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Heyo, 👋

I'm Jonas, I am currently doing my Master's degree in Bioinformatics at the University of Potsdam.

In my ongoing Master thesis project at the MDC's BIMSB Bioinformatics platform I am investigating the feasibility of using linear deconvolution models to improve the prediction accurracy of methods involving bulk RNA-seq data of tumor samples (repo).

In a previous project, I worked to improve code quality and prediction accurracy of the PiGx-SARS-Cov-2 pipeline.

I did my Bachelor's degree at the University of Tübingen, focusing on phenological shifts of plants and their pollinators. I investigated the results further leading to my first published paper, the analysis code of which can be found here.

My major experiences are with R and the tidyverse, but through my university courses I have some experience with other languages, most notably python (and snakemake), but also some C++.

Jonas Freimuth's Projects

adventofcode21 icon adventofcode21

My sporadic attempts to participate in https://adventofcode.com/2021/...

bayesprism icon bayesprism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

deconvr icon deconvr

The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.

easy-entrez icon easy-entrez

Retrieve PubMed articles, text-mining annotations, or molecular data from >35 Entrez databases via easy to use Python package - built on top of Entrez E-utilities API.

guix.install icon guix.install

Install (and import) R packages with Guix from within your R session

pigx-databases icon pigx-databases

Small database archives used for testing by the pigx-sars-cov-2 pipeline. May disappear at any point.

tcgaworkflow icon tcgaworkflow

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

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