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https://github.com/mschubert/mschubert

Last synced: 11 days ago
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Host: GitHub
URL: https://github.com/mschubert/mschubert
Owner: mschubert
Created: 2021-11-03T11:30:37.000Z (about 3 years ago)
Default Branch: main
Last Pushed: 2025-01-20T09:06:59.000Z (13 days ago)
Last Synced: 2025-01-20T10:24:27.709Z (13 days ago)
Size: 56.6 KB
Stars: 0
Watchers: 3
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md

Awesome Lists containing this project

README

        ### Hi there 👋

I'm Michael, a computational biologist. This means that I'm using computers and code to analyze biological data, often in collaboration with experimental scientists. I'm working on how cancer cells overcome their growth limitations and how we can use that to help patients. Here you can find some of the work I did, and more general purpose tools I wrote for anyone to use. Please reach out if you want to collaborate!

    

This is what I do for research 👨‍🔬 (full list 🔗)

| |             article             |         code          |

:- | :-: | :-:

| Developed a reliable method for estimating cell signaling pathways from gene expression | [![Nat Comm](https://img.shields.io/badge/Nat%20Comm-2018-blue.svg)](https://www.nature.com/articles/s41467-017-02391-6)
[![Cell](https://img.shields.io/badge/Cell-2016-blue.svg)](https://www.cell.com/cell/fulltext/S0092-8674(16)30746-2) | [github :octocat:](https://github.com/saezlab/footprints)
[bioc 📦](http://bioconductor.org/packages/release/bioc/html/progeny.html)

| Showed how gene coexpression networks often reflect cell mixtures instead of regulation | [![BBA-GRM](https://img.shields.io/badge/BBA--GRM-2020-blue.svg)](https://eriba.umcg.nl/wp-content/uploads/2021/07/Foijer-2019-10-23-Biochim-Biophys-Acta-Gene-Regul-Mech.pdf) | [github :octocat:](https://github.com/mschubert/GRN-aneup-purity)

| Found a way how cancer cells can tolerate abnormal DNA content (aneuploidy, ***c***hromosomal ***in***stability) and a potential treatment, in collaboration with experimental scientists | [![bioRxiv](https://img.shields.io/badge/bioRxiv-2021-yellow.svg)](https://www.biorxiv.org/content/10.1101/2021.12.03.471107v2)
[![Nature](https://img.shields.io/badge/Nature-2022-blue.svg)](https://www.nature.com/articles/s41586-022-04847-2) | [transposon :octocat:](https://github.com/mschubert/mad2-transposon)
[cgas_ko :octocat:](https://github.com/mschubert/cgas_ko) 

| Working on estimating DNA copy number of single-cell RNA sequencing | ^{_{coming soon}} |

  

Here are some of my open source contributions 🔠 (full list 🔗)

| | |             status             |         code          |

:-: | :- | :-: | :-:

| *clustermq* | R package for efficient high performance computing
[![Bioinformatics](https://img.shields.io/badge/Bioinformatics-2019-blue.svg)](https://academic.oup.com/bioinformatics/article/35/21/4493/5499081) [![downloads](https://cranlogs.r-pkg.org/badges/grand-total/clustermq)](https://github.com/mschubert/clustermq) | [![CRAN version](https://www.r-pkg.org/badges/version/clustermq)](https://cran.r-project.org/package=clustermq)
[![Build Status](https://github.com/mschubert/clustermq/actions/workflows/check-standard.yaml/badge.svg?branch=master)](https://github.com/mschubert/clustermq/actions) | [github :octocat:](https://github.com/mschubert/clustermq)
[cran 📦](https://cran.r-project.org/package=clustermq)
[testing :gear:](https://github.com/mschubert/clustermq-performance) 

| *narray* | R package for simplifying array operations
[![downloads](https://cranlogs.r-pkg.org/badges/grand-total/narray)](https://github.com/mschubert/narray) | [![CRAN version](https://www.r-pkg.org/badges/version/narray)](https://cran.r-project.org/package=narray)
[![Build Status](https://github.com/mschubert/narray/actions/workflows/check-standard.yaml/badge.svg?branch=master)](https://github.com/mschubert/narray/actions) | [github :octocat:](https://github.com/mschubert/narray)
[cran 📦](https://cran.r-project.org/package=narray)

| *ebits* | R bioinformatics toolkit incubator and data API | [![Build Status](https://github.com/mschubert/ebits/actions/workflows/check-standard.yaml/badge.svg?branch=master)](https://github.com/mschubert/ebits/actions) | [ebits :octocat:](https://github.com/mschubert/ebits)
[data :octocat:](https://github.com/mschubert/data)

| | Software build scripts for the [ArchLinux User Repository 🔗](https://aur.archlinux.org/packages/?K=mschu&SeB=m) and as [Gentoo overlay 🔗](https://en.wikipedia.org/wiki/Portage_(software)#ebuild) | [![pkgcheck](https://github.com/mschubert/overlay/actions/workflows/pkgcheck.yml/badge.svg)](https://github.com/mschubert/overlay/actions) | [pkgbuilds :octocat:](https://github.com/mschubert/PKGBUILDs)
[overlay :octocat:](https://github.com/mschubert/overlay)