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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://t1dexchange.org/research/biobank/

Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes.

Proper citation: T1D Exchange Biobank (RRID:SCR_017195) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/greenhouselab/Veta

Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS.

Proper citation: VETA (RRID:SCR_017201) Copy   

•   Source: SciCrunch Registry

https://github.com/llawas/Rice_HxD_Recovery_Metabolomics

Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress.

Proper citation: Rice_HxD_Recovery_Metabolomics (RRID:SCR_017204) Copy   

•   Source: SciCrunch Registry

https://www.plantsci.cam.ac.uk/bioinformatics

Core provides assistance in data analysis to support members of Plant Sciences.

Proper citation: University of Cambridge Department of Plant Sciences Bioinformatics Core Facility (RRID:SCR_017164) Copy   

•   Source: SciCrunch Registry

https://labs.gladstone.org/bioinformatics/index.html

Core provides consulting services, sequencing, data analysis, and programming assistance. Used for Experimental Design and Power Analysis Consultation, RNA-seq, ChIP-seq, ATAC-seq analysis, Statistics consulting, Variant calling, Data normalization across multiple projects, General programming, Custom Figures for publication, tutorials for learning common software tools.

Proper citation: UCSF Gladstone Institutes Bioinformatics Core Facility (RRID:SCR_017178) Copy   

•   Source: SciCrunch Registry

https://bonsai-rx.org/

Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world.

Proper citation: Bonsai (RRID:SCR_017218) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://en.vhir.org/portal1/article_menu_serveis.asp?s=serveis&contenttypeid=43&contentid=1250&t=Presentation

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://ous-research.no/bioinformatics/

Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services.

Proper citation: Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) Copy   

•   Source: SciCrunch Registry

https://usegalaxy.eu

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   

•   Source: SciCrunch Registry

http://rtools.cbrc.jp/centroidfold/

Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator.

Proper citation: CentroidFold (RRID:SCR_017253) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://mpd.bioinf.uni-sb.de/

Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are.

Proper citation: miRpathDB (RRID:SCR_017356) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/github/LTLA/batchelor/man/fastMNN.html

Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method.

Proper citation: fastMNN (RRID:SCR_017351) Copy   

•   Source: SciCrunch Registry