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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.
Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility.
Proper citation: Experimental Design Assistant (RRID:SCR_017019) Copy
Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way.
Proper citation: LION/web (RRID:SCR_017018) Copy
Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows.
Proper citation: Anima (RRID:SCR_017017) Copy
http://bioconductor.org/packages/gage/
Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.
Proper citation: GAGE (RRID:SCR_017067) Copy
https://www.scanco.ch/microct100.html
Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.
Proper citation: Scanco: Medical microCT 100 system (RRID:SCR_017119) Copy
Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts.
Proper citation: Empenn (RRID:SCR_017074) Copy
https://github.com/llawas/Rice_HxD_Metabolomics
Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress.
Proper citation: Source code for analysis of GC-MS data - Rice HxD Project (RRID:SCR_017073) Copy
https://github.com/Inria-Visages/Anima-Scripts-Public
Open source scripts for medical image processing. Provides set of scripts in Python shell. These scripts use essentially tools from Anima to perform more complex series like image preprocessing, model estimation, atlas creation.
Proper citation: Anima scripts (RRID:SCR_017072) Copy
https://github.com/nolanlab/VORTEX
Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids.
Proper citation: VORTEX (RRID:SCR_017047) Copy
https://github.com/dodomorandi/hatspil
Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability.
Proper citation: HaTSPiL (RRID:SCR_017059) Copy
https://github.com/Frederik-D-Weber/cosleep
Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.
Proper citation: COsleep (RRID:SCR_017053) Copy
http://bioconductor.org/packages/release/data/experiment/html/affydata.html
Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.
Proper citation: affydata (RRID:SCR_016976) Copy
https://www.ccpn.ac.uk/v2-software/software/analysis
Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix.
Proper citation: CCPN Analysis (RRID:SCR_016984) Copy
Issue
https://biit.cs.ut.ee/clustvis/
Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps.
Proper citation: ClustVis (RRID:SCR_017133) 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
Core to assist with analyzing and interpreting data produced by genomic technologies.
Proper citation: University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) Copy
https://www.cityofhope.org/research/shared-resources/integrative-genomics-and-bioinformatics
Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators.
Proper citation: City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility (RRID:SCR_017188) Copy
https://www.hsph.harvard.edu/hmac/
Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations.
Proper citation: Harvard School of Public Health Microbiome Analysis Core Facility (RRID:SCR_017187) Copy
https://github.com/ZSI-Bio/bdg-sequila
Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals.
Proper citation: SeQuiLa (RRID:SCR_017220) Copy
https://github.com/csbbcompbio/CSBB-v3.0
Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments.
Proper citation: Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) Copy
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