Use Galaxy

A Galaxy suite for tArgeted MEtagenomics

FROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels.

Analysis and bioinformatics for Marine Science.

This site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance.

Human Communication Science (HCS).

Set up you own general purpose genomics server running AWS using GVL and CloudMan.

A Galaxy-based metagenomics pipeline that is intuitive and easy to use.

Automated Nucleotide Aminoacid Sequences Translational plAtform for Systemic Interpretation and Analysis

Automate the analysis and visual reporting of T- and B-cell receptor repertoire sequencing data.

Run Galaxy inside the secure AnVIL environment on Google Cloud Platform.

Automated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data.

Antibiotic Resistance Gene Analyzer

Fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data.

Automated NOE assignment and NMR structure calculation

Analysis of genomic data in the field of public health and food safety, with the aim of deploying a comprehensive bioinformatics approach to the study of food-borne zoonoses and infectious diseases at the human and animal interface.

Integrates tools specifically chosen for metagenomic and metatranscriptomic studies and hierarchically organized to orient user choice toward the best tool for a given task.

ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility

Locally developed as well as standard tools are available on a 16-core server with 32GB memory, accessible to all users, and located in the BF2I lab.

A general genomics server. Includes the PROTEOFORMER pipeline tools.

Systems biology tools implemented by the Sybila team.

Taxonomic studies of environmental microbial communities

A general purpose Galaxy instance that includes most standard tools for DNA/RNA sequencing, plus extra tools for panel resequencing, variant annotation and some tools for Illumina SNParray analysis.

Detailed analysis of metagenomes.

Prepare, simulate and analyse and visualise molecular simulations, especially molecular dynamics and free energies.

A Galaxy framework for exploring unmapped RNA-Seq data

A general purpose Galaxy instance that includes EMBOSS (a software analysis package for molecular biology) and fibronectin (diversity analysis of synthetic libraries of a Fibronectin domain).

Create generative models of the spatial organization of cells from microscope images and automatically provide geometries for spatial simulations of cell processes and behaviors

Phage biology and automated annotation.

Chemometrics without programming: infrared spectrometry on a Galaxy platform.

Retrieves annotations on biological effects of chemicals and determines which ones are enriched.

For processing, analysing and visualising chemical data, and performing molecular simulations.

Fusion gene discovery from transcriptome-sequencing (RNA-seq) datasets.

ChIP-chip/seq and gene expression data

A comprehensive set of analysis tools and consolidated workflows for climate analysis and visualisation

The CLIMB project (Cloud Infrastructure for Microbial Bioinformatics) develops and deploys a world leading cyber-infrastructure for microbial bioinformatics; providing free cloud-based compute, storage, and analysis tools for academic microbiologists in the UK.

The CLIP-Explorer is a webserver to process, analyse and visualise CLIP-Seq data.

Easily generate codon harmonized variants of gene sequences for heterologous expression

a unified web interface to perform co-localization analysis of genomic features

A modular, easy to install application that provides a web based environment for Mycobacterium tuberculosis bioinformatics

Standard Tools for Acroporid Genotyping (STAG)

Align complete assemblies of SARS-CoV-2 genomes wih the reference genomic sequence, to obtain a list of polymorphic positions and to annotate genetic variants.

A companion to our study describing the analysis of early COVID-19 data

Provides numerous workflows for COVID-19 analysis.

A Docker image containing a fully-operational Galaxy instance with pre-installed demonstration material for CRAVAT-P.

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

Annotates raw sequencing reads from next-generation sequencers(NGS) with high throughput, which are registered in DDBJ Read Archive (DRA).

deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments.

Explore transcriptional switches from pairwise, temporal, and population RNA-Seq using deepTS.

GWA and NGS tools and modules for functional annotation of genes and gene products

Galaxy Docker for DNA methylation analysis in WGBS

Galaxy instances on a European wide federation of research cloud providers.

Compare user-provided epigenomic datasets with thousands of public datasets.

Galaxy Docker image for epigenomics analysis

Computational immunology for the development of novel epitope-based vaccines.

General purpose genomics analysis, featuring many standard tools plus many additional tools.

Galaxy Docker image for population epigenetics data analysis

Galaxy for metagenomic analysis.

G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders.

Integrative 'omics data analysis

Devoted to assisting researchers on the African continent accelerate their genomics research and analyses.

Galaxy Docker repository for basic sequence data analysis.

A complete and production ready Galaxy instance with installed BLAST+ tools.

Galaxy Docker image for ChipSeq analysis

Galaxy instance with tools for Constructive Solid Geometry shipped in a Docker container.

The Galaxy Docker Image is an easily distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features.

Galaxy Docker repository for Exome sequencing data analysis

A web platform to get, process, analyze and visualize ecological data

Galaxy for genome annotation

Galaxy Docker repository for image analysis

This is the Indian galaxy server, Welcome Home!

Proteomics Informed by Transcriptomics (PIT) methodology, and selection of surrogate peptides for targeted proteomics.

This is a standard Galaxy instance implemented with specific tools for Biodiversity (Biodiversity Virtual Lab) and NGS (Ion Torrent from the PGTB facility) analysis.

Beta version of Galaxy Main

Galaxy Docker image for mass spec imaging

Galaxy-CEFAP offers a set of tools to perform RNA-Seq and miRNA analysis.

Gene Set Analysis tools

Synthetic biology and metabolic engineering

General purpose genomics analysis server.

General purpose genomics analysis server.

Includes bioinformatics tools developed by the research teams working in the perimeter of the PRABI core facility, including kissplice/kissDE, TETools, SEX-DETector, and priam.

Standard and custom-built bioinformatics tools with special focus on ChIP-Seq, RNA-Seq, single-cell RNA-Seq, Gene Expression and Cancer Genomics (e.g. TCGA).

Supporting food-borne pathogen research

Supports PIPE-T, a tool for Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis.

GCAC is a web enabled platform for predictive model building using R and caret package for virtual screening.

NASA GeneLab is a comprehensive space-related omics database in which users can upload, download, share, store, and analyze spaceflight and corresponding model organism data.

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

Globus Genomics provides hardened high-performance Galaxy servers running with Globus on AWS.

GrAPPA is a web-based interface constructed on the Galaxy framework for graph theoretical tools. It contains novel combinatorial methods integrated into a complete microarray analysis toolchain, from uploading raw high-throughput data to visualization of results.

Visualize halogen bond contacts in the protein binding site. Analyze a protein binding site for halogen bonding hotspots. Evaluate halogen contacts with the protein backbone using the scoring function XBScore.

A simplified, workflow-centic interface to Galaxy, focused on genomics data from hardwood trees.

Tools to process and visualize chromosome conformation.

A general purpose genomics server

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

Tools for HIV sequencing analysis.

Software, tools and pages written by IBERS researchers for release to the wider community.

Inter-Domain Ecological Network Analysis Pipeline

Image analysis and processing.

Flow Cytometry Analysis.

Machine learning-based analysis and classification of adaptive immune receptors and repertoires (AIRR).

Provides a set of tools for easy detection and quantitation of immunoglobulin heavy chain alternative transcripts.

Construction, analysis, and visualization of gene-gene interaction networks for sequencing data.

A one-stop resource offering a wide range of computational analyses from proteome-wide interactomes to structure of protein complexes

Part of the IPK Crop Analysis Tools Suite (CATS). Offers access to genomic references published by IPK and collaborative projects

Immune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data.

Tool suite uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay.

Web based access to tools created by the Koslicki Lab at Oregon State University.

Kinetic Re-Epithelialization Analysis Pipeline

Prediction of the unobserved character states in a community of organisms from phylogenetic information.

Web interface to a centralized repository of a wide range of language technology tools, all installed on a high-performance computing (HPC) cluster.

Laniakea provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians, with built-in storage encryption for user data.

An open, interoperable web service platform for natural language processing (NLP) research and development.

Includes the SpCLUST tool set for fast and reliable clustering of potentially divergent biological sequences

a Galaxy instance to satisfy the computational needs of the Norwegian research community in life sciences but also of any other user willing to use the service.

A platform for Virtual Screening.

A comprehensive set of data preprocessing, machine learning, deep learning and visualisation tools, consolidated workflows for end-to-end machine learning analysis and training materials to showcase the usage of these tools.

Detection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data.

Metabolic Reaction Enrichment Analysis and visualization of RNA-seq data

Simplifying control, usage, access, and analysis of microbiome, metabolome, and immunome data (the Metabiome).

A community driven metabolomics Galaxy service

a webserver to process, analyse and visualize Metagenomic and Microbiota data in general.

Metaproteomics gateway providing access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows

Identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences.

Shotgun whole-genome metagenomic analysis using DNA-DNA alignment

Leverage cloud technologies to provide an easy-to-use streamlined NGS data analysis using local computational hardware

A general purpose genomics server with an emphasis on metagenomics, including FROGS and several Migale developed tools.

NacreousMap mapping/plotting tool of MiModD for users of MiModD who do not want to install the required dependencies (R and rpy2) for graphical output from this tool on their local system.

NGS data analysis focusing on microRNAs and their sequence variants—isomiRs.

Support for analyses of RNA and small RNA sequencing datasets as well as for epigenetics or metagenomics studies.

A disease-specific open source web portal for Diabetes Mellitus.

A disease-specific web portal for Tuberculosis for drug discovery and development.

Hosts the MIRPIPE, ADMIRE, and LimiTT tools

a webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies.

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

Set up a Galaxy server on Australia's Nectar research cloud.

Plataforma de servicios para análisis de datos biomédicos en bioinformática featuring standard Galaxy Tools

Life Science platform for Norwegian academic researchers.

For mapping and quantification of raw RNA-seq data

A Semantic Framework for High-throughput Marker Gene (Amplicon) Analysis

Robust phylogenetic analysis for everyone.

Human Communication Science (HCS).

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

Drug discovery

Phylogenetics

Microsatellite development.

Integrated workflow tool for mapping of massive peptide repertoires on whole proteomes and delivering streamlined, systems-level biological interpretation.

Predict promoter sequences in phage genomes, using machine learning models.

Large scale computing for medical informatics

Phylogenetics and gene interaction

Reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP.

Detect, classify and annotate TEs of non-model organisms.

A community driven plant data analsys Galaxy service

Plant Genome Integrative Explorer Galaxy instance

Predicting Specific Tissue Interactions of Genes and Enhancers

Provides access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized proteogenomics workflows. The main goal of this server is to provide documentation to facilitate training and mastery of these software and workflows.

ProteoRE (Proteomics Research Environment)

All-in-one genome description tool, aimed at simplifying gathering the data required for writing protologues. This includes providing taxonomic, functional and ecological insights.

QIIME 2 Galaxy Docker image.

Hosts custom tools developed by members of the Quantitative Biomedical Research Center @ University of Texas Southwestern for statistical analysis of various High Throughput Sequencing experiments.

A Docker image containing a fully-operational Galaxy instance with pre-installed QuanTP tools.

RDF2Graph recovers the structure of an RDF resource.

Graph-based clustering and characterization of repetitive sequences, and detection of transposable element protein coding domains.

Tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique.

Tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice−bacterial pathogen diagnostics, and a suite of published genomic prediction methods.

Galaxy Docker image for RNA analysis and modification calling

more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction.

Supports comparative analysis of host response to pathogens. It provides an RNA-Seq pipeline to characterize the transcriptome of all NIAID Bioinformatic Resource Center (BRC) pathogens and their key hosts.

RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure.

Galaxy Docker image for submitting SARS-CoV-2 data to ENA

Galaxy server for microbiological genomics applications with a focus on public health.

A user-friendly website for metataxonomic analysis from raw reads to statistical analysis

RNA structure and design tools including RNA2D3D and StructureLab

Specificity Inference For TAL-Effector Design (SIFTED)

The Single Cell Omics workbench is a comprehensive set of analysis tools and consolidated workflows

SMAGEXP (Statistical Meta-Analysis for Gene EXPression) provides a unified way to carry out meta-analysis of gene expression data, while taking care of their specificities.

A national-scale cloud infrastructure for Swedish Academia

Genomic resource analysis of southern and Mediterranean plants.

Prediction of neuronal maturation using splicing profiles

Database of curated cancer stem cell experiments coupled to Galaxy.

a Galaxy dedicated for the Street Science Community

Running reproducible Galaxy instances in a secure multicloud environment for Dutch scientists.

a platform for detecting internally symmetric protein structures

Run Galaxy inside the Terra cloud platform.

The TGM pipeline is a workflow combining tranSMART server, Galaxy Server and MINERVA platform to enable visually-aided exploration, analysis and interpretation of high-throughput translational medicine data.

The Trinity CTAT Galaxy provides users with access to large memory resources required for de novo transcriptome assembly and downstream analysis.

General purpose genomics Galaxy server

General purpose Galaxy server

The free public European Galaxy server

General purpose genomics Galaxy server

A central, joint & free Galaxy instance for Norway-based researchers and their collaborators, with ~2000 bioinformatics tools, 200GB short-term storage and project storage on nels.bioinfo.no.

The Australian UseGalaxy server.

This Galaxy implementation is meant to demonstrate integration of microbial domain Biological Resource Center (mBRC) catalogues into the bioinformatics data integration environment.

Reliable prediction of different types of variants even at low frequencies.

A free, interactive, web-based platform for large-scale data analysis focused on eukaryotic pathogens. Merges the former VectorBase and EuPathDB servers.

RNA structure-probing data analysis to improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated.

A flexible and fully automated system for the functional annotation and prioritization of genetic variants.

Determine the composition of a viral population

VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data.

A comprehensive set of analysis tools and consolidated workflows for virology work, including SARS-CoV-2.

Includes microarray tools, the MUMmer suite, and many conversion tools. Strong focus on multi-omics: next to genomics tools it also contains proteomics and metabolomics tools

A collaborative portal dedicated to metabolomics data processing, analysis and annotation.

QAP is an open source software that can be used to analyze virus quasispecies using CBS, NGS and TGS data. wQAP (web QAP), is the online version of QAP.