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https://github.com/mzlab-research/SMIntegration

Software open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Enables to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression.

Proper citation: SMIntegration (RRID:SCR_027925) Copy   

•   Source: SciCrunch Registry

https://github.com/janclemenslab/glm_utils

Software tools for fitting Generalized Linear Models (GLMs) with time dependence (a.k.a. filters).

Proper citation: GLM utilities (RRID:SCR_027862) Copy   

•   Source: SciCrunch Registry

https://github.com/micom-dev/micom

Software Python package to study microbial communities using metabolic modeling. Metagenome-scale modeling to infer metabolic interactions in the gut microbiota.

Proper citation: micom (RRID:SCR_027982) Copy   

•   Source: SciCrunch Registry

https://mic.massgeneralbrigham.org

Core facility that provides microscopy training, imaging solutions, image processing and analysis services, and consultation. Offers imaging techniques and expertise, including spinning disc confocal microscopy, two-photon confocal microscopy, super resolution microscopy, total internal reflection microscopy, wide field microscopy, fluorescence spectroscopy, photo-manipulation techniques (e.g. FRAP, photoablation, optogenetics, and optical tweezers) and live cell imaging.

Proper citation: Massachusetts General Hospital Brigham Center of Excellence for Molecular Imaging Core Facility (RRID:SCR_027865) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/sivic/

Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.

Proper citation: Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) Copy   

•   Source: SciCrunch Registry

https://www.pancreatlas.org/datasets

Exeter Archival Diabetes Biobank (EADB), formerly the Alan Foulis collection. The collection is managed by the University of Exeter Medical School, with images from the biobank made accessible via Pancreatlas. Collection of pancreatic tissues, largely from children who died shortly after a type 1 diabetes (T1D) diagnosis. Provides high-quality digital images of historical, formalin-fixed, paraffin-embedded samples.

Proper citation: Exeter Archival Diabetes Biobank (EADB) (RRID:SCR_027352) Copy   

•   Source: SciCrunch Registry

http://nmr.chem.cornell.edu

Core specializes in the analysis of small organic and organometallic analytes. Provides access to mass spectrometers for all.

Proper citation: Cornell University Chemistry MS Core Facility (RRID:SCR_028079) Copy   

•   Source: SciCrunch Registry

http://nmr.chem.cornell.edu

Facility provides access to nuclear magnetic resonance spectroscopy for all. Houses spectrometers ranging in field strength from 400 to 600 MHz, including two 500 MHz Brukers equipped with nitrogen-cooled Prodigy CryoProbes. New users may operate a particular spectrometer independently once they complete the required training and demonstrate the knowledge required for operating each instrument.

Proper citation: Cornell University NMR Core Facility (RRID:SCR_028078) Copy   

•   Source: SciCrunch Registry

https://www.cdt-africa.org/

World Bank-supported regional center of excellence focused on building capacity for clinical trials, and developing novel vaccines, diagnostics, and therapeutics. Provides training in clinical trials and translational medicine, to foster homegrown health solutions.Training researchers, scientists, and clinical trial staff across Africa in trial management, data management, and scientific writing.

Proper citation: Addis Ababa University Center for Innovative Drug Development and Therapeutic Trials for Africa Core Facility (RRID:SCR_028125) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/DMRcate.html

Software application for de novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

Proper citation: DMRcate (RRID:SCR_028007) Copy   

•   Source: SciCrunch Registry

https://wucci.wustl.edu/

Core offers access to advanced imaging technologies, expert consultation, training, and collaborative partnerships across the School of Medicine and Washington University research community. Provides access to light and electron microscopy platforms, guidance in experimental design, sample preparation, data acquisition, quantitative image analysis, expertise, and training to enable investigators to explore cellular and tissue architecture across scales.

Proper citation: Washington University in St. Louis Washington University Center for Cellular Imaging Core Facility (RRID:SCR_028069) Copy   

•   Source: SciCrunch Registry

https://bican.mccarrolllab.org/app/bican?_inputs_&geneList=%22XIST%20PDE10A%20%20PENK%20PDYN%22&navbarPage=%22panelGeneExpr%22&plotExpressionButton=0&exprPlotUseCommonYScale=true&cellTypeSelector=%5B%22MSN%22%2C%22MSN_D1%22%2C%22MSN_D2%22%2C%22MSN_D1_matrix%22%2C%22MSN_D2_matrix%22%2C%22MSN_D1_striosome%22%2C%22MSN_D2_striosome%22%5D&exprPlotRegionSelector=%22Pu%22&GeneExprPlot_hover=null

Project provides data currently generated with support from the NIH Brain Initiative Cell Atlas Network (BICAN). Broad Institute collaboration supported by the NIH BRAIN Initiative, to create comprehensive atlas of cellular variation in the healthy human brain. It maps data from millions of cells across diverse individuals to understand how brain biology differs, helping researchers distinguish healthy variation from disease states.

Proper citation: Human Brain Variation Project (RRID:SCR_028065) Copy   

•   Source: SciCrunch Registry

https://github.com/google-deepmind/alphafold3

Software package provides implementation of the inference pipeline of AlphaFold 3.

Proper citation: AlphaFold3 (RRID:SCR_028034) Copy   

•   Source: SciCrunch Registry

https://www.cdc.gov/rdc/

Secure facility that provides qualified researchers with access to restricted-use, non-public health data. It protects participant confidentiality while allowing analysis of detailed survey data, such as specific geographic locations or sensitive health info. Provides access to restricted data from the National Center for Health Statistics and from other federal government agency surveys and studies. Access is granted only to approved researchers under strict supervision, and all results undergo disclosure review before leaving the RDC.

Proper citation: CDC Research Data Center (RRID:SCR_027996) Copy   

•   Source: SciCrunch Registry

https://github.com/adamewing/methylartist

Software tools for parsing and plotting methylation patterns. Used for plotting methylation data in various ways.

Proper citation: methylartist (RRID:SCR_028164) Copy   

•   Source: SciCrunch Registry

https://www.gbo.com/en-us/

Global medical technology company specializing in high-quality plastic laboratory products for diagnostics, biotechnology, and pharmaceutical industries. With over 60 years of experience, they produce VACUETTE® blood collection systems, CELLSTAR® cell culture products, and specialized labware for sample storage.

Proper citation: Greiner Bio-One (RRID:SCR_028044) Copy   

•   Source: SciCrunch Registry

https://github.com/nloyfer/wgbs_tools

Software tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies.

Proper citation: wgbstools (RRID:SCR_028257) Copy   

•   Source: SciCrunch Registry

https://github.com/HuiyangYu/PanDepth

Software tool for calculating sequence depth.

Proper citation: PanDepth (RRID:SCR_028256) Copy   

•   Source: SciCrunch Registry

https://github.com/SCANDAN-Team/SCANDAN-DICOM-labelling

Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag.

Proper citation: SCANDAN-DICOM-labelling (RRID:SCR_028365) Copy   

•   Source: SciCrunch Registry

http://obsproject.com

Software used for live streaming and high-quality screen recording on Windows, Mac, and Linux. Allows to capture, mix, and arrange multiple audio/video sources—such as webcams, desktop screens, and games—in real-time to create, broadcast, or record customized video content. Cross-platform screencasting and live streaming software application.

Proper citation: OBS Studio (RRID:SCR_028179) Copy   

•   Source: SciCrunch Registry