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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://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Predict1/Predict1.html
Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program.
Proper citation: RNAstructure (RRID:SCR_017216) Copy
https://www.bmh.manchester.ac.uk/research/facilities/bioinformatics/
Core provides assistance in integrative analysis of genomic datasets to support faculty.
Proper citation: University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) Copy
http://kim.bio.upenn.edu/software/pivot.shtml
Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows.
Proper citation: PIVOT software (RRID:SCR_017210) Copy
Core at Vall dHebron Institut de Recerca, Barcelona, Spain to provide data analysis, softwares and training programs in statistics and bioinformatics for clinical research at VHIR.
Proper citation: Vall dHebron Institut de Recerca Statistics and Bioinformatics Unit Core Facility (RRID:SCR_017175) Copy
https://genome.duke.edu/cores-and-services/genomic-analysis-and-bioinformatics
Genomic Analysis and Bioinformatics core for data analysis associated with performing complex and data intensive projects in life science research of Duke University and Duke Medical School. Provides expertise, training, data analysis in next generation sequencing, array and proteomic based technologies.
Proper citation: Duke University Omics Data Analysis Core Facility (RRID:SCR_017174) Copy
https://github.com/raamana/neuropredict
Software tool for assessment of predictive power, with support for neuroimaging features. Easy machine learning and standardized predictive analysis of biomarkers.
Proper citation: neuropredict (RRID:SCR_017405) Copy
https://www.liebertpub.com/doi/pdf/10.1089/15279160150518540
Software package for statistical analysis by SAS Institute Inc, Cary, NC.
Proper citation: StatView Version 5.0 (RRID:SCR_017411) Copy
Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging.
Proper citation: Mass spectrometry imaging workbench (RRID:SCR_017410) Copy
http://www.bio-rad.com/en-eh/product/cfx-manager-software
Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CFX Manager (RRID:SCR_017251) Copy
https://CRAN.R-project.org/package=ape
Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R.
Proper citation: ape (RRID:SCR_017343) Copy
https://github.com/zuoxinian/CCS
Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.
Proper citation: Connectome Computation System (RRID:SCR_017342) Copy
https://CRAN.R-project.org/package=macc
Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method.
Proper citation: Mediation Analysis of Causality under Confounding (RRID:SCR_017442) Copy
https://github.com/biocore/redbiom
Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data.
Proper citation: redbiom (RRID:SCR_017285) Copy
https://github.com/Mark-Kramer/Seizure-Waves
Analysis and modeling code for waves of seizure activity.
Proper citation: Seizure-Waves (RRID:SCR_017455) Copy
Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats.
Proper citation: PILER (RRID:SCR_017333) Copy
Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu .
Proper citation: Excel Statistics (RRID:SCR_017294) Copy
http://140.120.197.173/Ecology/prod02.htm
Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan.
Proper citation: TWOSEX-MSChart (RRID:SCR_017298) Copy
Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.
Proper citation: SynGO (RRID:SCR_017330) Copy
https://cran.r-project.org/web/packages/phangorn/index.html
Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.
Proper citation: Phangorn (RRID:SCR_017302) Copy
https://beast.community/tempest
Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019.
Proper citation: TempEst (RRID:SCR_017304) Copy
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