Campus IFOM IEO

Includes CARPET - Collection of Automated Routine Programs for Easy Tiling

Campus IFOM-IEO

Cistrome Analysis Pipeline

ChIP-chip/seq and gene expression data

The Cistrome Analysis Pipeline has the standard Galaxy tools, plus 29 additional ChIP-chip and ChIP-seq specific tools, including preliminary peak calling and correlation analyses, downstream genome feature association, gene expression analyses, and motif discovery.

Requires login, anyone can create a login.

Cistrome

DBCLS Galaxy

Adds text mining tools, DBCLS DBSearch Tools, semantic web tools

Can be used without understanding Japanese

Database Center for Life Science

Galaxy Main

Biomedical research

Strong on genomics; good central repository for shared Galaxy objects.

Storage and computational quotas

Galaxy Project

Galaxy Test

Beta version of Galaxy Main

Not stable or persistent

Storage and computational quotas

Galaxy Project

GeneNetwork Galaxy Mirror

Mirrors Galaxy Main

University of Tennessee Center for Integrative and Translational Genomics

Genboree

Has several Genboree specific additions.

Bioinformatics Research Laboratory at Baylor College of Medicine

Genomic Hyperborwser

"statistical methodology and computing power to handle a variety of biological inquires on genomic datasets"

Norwegian Functional Genomics Program

Gene Ontololgy (GO)

The Gene Ontology's Galaxy installation.

A Galaxy install tailored for manipulating ontologies. Includes OBO, OWL, Pellet and other annotation manipulation tools.

Gene Ontology Project

Hannon Lab

Offers several tools published by the Hannon Laboratory for cross-tabulation, column normalization, as well as several Unix Tools

Hannon Lab

Huttenhower Lab

"metagenomic and functional genomic analyses, intended for research and academic use"

Implements "LDA Effect Size (LEfSe) (Segata et. al 2011), an algorithm for high-dimensional biomarker discovery and explanation that identifies genomic features (genes, pathways, or taxa) characterizing the differences between two or more biological conditions"

Huttenhower Lab

INRA-URGI

Offers S-MART conversion and MAPHiTS tools.

"Mapping Analysis Pipeline for High-Throughput Sequences" (MAPHiTS). "The pipeline allows the detection of single nucleotide polymorphisms (SNPs) and small insertion/deletions (indels) by comparing high-throughput Illumina short-reads (GAIIx or HighSeq) with a reference sequence from the same or a different species. This pipeline is based on public softwares (BWA, Bowtie, SAMtools, VarScan and Tablet) and homemade tools. In particular, we developed tools to filter out short-reads of low quality and to prepare the mapping and SNP calling. We also developed tools to filter out the called SNPs according to genome coverage, allele frequency, pValue, and SNP positions in the read."

INRA URGI

MGTAXA

Prediction of metagenomic taxonomy

Provides a flexible interface to the tools the MGTAXA team have developed for the prediction of metagenomic taxonomy.  Server also exposes some of the standard Galaxy tools that can be useful in the context of the MGTAXA project. 

JCVI

Nebula

"allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data."

"Nebula is a web service provided by Institut Curie."

Institut Curie

Netherlands Metabolomics Centre

Metabolomics

Include MTSiP package

Netherlands Metabolimics Centre

Oqtans

Customized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis.

Machine Learning in Biology (MLB) Group at the Friedrich Miescher Laboratory of the Max Planck Society

Regulatory Genomics Galaxy

Regulatory genomics, including the Pyicos package. Chip/clip/rna seq data analysis.

"This Galaxy instance is on a TESTING phase and contains experimental software. Use at your own risk" A paper and the source are also available.

Regulatory Genomics Group @ Pompeu Fabra University

Sombrero

NBIC's development Galaxy server

Beware that your data may vanish without notice

Netherlands Bioinformatics Centre (NBIC)

Stem Cell Discovery Engine (SCDE)

Database of curated cancer stem cell experiments coupled to Galaxy.

Includes tools for stem cell gene list comparisons. From the web site:
→ Compare your genes to curated experiments from the SCDE Bioinvestigation Index
→ Compare your uploaded list (SCDE ListMatch) or multiple lists (SCDE ListCompare) against curated gene signatures from the GeneSigDB and mSigDB databases
→ Compare your genes against pathways in WikiPathways, and show the overlap on a pathway diagram

Hide Lab @ Harvard School of Public Health, Harvard Stem Cell Institute.

SymD

"SymD is a tool for detecting internally symmetric protein structures."

US National Cancer Institute (NCI)

Wageningen University Galaxy

Includes microarray tools, the MUMmer suite, and many conversion tools.

Part of the Plant Research International ChIP-seq Analysis Tool (PRI-CAT)

Requires login, anyone can create a login.

Wageningen University