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Achievement: Starstruckx2Achievement: Galaxy BrainAchievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2

Achievements

Achievement: Starstruckx2Achievement: Galaxy BrainAchievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2

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@EBI-predocs @NKI-CCB

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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 Nat Comm
Cell		 github :octocat:
bioc 📦
Showed how gene coexpression networks often reflect cell mixtures instead of regulation BBA-GRM github :octocat:
Found a way how cancer cells can tolerate abnormal DNA content (aneuploidy, chromosomal instability) and a potential treatment, in collaboration with experimental scientists bioRxiv
Nature		 transposon :octocat:
cgas_ko :octocat:
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 downloads		 CRAN version
Build Status		 github :octocat:
cran 📦
testing ⚙️
narray R package for simplifying array operations
downloads		 CRAN version
Build Status		 github :octocat:
cran 📦
ebits R bioinformatics toolkit incubator and data API Build Status ebits :octocat:
data :octocat:
Software build scripts for the ArchLinux User Repository 🔗 and as Gentoo overlay 🔗 pkgcheck pkgbuilds :octocat:
overlay :octocat:

Pinned Loading

  1. clustermq clustermq Public

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

    R 147 27

  2. narray narray Public

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

    R 27 1

  3. saezlab/progeny saezlab/progeny Public

    R package for Pathway RespOnsive GENe activity inference

    R 93 19

  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 20 8

  6. PKGBUILDs PKGBUILDs Public

    Build scripts for the Archlinux User Repository

    Shell 2 1