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mschubert (Michael Schubert) · GitHub

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mschubert/README.md

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
github
bioc 📦
Showed how gene coexpression networks often reflect cell mixtures instead of regulation github
Found a way how cancer cells can tolerate abnormal DNA content (aneuploidy, chromosomal instability) and potential treatments, in collaboration with experimental scientists

transposon
cgas_ko
ToxicGenes
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
github
cran 📦
testing ⚙️
narray R package for simplifying array operations
github
cran 📦
ebits R bioinformatics toolkit incubator and data API ebits
data
Software build scripts for the ArchLinux User Repository 🔗 and as Gentoo overlay 🔗 pkgbuilds
overlay

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  1. clustermq clustermq Public

    R package to send function calls as jobs on LSF, SGE, Slurm, PBS/Torque, or each via SSH

    R 152 29

  2. narray narray Public

    R package for subset- and name-aware array utility functions

    R 26 1

  3. saezlab/progeny saezlab/progeny Public

    R package for Pathway RespOnsive GENe activity inference

    R 130 24

  4. ebits ebits Public

    R bioinformatics toolkit incubator

    R 6 3

  5. saezlab/footprints saezlab/footprints Public

    Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"

    R 24 8

  6. PKGBUILDs PKGBUILDs Public

    Build scripts for the Archlinux User Repository

    Shell 2 1

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