Learning for Computer Vision course
makrez/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
makrez/shiny_deployment_example
makrez/ShinyApps
makrez/Nature_bx_metabolisation_MS
Code for the manuscript
makrez/soil_metagenomics
makrez/test-datasets
Test data to be used for automated testing with the nf-core pipelines
makrez/website
Code and files for the main nf-core website.