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Pjotr Prins

Login: pjotrp

Company: University Medical Center Utrecht

Location: Wageningen

Bio: Bioinformatician at large @genenetwork

Blog: http://thebird.nl/

Member of

Repositories

arvados: an open source platform for managing and analyzing biomedical big data
ascilib: A science library - SWIG mappings
bcbb: Incubator for useful bioinformatics code, primarily in Python and R
bigbio: Big data bioinformatics repository
BioD: Development moved to http://github.com/biod/BioD
biogems.info: Tools for keeping track of biogems through http://biogems.info/
bioinformatics: Tools for bioinformatics
biolib: BioLib brings together a set of opensource libraries written in C/C++ and makes them available for all Bio* languages
biolib_hpc: High performance computing for Big Data
biolib_staden_io_lib: Biolib: Git copy of the SVN repository hosted as sourceforge
bio-locus: Bio-locus
bio-nexml: BioRuby plugin to read and write NeXML data
bionix: Bio packages for the Nix package system
BioNode: BioNode Debian based VM tools
bio---numcalc: Trial repository for numcalc
biopp: A reference repository of the Bio++ project (no history)
bioruby: Central testing repository for the Bioruby project
bioruby-affy: TODO: one-line summary of your gem
bioruby-alignment: TODO: one-line summary of your gem
bioruby-bioinformatics-impact: Calculate impact for researchers in bioinformatics
bioruby-core-plugin: Bioruby core plugin - adds/replaces core functionality
bioruby-exominer: Mining publications for gene names
bioruby-foo: TODO: one-line summary of your gem
bioruby-gem: BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package
bioruby-gff3-pltools: Ruby wrapper library for gff3-pltools
bioruby-gff3-plugin: GFF3 plugin for BioRuby - allows parsing big data GFF3
bioruby-grid: Utility to create and distribute jobs on a queue system
bioruby-logger-plugin: BioRuby logger
bioruby-maf: MAF parser for BioRuby
bioruby-ngs: This plugins is intended to wrap the common software used for Next Generation Sequencing data
bioruby-pipeline: TODO: one-line summary of your gem
bioruby-qtlHD: TODO: one-line summary of your gem
bioruby-rdf: Bioinformatics parsing and filtering data for triple-stores
bioruby-sparql-examples: SPARQL examples with Ruby
bioruby-support: Supporting files and scripts for the Bioruby project
bioruby-table: Swiss knife of tabular data
bioruby-vcf: Smart VCF parser
bioscala: Bioinformatics for the Scala programming language
biotools: A set of tools and filters
blastxmlparser: Fast big data XML parser and library, written in Ruby
bosc2015: Content from BOSC2015 unconference sessions on building successful open source bioinformatics communities
browsertest: Javascript test snippets
cfruby: CFRuby project
cloudbiolinux: CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
CloudCluster: null
cmake-support: CMake scripts for BioLib and ASciLib
course: null
course2: null
course3: null
course_adv_bioinf: null
Cross-language-interfacing: Testing cross-language interfaces
CTLmapping: Correlated Trait Locus (CTL) mapping
d2tags: d2tags - converts DMD2's JSON output to Exuberant Ctags format.
deploy: Pjotr's deployment tools
elixir-lang.github.com: Website for Elixir
emboss: Unofficial mirror of the EMBOSS source
EMBOSS-biolib: Git import of EMBOSS CVS repository for Biolib
faster_lmm_d: A faster lmm for GWAS. GPU support coming soon.
gcta: Source for a project some user wanted to see added to MacPorts. With included Eigen headers.
gemma-annotate: Annotation tools for GEMMA
genenetwork2: GeneNetwork (2nd generation)
genfrag: TDF predictor - copy of Rubyforge site
gff3-pltools: A fast parallel GFF3 parser
gnrest: GeneNetwork REST API
gnu-install-bin: Moved to
GSoC: OBF Google Summer of Code
GSoC2013: OBF Google Summer of Code 2013
guix: GNU Guix
guix-conda: null
guix-notes: This repo has moved to https://gitlab.com/pjotrp/guix-notes Notes on Guix
guix-relocatable-binary-packages: Moved to
guix-relocate: Moved to
heyu-run: Heyu/X10 electrical appliances runner and state-machine that can run on OpenWRT wifi routers
htslib: C library for high-throughput sequencing data formats
joss: The Journal of Open Source Software
kemri: kemri example
knuth-interview-2006: The transcript of a Donald Knuth interview in 2006
lepra2: Lepra2 Rails app.
libsequence: The libsequence library (for BioLib)
maru: Elixir RESTful Framework
math--gsl: Perl interface to the GNU Scientific Library
mixed_models: Statistical mixed effects models in Ruby
mlmm: An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations
mpi-ruby: MPI Ruby Bindings
mpi-with-ruby: Super computing tests
NA-BioRuby.org: New age BioRuby website
nix-no-root: Empowered Nix/Guix without root
nixpkgs: Nix Packages collection
nokogiri: Nokogiri (?) is an HTML, XML, SAX, and Reader parser with XPath and CSS selector support.
nokogiri.org-tutorials: The Official Tutorial Archive? of Nokogiri �
Nyaplotjs: JavaScript plotting library
once-only: Execute scripts only once when input is unchanged
open-data-journal: The Journal of Open Data is being developed under Open bioinformatics foundation in Google Summer of Code '17.
orgtexer: Mixing Org mode with LaTeX
OSM: Openstreetmap tools and styles
patchelf: A small utility to modify the dynamic linker and RPATH of ELF executables
pfff: --
Pjotr-s-Debian-packages: null
ptodo: Command line todo organizer (interacts with remind and org-mode)
qnorm: High performance quantile normalization (for BioLib)
qnormalization: A library of parallel methods for gene-expression Q-normalization
qtl: MQM
qtl2cl: Command-line interface for R/qtl2
qtlHD: Re-implementation of R/qtl with clean code, aimed at high-density, high-throughput data
QTLReaper: null
rbib: A ruby parser for BibTeX files
rdf: RDF.rb is a pure-Ruby library for working with Resource Description Framework (RDF) data.
regressiontest: Tools for regression testing
rq: Ruby Queue
rq.deb: Debian package for rq (Ruby Queue)
rqtl: R/qtl mapping software
rqtl-mqm: R/QTL with MQM support
rubydoctest: Ruby version of Python's doctest tool, but a bit different
sambamba: Library for working with SAM/BAM/CRAM formats written in D programming language
samtools: SAM tools repository for BioLib
Scalability: Scalability tests
sciruby: Tools for scientific computation in Ruby/Rails
sciruby.com: Octopress source for sciruby.com
smb_performance: Sambamba vs samtools
somatic_pipeline: Scripts for simple somatic pipeline(s)
sparql-query: command line SPARQL query tool
swig2doc: Convert SWIG generated to documentation
test_gn_pylmm: Testing frame for GeneNetwork2's pylmm
vcf-explorer: Vcf-explorer
WGCNA: GN2�adaption�of�the�CRAN�R�package�repository. WGCNA�?�Weighted�Correlation�Network�Analysis.�Homepage:�http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/
wikitexer: Mixing wiki style syntax with LaTex to generate HTML docs (and pure LaTeX)
yaj: Pilot project for Biohackathon 2017

Commits To

Repository	Most Recent Commit	# Commits
pjotrp/bigbio	2014-05-21 07:57:49.0	165
bioscala/bioscala	2017-03-26 19:35:06.0	214
pjotrp/bioinformatics	2018-03-18 15:10:05.0	80
genenetwork/guix-bioinformatics	2017-07-04 07:30:37.0	254

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.