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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development.
Proper citation: Stem Cell Commons (RRID:SCR_004415) Copy
https://deeptools.readthedocs.io/en/develop/
Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches.
Proper citation: Deeptools (RRID:SCR_016366) Copy
https://github.com/sblanck/smagexp
Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.
Proper citation: SMAGEXP (RRID:SCR_016360) Copy
http://bit.do/canidmeth-github
Software tool for visualisation and quantification of DNA methylation at candidate features.
Proper citation: CandiMeth (RRID:SCR_017974) Copy
Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP.
Proper citation: CLIP-Explorer (RRID:SCR_018128) Copy
https://nanopore.usegalaxy.eu/
Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.
Proper citation: NanoGalaxy (RRID:SCR_018912) Copy
https://github.com/howisonlab/softcite-dataset
Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.
Proper citation: SoftCite (RRID:SCR_024411) Copy
A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PIPE-CLIP (RRID:SCR_005820) Copy
http://www.cgat.org/~andreas/documentation/cgat/cgat.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3, 2023. A collection of tools for the computational genomicist written in the python language to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. Please note that the tools are part of a larger code base also including genomics and NGS pipelines. Everyone who uses parts of the CGAT code collection is encouraged to contribute. Contributions can take many forms: bugreports, bugfixes, new scripts and pipelines, documentation, tests, etc. All contributions are welcome.
Proper citation: Computational Genomics Analysis Tools (RRID:SCR_006390) Copy
https://github.com/anuprulez/galaxy_tool_recommendation
Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network.
Proper citation: Tool recommender system in Galaxy (RRID:SCR_018491) Copy
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