Light

Michael Schubert photo

mschubert Goto Github PK

followers: 111.0 following: 90.0 repos: 48.0 gists: 14.0

Name: Michael Schubert

Type: User

Bio: Postdoctoral scientist at the Netherlands Cancer Institute (NKI). Previously EMBL-EBI/Cambridge Uni.

Twitter: _ms03

Location: Amsterdam, NL

Blog: http://mschubert.github.io

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 a potential treatment, in collaboration with experimental scientists		transposon 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		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

Michael Schubert's Projects

aneufinder2

Find CNVs in single cell sequencing data.

arrayexpress

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/ArrayExpress.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=ArrayExpress.

bhtsner

R package for Barnes-Hut t-SNE

biomodels_curation

Scripts used for curation of Blood Coagulation models for the BioModels database

boundie

R package for differential expression on count data with parameter bounds

cgas_ko

clustermq

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

clustermq-performance

Performance testing for https://github.com/mschubert/clustermq

cppzmq

Header-only C++ binding for libzmq

data

A data API for molecular biology

docker-actions-test

ebits

R bioinformatics toolkit incubator

ensembl-rest

Exercises for the Ensembl REST API

footprints

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

genie3

GENIE3 (GEne Network Inference with Ensemble of trees) R-package

gentoo

The official mirror the Gentoo ebuild repository (now in true git!)

gentoo_prefix_ci

A Gentoo Prefix continuous integration repo. Find precompiled Gentoo Prefix in the releases section

git-annex

grn-aneup-purity

Analysis code for "Gene networks in cancer are biased by aneuploidies and sample impurities"

honeybadger

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

lincs-data-processing

mad2-transposon

Analysis code for "Cancer tolerance to chromosomal instability is driven by Stat1 inactivation in vivo"

mcp

Regression with Multiple Change Points

mschubert

mschubert.github.io

narray

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

nmfconsensus

Parallel version of the BROAD nmfconsensus.R script

overlay

Gentoo overlay for (mainly scientific) software that's not quite ready for the main tree

pkgbuilds

Build scripts for the Archlinux User Repository

probabilistic-programming-and-bayesian-methods-for-hackers

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming in data analysis with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

1
2

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.