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https://sleepdata.org/datasets/shhs

Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light.

Proper citation: Sleep Heart Health Study (RRID:SCR_016559) Copy   

•   Source: SciCrunch Registry

https://github.com/xu-lab/SINCERA

Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis.

Proper citation: SINCERA Pipeline (RRID:SCR_016563) Copy   

•   Source: SciCrunch Registry

http://mib.helsinki.fi/

Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.

Proper citation: Microscopy Image Browser (RRID:SCR_016560) Copy   

•   Source: SciCrunch Registry

http://www2.chemie.uni-erlangen.de/software/cactvs/

Computational chemistry related-software used for the computation management, analysis and visualisation of chemical information of any defined type. This software uses a worldwide network of databases with property descriptions, computational modules, data analysis tools, visualization servers, data type handlers and I/O modules to increase the software�s capacity extensibility.

Proper citation: CACTVS System (RRID:SCR_014919) Copy   

•   Source: SciCrunch Registry

http://niag.ir/

Project to house templates used to build other projects. It is also known as the NeuroImaging and Analysis Group, which employs various physiological, functional and structural neuroimaging methodologies in both research and clinical domains.

Proper citation: Template Project (RRID:SCR_015516) Copy   

•   Source: SciCrunch Registry

http://shiny.chemgrid.org/boxplotr/

Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.

Proper citation: BoxPlotR (RRID:SCR_015629) Copy   

•   Source: SciCrunch Registry

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   

•   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://bioservices.uncc.edu

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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/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   

•   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://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://www.agilent.com/cs/library/usermanuals/Public/G2505-90019_ScannerC_User.pdf

Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays.

Proper citation: Agilent: G2565CA Microarray Scanner (RRID:SCR_017206) 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

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   

•   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