Björn Grüning

Login: bgruening

Company: University of Freiburg

Location: Freiburg (Germany)

Bio: null

Blog: orcid.org/0000-0002-3079-6586

Blog: orcid.org/0000-0002-3079-6586

Member of

  2. BioContainers
  3. Bioinformatics Lab - Department of Computer Science - University Freiburg
  4. Biopython Project
  5. GalaxyP
  6. Galaxy Project
  7. GenericWorkflowNodes
  8. Intergalactic Utilities Commission
  9. Involucro
  10. The deepTools ecosystem

Repositories

ansible-galaxy-extras
Ansible roles to configure assorted compontents for an Ubuntu VM or container configured with https://github.com/galaxyproject/ansible-galaxy with production services including nginx, uwsgi, supervisor, protftp, and slurm.
ansible-galaxy-os
An Ansible role is for configuring the base operating system useful for running Galaxy.
antarna
RNA inverse folding using ant-colony optimization
aRchive_source_code
aRchive for Bioconductor packages
argparse2galaxy
Convert a python argparse defintion in a Galaxy Tool XML
bc
Template for Software Carpentry bootcamp site repository.
bcbb
Useful bioinformatics code, primarily in Python and R
bcfind
Brain cell finder
bedtools
A powerful toolset for genome arithmetic.
bedtools2
A powerful toolset for genome arithmetic.
bedtools-galaxy
null
bgbio
bioinformatic tools, primarily in Python
bgchem
cheminformatic tools, primarily in Python
bioblend
A python library for interacting with CloudMan and Galaxy API
bioconda_biocontainers_talk
BioConda & BioContainers
bioconda-recipes
Conda recipes for the bioconda channel.
BioDocklets
null
biom-format
The Biological Observation Matrix (BIOM) Format Project
biopython
Biopython fork
biopython_docker
Dockerfiles to build Biopython instances
bitarray
efficient arrays of booleans for Python
bosc2015
Content from BOSC2015 unconference sessions on building successful open source bioinformatics communities
camera
CAMERA for Galaxy
cardiac-epigenome-browser-mm9-cm
Cardiac epigenome browser mm9-cm
cegr-galaxy
CEGR proprietary Galaxy components: pre-processing pipeline, ChIP-exo statistics tools, etc.
cellorganizer-galaxy-tools
CellOrganizer tools and scripts for Galaxy Project
cf-scripts
Flagship repo for cf-regro-autotick-bot
CIRCexplorer
A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)
circos_galaxy_wrapper
Every first version of the Circos Galaxy wrapper
coding_for_big_data
X things you should take into consideration if you code for big data analysis
conda-build
Commands and tools for building conda packages
conda-forge.github.io
Documentation for conda-forge
conda-recipes
build and test recipes for conda
conda_r_skeleton_helper
Cleaning up Conda r-packages
confab
Automatically exported from code.google.com/p/confab
confab.docs
Automatically exported from code.google.com/p/confab.docs
containers
Bioinformatics containers
crossbio
Cross-filtered biological data
CTDopts
Gives your Python tools a CTD-compatible interface
dagobah-training
Galaxy admin trainings for aspiring Skywalkers
deepTools
Tools to process and analyze deep sequencing data.
devteam2git
null
docker
Docker - the open-source application container engine
docker-build
Playing around with building Galaxy dependencies in Docker, nothing interesting to see here.
docker-busybox-bash
Minimal Docker Container with bash
docker-galaxy-blast
:whale: Galaxy Docker repository with NCBI Blast tools (Galaxy Blast flavour)
docker-galaxy-chemicaltoolbox
:books::whale: Galaxy flavor for Cheminformatics
docker-galaxy-ChIP-exo
Galaxy Docker repository with ChIP-exo tools (Galaxy ChIP-exo flavor)
docker-galaxy-computational-chemistry
null
docker-galaxy-csg
Galaxy Docker repository with Constructive Solid Geometry tools (Galaxy CSG flavour)
docker-galaxy-epigenetics
:whale::bar_chart::books: Docker Images for epigenetics data analysis
docker-galaxy-exome-seq
Galaxy Docker Image for Exome sequencing
docker-galaxy-imaging
:whale: Galaxy Docker repository with Imaging tools (Galaxy Imaging flavour)
docker-galaxy-machine-learning
Galaxy machine learning flavour
docker-galaxy-ngs-preprocessing
:whale::bar_chart::books: Docker Images for NGS data preprocessing
docker-galaxy-phylogenetics
:whale::bar_chart::books: Docker Images for molecular phylogenetics
docker-galaxy-ploen
Special Galaxy Docker Image for the MPI for Evolutionary Biology
docker-galaxy-protease-prediction
Docker Image for protease predictions based on cleavage sites
docker-galaxy-sequence-tools
Galaxy flavor with a basic set of sequence manipulation tools
docker-galaxy-stable
:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
dockeri.co
Badges for Docker
docker-ipython-notebook
:whale: :microscope: :books: IPython running in a docker container. This image can be used to integrate IPython into Galaxy
docker-jupyter-notebook
:whale: :microscope: :books: Jupyter running in a docker container. This image can be used to integrate Jupyter into Galaxy
docker-paraviewweb
:whale: ParaViewWeb running in a docker container. This image can be used to integrate ParaViewWeb into Galaxy
docker-recipes
:whale: Dockerfiles to build Galaxy images
docker-stacks
Opinionated stacks of ready-to-run Jupyter applications in Docker.
docker-usegalaxy
:whale: Galaxy Docker repository with tools from usegalaxy.org (UseGalaxy.org flavour)
documentation
Sphinx-based documentation for the Open Babel project
download_store
universal storage
dunovo
Reference-free duplex sequencing pipeline.
EDeN
Python Explicit Decomposition with Neighborhoods
FancySelector
Select replacement, but fancy!
fasrc-galaxy
Galaxy app in a container
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)
featurecounts_galaxy_wrapper
featureCounts Galaxy Wrapper
find_subsequence
null
flexbar
flexible barcode and adapter removal
freebayes
Bayesian haplotype-based polymorphism discovery and genotyping.
galaxy
Data intensive biology for everyone.
galaxy-admin-utils
Utility scripts for working with local instances of Penn State's Galaxy platform http://wiki.galaxyproject.org/
galaxy-bgisoap
Galaxy wrappers for BGI's SOAP tools including SOAPdenovo2.
galaxy_blast
Galaxy wrappers for NCBI BLAST+ and related BLAST tools.
galaxy-config
Various configuration files from the Galaxy-FR server
GalaxyConfigGenerator
Given a CTD file, GalaxyConfigGenerator generates a Galaxy wrapper
galaxy-downloads
Misc. Galaxy related downloads.
galaxy_ie_helpers
Helper scripts to work with Galaxy's Interactive Environments
galaxy-image-analysis
Galaxy tools for image analysis
galaxy-ipython
:microscope::books: IPython Integration into Galaxy
galaxy-lib
Subset of Galaxy (http://galaxyproject.org/) core code designed to be used as a library.
galaxy-maps
null
galaxy-neurolincs
The NeuroLINCS Galaxy Flavor
galaxy-open-molecule-generator
:books::whale: Galaxy flavour for the Open Molecule Generator
galaxy-RNAcommender
Production ready Galaxy instance with RNAcommender
galaxy-rna-seq
:whale::bar_chart::books: Galaxy Docker Image to analyse RNA-Seq data
galaxy-rna-structural-analysis
Galaxy flavor for RNA structural analysis
galaxy-rna-workbench
Galaxy RNA workbench
galaxy-rna-workbench-extra
:books::whale: Galaxy RNA workbench (de.NBI project) for taining courses
galaxy-site
Galaxy project website, aka Galaxy Community Hub
galaxy-tool-encode-data-submission
A Galaxy Tool that was used to submit experimental results to Encode DCC circa 2012
galaxytools
:microscope::books: Galaxy Tool wrappers
galaxy_tools
Wrappers for galaxy tools
galaxy_tools-1
Contains a set of Galaxy Tools mostly written by the Bioinformatics core at NML
galaxy-toolshed-hooks
Easy deployment of large and complex toolshed repositories.
galaxy-training-builder
Proof of concept project to build Galaxy training material
galaxy-tricks
Useful tricks and tipps for Galaxy users
galaxy-universe
A community project to get an overview about the Galaxy project
galaxy-webhooks
Repository to store and share Galaxy webhooks
gemini
a lightweight db framework for disease and population genetics.
gemini-versioned-install
Instalation script with a more conservative dependency definitions (for use by Galaxy)
gnuplot-feedstock
A conda-smithy repository for gnuplot.
goatools
Python scripts to find enrichment of GO terms
gobyexample
Go by Example
gops
Galaxy Operations Python Package
grequests-feedstock
A conda-smithy repository for grequests.
gsh
Galaxy Shell
gsl
Collection of links (for eric)
gvl_commandline_utilities
Scripts for users of GVL cloud instances. These scripts configure GVL servers as command line bioinformatics platforms.
hackathonfr
Source and documention of the OpenData Hackathon 2015 in Freiburg
HiCExplorer
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
idc
Intergalactic (reference) Data Commission
idea-incubator
null
ig-checkfcs
null
infernal
RNA secondary structure/sequence profiles for homology search and alignment
intro.js
A better way for new feature introduction and step-by-step users guide for your website and project.
iobio-galaxy.bam_iobio_io
The docker container that is created for embedding bam.iobio inside Galaxy
iobio-galaxy.vcf_iobio_io
The docker container that is created for embedding vcf.iobio inside Galaxy
ipython
Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.
ipython-galaxy-publication
Our initial proposal for a Docker/IPython/Galaxy paper
jsonschema
An(other) implementation of JSON Schema for Python
libgd-feedstock
A conda-smithy repository for libgd.
libgtextutils
Gordon's Text utils Library
Lighter
Fast and memory-efficient sequencing error corrector
M7I-annotation
Genome Annotation
MACS
MACS -- Model-based Analysis of ChIP-Seq
magictools
:video_game: :pencil: A list of Game Development resources to make magic happen.
MALDI-tools-dev
MALDI tools development
matplotlib-feedstock
A conda-smithy repository for matplotlib.
methtools
tools for the processing of genome-wide bisulfite sequencing data
modENCODE-Galaxy
modENCODE Galaxy on Amazon Cloud
moFF
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
mono-feedstock
A conda-smithy repository for mono.
mQC
Ribosome profiling mapping quality control tool
mulled
null
mulled-1
null
mulled-utils
Python script to work with mulled based Docker containers
multireqcontainers
Testing building mulled containers for multi-requirement tools.
ngl
WebGL protein viewer
ngsutils
Tools for next-generation sequencing analysis
nmr_alignment
null
nosebook
a nose plugin for finding and running IPython notebooks as nose tests
notebook
Jupyter Interactive Notebook
notebooks
:books: Collection of IPython notebooks
NP-Likeness
Natural Product-likeness calculator v-2.1 : calculates natural product-likeness of small molecules based on open-data of natural products.
omnia-conda-recipes
conda build recipes for the Omnia project
openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
OpenMS
The codebase of the OpenMS project
pannenkoek
A tool for generating LEfSe ready data from an OTU table and mapping file. Sample metadata is added as a new row based on user inputs.
ParaView
VTK-based Data Analysis and Visualization Application
peakzilla
Peakzilla is a new algorithm to identify transcription factor binding sites from ChIP-seq data. I would be very happy if you try it and provide me with feedback, so I can improve peakzilla and make you a happier user. Please feel free to send an e-mail to: jonas.steinmann@imba.oeaw.ac.at
PEAR
Pair-End AssembeR
peptide-shaker
Interpretation of proteomics identification results
perl-feedstock
A conda-smithy repository for perl.
pgchem_tigress
Pgchem::tigress is the chemoinformatics extension to the PostgreSQL DBMS. It enables PostgreSQL to handle molecules through SQL statements.
Phinch
Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Berkeley, CA, and biological researchers at UC Davis.
picard
Galaxy wrappers for Picard tools
pico_galaxy
Galaxy tools and wrappers for sequence analysis
PileOMeth
A (mostly) universal methylation extractor for BS-seq experiments.
pizzly
Fast fusion detection using kallisto
planemo
Command-line utilities to assist in developing tools for the Galaxy project.
planemo-machine
A packer.io configuration for building out Galaxy (http://galaxyproject.org/) tool development environments.
planemo-monitor
Planemo scripting to monitor repositories and register tool containers.
planemo-workflow-test-template
null
planets
Software Carpentry Workshop Freiburg
presentations
:books: talks, presentations and ideas
proBAMconvert
proBAMconvert, a conversion tool for peptide identification files (MzIdentML,pepXML,mzTAB) to the proBAM format
project-ideas
A collection of project ideas suitable for Master and Bachelor students
proteomics-datatypes
Proteomics datatypes definitions for Galaxy
protk
Proteomics Toolkit in Ruby
protk-galaxytools
Galaxy tool wrappers for protk
pyBigWig
A python extension for quick access to bigWig files
pytables-feedstock
A conda-smithy repository for pytables.
qiime
Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests
r-agricolae-feedstock
A conda-smithy repository for r-agricolae.
r-aroma.apd-feedstock
A conda-smithy repository for r-aroma.apd.
r-assertthat-feedstock
A conda-smithy repository for r-assertthat.
r-base-feedstock
A conda-smithy repository for r-base.
rbc_docs
RBC de.NBI documents
r-broom-feedstock
A conda-smithy repository for r-broom.
r-circlize-feedstock
A conda-smithy repository for r-circlize.
r-class-feedstock
A conda-smithy repository for r-class.
r-cowplot-feedstock
A conda-smithy repository for r-cowplot.
r-d3heatmap-feedstock
A conda-smithy repository for r-d3heatmap.
r-dendextend-feedstock
A conda-smithy repository for r-dendextend.
r-digest-feedstock
A conda-smithy repository for r-digest.
rdkit
The official sources for the RDKit library
rdkit-feedstock
A conda-smithy repository for rdkit.
r-dosnow-feedstock
A conda-smithy repository for r-dosnow.
r-dplyr-feedstock
A conda-smithy repository for r-dplyr.
reago-1.1
null
registrator
Service registry bridge for Docker with pluggable adapters
r-emdbook-feedstock
A conda-smithy repository for r-emdbook.
r-feedstock
A conda-smithy repository for r.
r-fftwtools-feedstock
A conda-smithy repository for r-fftwtools.
r-fields-feedstock
A conda-smithy repository for r-fields.
r-fpc-feedstock
A conda-smithy repository for r-fpc.
r-future-feedstock
A conda-smithy repository for r-future.
r-gamlss-feedstock
A conda-smithy repository for r-gamlss.
r-geomap-feedstock
A conda-smithy repository for r-geomap.
r-getoptlong-feedstock
A conda-smithy repository for r-getoptlong.
r-ggally-feedstock
A conda-smithy repository for r-ggally.
r-ggbeeswarm-feedstock
A conda-smithy repository for r-ggbeeswarm.
r-gridextra-feedstock
A conda-smithy repository for r-gridextra.
r-hdrcde-feedstock
A conda-smithy repository for r-hdrcde.
r-htmlwidgets-feedstock
A conda-smithy repository for r-htmlwidgets.
r-jsonlite-feedstock
A conda-smithy repository for r-jsonlite.
r-klar-feedstock
A conda-smithy repository for r-klar.
r-lokern-feedstock
A conda-smithy repository for r-lokern.
r-lubridate-feedstock
A conda-smithy repository for r-lubridate.
r-markdown-feedstock
A conda-smithy repository for r-markdown.
r-matrix-feedstock
A conda-smithy repository for r-matrix.
r-mixtools-feedstock
A conda-smithy repository for r-mixtools.
r-modelr-feedstock
A conda-smithy repository for r-modelr.
RNAcommender
genome-wide recommendation of RNA-protein interactions
RNAlien
RNAlien - unsupervised model construction
r-nloptr-feedstock
A conda-smithy repository for r-nloptr.
ROCED
ROCED cloud scheduler
r-openssl-feedstock
A conda-smithy repository for r-openssl.
r-prabclus-feedstock
A conda-smithy repository for r-prabclus.
r-progress-feedstock
A conda-smithy repository for r-progress.
r-psych-feedstock
A conda-smithy repository for r-psych.
rpy2-feedstock
A conda-smithy repository for rpy2.
r-rainbow-feedstock
A conda-smithy repository for r-rainbow.
r-r.filesets-feedstock
A conda-smithy repository for r-r.filesets.
r-rfoc-feedstock
A conda-smithy repository for r-rfoc.
r-rgl-feedstock
A conda-smithy repository for r-rgl.
r-rmarkdown-feedstock
A conda-smithy repository for r-rmarkdown.
r-rmpfr-feedstock
A conda-smithy repository for r-rmpfr.
r-rmysql-feedstock
A conda-smithy repository for r-rmysql.
r-r.rsp-feedstock
A conda-smithy repository for r-r.rsp.
r-rseis-feedstock
A conda-smithy repository for r-rseis.
r-spdep-feedstock
A conda-smithy repository for r-spdep.
r-sqldf-feedstock
A conda-smithy repository for r-sqldf.
r-stanheaders-feedstock
A conda-smithy repository for r-stanheaders.
r-svdialogs-feedstock
A conda-smithy repository for r-svdialogs.
r-tidyverse-feedstock
A conda-smithy repository for r-tidyverse.
r-tsne-feedstock
A conda-smithy repository for r-tsne.
r-venndiagram-feedstock
A conda-smithy repository for r-venndiagram.
sailfish
Rapid Alignment-free Isoform Quantification from RNA-Seq Reads
searchgui
Graphical user interface for proteomics identification search engines
silicos-it_store
Storage for silicos-it tarballs
simplestyle-spec
A simple styling convention for GeoJSON data
singularity-galaxy-tests
Test files for singularity in Galaxy
SpliceVista
SpliceVista
staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
tcoffee
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
the-art-of-command-line
Master the command line, in one page
tool-bank-golm-lib_search
Tool using the Golm Library Search WS.
tools
collection of own scripts and tools
tools-artbio
Collection of galaxy tools developed by the artbio-platform at the IBPS (Institut de Biologie Paris-Seine)
tools-devteam
Repository encapsulating a set of Galaxy tools mostly written by the Galaxy Team.
tools-iuc
Tool Shed repositories maintained by the Intergalactic Utilities Commission
training_data
Small trainging data sets used by tours.
training-material
A collection of training material from offered Galaxy courses
Unicycler
hybrid assembly pipeline for bacterial genomes
vcflib-tools
A collection of Galaxy wrappers for vcflib utilities
vennt
Dynamic Venn diagrams for differential gene expression
viramp-project
null
Voronoia
Voronoia - Protein packing calculation
vt
A tool set for short variant discovery in genetic sequence data.
vue
? A progressive, incrementally-adoptable JavaScript framework for building UI on the web.
w4m-config
This repository contains the W4M tool list
where_does_my_trash_need_to_go
Trash sorting guide
XMLparser-wrapper
Create Galaxy/Pise wrapper from XML or StdOut (myprog --help), or just display options from wrapper...
yaml-pm
YAML Perl Module

Commits To

RepositoryMost Recent Commit# Commits
arq5x/bedtools-galaxy2014-01-10 17:17:38.09
galaxyproject/bioblend2016-09-23 12:20:49.02
modENCODE-DCC/Galaxy2014-11-12 23:04:33.013
galaxyproject/Galaxy-XSD2016-09-15 11:32:02.03
deeptools/deepTools2018-03-01 15:11:30.0355
peterjc/galaxy_blast2014-12-25 01:00:55.016
biopython/galaxy_packages2015-12-03 23:31:05.06
peterjc/pico_galaxy2015-10-10 11:40:29.04
iracooke/protk2015-05-23 14:43:29.015
bgruening/docker-recipes2017-05-31 19:55:59.0210
BioContainers/BioContainers.github.io2017-06-15 20:39:09.01
compomics/moFF2016-06-12 14:27:20.012
dpryan79/MethylDackel2015-06-28 11:45:31.01
erasche/argparse2tool2015-04-22 12:43:57.01
galaxyproject/docker-galaxy-requirements2016-10-29 18:17:02.08
galaxyproject/planemo-machine2016-06-15 17:45:12.024
bgruening/docker-galaxy-blast2017-06-04 16:21:04.038
galaxyproteomics/docker-galaxyp2017-12-09 12:02:54.061
galaxy-genome-annotation/docker-galaxy-genome-annotation2017-06-30 09:40:00.012
iracooke/proteomics-datatypes2015-06-20 09:17:20.07
shiltemann/galaxy-metagenomics2017-05-31 18:11:58.030
bgruening/galaxy-tricks2018-01-25 21:33:36.011
aidanbudd/bosc20152015-08-11 22:18:50.09
galaxyFlavorsGenerators/galaxyFlavorGenerator2015-10-23 11:34:42.02
bgruening/galaxy-maps2017-03-30 14:28:14.034
compomics/peptide-shaker2016-06-12 22:19:10.01
BioContainers/containers2017-10-10 16:45:42.01
bgruening/docker-galaxy-ngs-preprocessing2017-11-06 11:29:33.044
BioContainers/mulled2016-08-12 23:58:46.0132
galaxyproject/galaxy-tours2016-08-03 19:15:13.05
bgruening/galaxy_ie_helpers2018-03-06 18:12:06.07
torognes/inf93802016-04-30 20:53:28.07
galaxy-genome-annotation/galaxy-circos-tool2016-06-21 15:34:38.04
BMCV/galaxy-image-analysis2016-07-24 14:37:28.01
fraenkel-lab/galaxy-neurolincs2017-12-23 18:48:38.01
bgruening/galaxy-rna-seq2017-11-11 20:45:45.031
BackofenLab/docker-galaxy-graphclust2017-11-10 13:57:45.062
65MO/Galaxy-E2018-02-02 10:47:01.02
OpenGene/fastp2018-03-12 08:57:25.01
ISA-tools/bioconda-recipes2018-01-14 21:44:51.068

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.