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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.
https://github.com/aidenlab/juicer.git
Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.
Proper citation: Juicer (RRID:SCR_017226) Copy
https://github.com/anaphaze/ot-tools
Software tools for analysis of cellular cryo-ET data.
Proper citation: ot-tools (RRID:SCR_017191) Copy
http://www.igc.gulbenkian.pt/facilities/bioinformatics
IGC Core in Oeiras, Portugal, promotes use of computational methods in biological research, through training and development of resources and materials, supports biological data analysis using computational methods, conducts research and development in bioinformatics, in particular in data flows, data warehousing and data analyses.
Proper citation: Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility (RRID:SCR_017190) Copy
Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.
Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy
Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs.
Proper citation: BSA4Yeast (RRID:SCR_017113) Copy
https://www.ed.ac.uk/igmm/facilities/bioinformatics-analysis-core
Core provides advice, training, provision of computational tools and collaborative expertise to all IGMM researchers.
Proper citation: University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility (RRID:SCR_017194) Copy
https://www.a-star.edu.sg/gis/Our-Science/Technology-Platforms/Scientific-and-Research-Computing
Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers.
Proper citation: Genome Institute of Singapore Scientific and Research Computing Core Facility (RRID:SCR_017193) Copy
https://www.trophoblast.cam.ac.uk/Resources/BioInformatics
Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training.
Proper citation: University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) Copy
https://github.com/tseemann/shovill
Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.
Proper citation: shovill (RRID:SCR_017077) Copy
https://inutano.github.io/cwl-metrics/
Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux.
Proper citation: cwl-metrics (RRID:SCR_017076) Copy
Provides assistance in computing, nanotechnology, and biological fields. Provides scientific support and resources to the UMA research groups, public institutions and private companies.
Proper citation: University of Malaga Andalusian Platform of Bioinformatics Core Facility (RRID:SCR_017169) Copy
http://mayoresearch.mayo.edu/mayo/research/biostat/index.cfm
Core assists in genomics, proteomics and metabolomics data acquisition, management, analyses and interpretation to Mayo investigators. Participates in Basic science research, Clinical trials, Population health, and Translational science to execute analytical workflows and manage large omics data sets. Provides support to Mayo Clinic Center for Individualized Medicine and Mayo Clinic Cancer Center. Has its academic home in Department of Health Sciences Research within Division of Biomedical Statistics and Informatics.
Proper citation: Mayo Clinic Rochehster Bioinformatics Core Facility (RRID:SCR_017161) Copy
https://www.ie-freiburg.mpg.de/bioinformaticsfac
Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing.
Proper citation: Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility (RRID:SCR_017160) Copy
https://medicine.umich.edu/dept/dcmb/center-computational-medicine-bioinformatics
University interdisciplinary academic center for bioinformatics, biomedical data science, and translational precision health informatics. Core provides training programs.
Proper citation: University of Michigan School of Medicine Center of Computational Medicine and Bioinformatics Core Facility (RRID:SCR_017179) Copy
https://www.ibm.com/us-en/marketplace/marketscan-research-databases
Software suite of proprietary databases that contain one of longest running and largest collection of privately and publicly insured, de identified patient data in USA. Family of data sets that fully integrate many types of data for healthcare research.
Proper citation: IBM® MarketScan® Research Databases (RRID:SCR_017212) Copy
https://www.beckman.it/flow-cytometry/research-flow-cytometers/cytoflex/software
Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter.
Proper citation: CytExpert Software (RRID:SCR_017217) Copy
https://github.com/EpistasisLab/pennai
Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems.
Proper citation: PennAI (RRID:SCR_017215) Copy
https://www.medsci.ox.ac.uk/research/labtalk/labtalk
Core provides genomics training, as well as assistance in next generation sequencing analyses.
Proper citation: University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility (RRID:SCR_017173) Copy
https://ircm.qc.ca/en/technological-services/bioinformatics
Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses.
Proper citation: Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) Copy
https://biocore.crg.eu/wiki/Main_Page
Provides services of consultation and data analysis, with focus on Next Generation Sequencing and other high throughput experiments, software and database development, and training in basic and advanced bioinformatics techniques. Services provided for fee to support collaborative grant funded investigations.
Proper citation: Centre for Genome Regulation Bioinformatics Core Facility (RRID:SCR_017145) Copy
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