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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.
http://bioconductor.org/packages/release/bioc/html/MetaCyto.html
Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.
Proper citation: MetaCyto (RRID:SCR_016415) Copy
https://github.com/MRCIEU/PhenoSpD
Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool.
Proper citation: PhenoSpD (RRID:SCR_016359) 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
https://github.com/mikessh/migec
Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires.
Proper citation: migec (RRID:SCR_016337) Copy
http://www.nitrc.org/projects/mica/
Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.
Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy
https://www.mousephenotype.org/imits/
This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products.
Proper citation: iMITS (RRID:SCR_016552) Copy
Software analysis tools for electrophysiological somatosensory cortex databank. Allows to estimate the information content of spiking in single neuron resolution. It accompanies the open source intracellular recording database by Lantyer and colleagues.
Proper citation: Frozen Noise (RRID:SCR_016558) Copy
Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.
Proper citation: CajaDB (RRID:SCR_016506) Copy
http://www.flywings.org.uk/morphoj_page.htm
Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data.
Proper citation: MorphoJ (RRID:SCR_016483) Copy
Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
Proper citation: cisTEM (RRID:SCR_016502) Copy
Portal to discover COVID-19 open research data on Figshare. Figshare collection of COVID-19 related research data.
Proper citation: COVID-19 research data on Figshare (RRID:SCR_018277) Copy
Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19.
Proper citation: outbreak.info (RRID:SCR_018282) Copy
https://discourse.data-against-covid.org/t/list-of-pis-supporting-this-endeavour/124
Group of volunteer data scientists, machines learning experts, bioinformaticians and professional software developers who have joined together to offer their expertise for any data analysis problems that arise in context of ongoing coronavirus pandemic.
Proper citation: Data-Against-COVID Team (RRID:SCR_018288) Copy
https://timothyspringer.org/files/tas/files/biacore3000-instrument.pdf
Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants.
Proper citation: GE: Biacore 3000 Real Time Biomolecular Interaction Analyzer (RRID:SCR_018044) Copy
Cloud resources for COVID-19 research provided by Rescale, Google Cloud, and Microsoft Azure. High performance computing resources immediately available for COVID-19 research.
Proper citation: Cloud resources for COVID-19 research (RRID:SCR_018286) Copy
http://www.milesculabs.org/QuB.html
Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: QuB (RRID:SCR_018076) Copy
Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials.
Proper citation: Vivli (RRID:SCR_018080) Copy
http://www.imperial.ac.uk/research/animallectins
Resource presents information about animal lectins involved in various sugar recognition processes.
Proper citation: genomics resource for animal lectins (RRID:SCR_018122) Copy
https://bioportal.bioontology.org/ontologies/PCL/
Collection of ontology of provisional cells determined by experimental methods.
Proper citation: Provisional Cell Ontology (RRID:SCR_018332) Copy
Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.
Proper citation: EpiModel (RRID:SCR_018539) Copy
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