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Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
https://immunedb.readthedocs.io/en/latest/
Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.
Proper citation: ImmuneDB (RRID:SCR_017125) Copy
http://bioconductor.org/packages/CATALYST/
Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation.
Proper citation: CATALYST (RRID:SCR_017127) 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://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
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://github.com/theaidenlab/3d-dna.git
Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.
Proper citation: 3D de novo assembly (RRID:SCR_017227) 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
Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.
Proper citation: exRNA Atlas (RRID:SCR_017221) 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/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
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
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
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
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
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://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
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
http://bio3d.colorado.edu/SerialEM/
Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function.
Proper citation: SerialEM (RRID:SCR_017293) Copy
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