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http://www.scbi.uma.es/site/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.beckman.fr/flow-cytometry/instruments/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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/epistasislab/hibachi

Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods.

Proper citation: Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) Copy   

•   Source: SciCrunch Registry

https://github.com/aldenleung/OMTools

Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.

Proper citation: OMTools (RRID:SCR_017143) Copy   

•   Source: SciCrunch Registry

https://github.com/dgrun/FateID

Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations.

Proper citation: FateID (RRID:SCR_017244) Copy   

•   Source: SciCrunch Registry

https://github.com/jefferis/nat

Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons.

Proper citation: NeuroAnatomy Toolbox (RRID:SCR_017248) Copy   

•   Source: SciCrunch Registry

https://github.com/powellgenomicslab/ascend

Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.

Proper citation: ascend (RRID:SCR_017257) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vini/

Software Python tool as viewer for MRI data and numpy arrays.

Proper citation: vini: A viewer for fMRI data (RRID:SCR_017250) Copy   

•   Source: SciCrunch Registry

http://www.iqtree.org/

Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference.

Proper citation: IQ-TREE (RRID:SCR_017254) Copy   

•   Source: SciCrunch Registry

http://trackvis.org/dtk/

Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography.

Proper citation: Diffusion Toolkit (RRID:SCR_017345) Copy   

•   Source: SciCrunch Registry

http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

https://ccb-web.cs.uni-saarland.de/tissueatlas

Human miRNA tissue atlas. Database showing distribution of miRNA expression across human tissues.

Proper citation: TissueAtlas (RRID:SCR_017352) Copy   

•   Source: SciCrunch Registry