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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://cran.r-project.org/web/packages/compareGroups/

Software R package to create tables displaying results of univariate analyses, stratified or not by categorical variable groupings.

Proper citation: compareGroups (RRID:SCR_027994) 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://alleninstitute.github.io/scrattch.taxonomy/

Software R package from the Allen Institute designed to build, standardize, and analyze single-cell RNA-seq-based cell type taxonomies. It utilizes a structured Allen Institute schema (AIT) to organize cell annotations and metadata, enabling hierarchical, data-driven cell type classification

Proper citation: scrattch taxonomy (RRID:SCR_027910) 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

https://github.com/AlexanRNA/nanowgs/releases/tag/v0.0.2

Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project.

Proper citation: NanoWGS (RRID:SCR_028113) 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

https://ipfx.readthedocs.io/

Software Python package for computing intrinsic cell features from electrophysiology data. Used to compute intrinsic cell features from intracellular electrophysiology data.

Proper citation: Intrinsic Physiology Feature Extractor (RRID:SCR_028075) 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://bioconductor.org/packages/release/bioc/html/tximeta.html

Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility.

Proper citation: tximeta (RRID:SCR_028005) 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://jokergoo.github.io/rGREAT/

Software R package for functional enrichment on genomic regions. Functional enrichment analysis directly performed on genomic regions.

Proper citation: rGREAT (RRID:SCR_028008) 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://nda.nih.gov/oai

Centralized, annotated repository for the Osteoarthritis Initiative (OAI) study, designed to accelerate research by organizing and linking extensive clinical, imaging (MRI/X-ray), and biomarker data. It aims to help researchers analyze knee osteoarthritis prevention, treatment, and progression.

Proper citation: OAI Knowledge base (RRID:SCR_028107) 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.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://ur.ac.rw/

National University of Rwanda located in the city of Butare and was established in 1963 by the government in cooperation with the Congregation of the Dominicans from the Province of Quebec, Canada.

Proper citation: University of Rwanda; Butare; Rwanda (RRID:SCR_028139) Copy   

•   Source: SciCrunch Registry

http://www.uem.mz/index.php

Public university, founded in 1962. It is a comprehensive institution focused on higher education, scientific research, and community extension services to promote innovation and sustainable development. The university offers various faculties, including agriculture, engineering, arts, sciences, and medicine.

Proper citation: Eduardo Mondlane University; Maputo; Mozambique (RRID:SCR_028146) Copy   

•   Source: SciCrunch Registry

http://www.aau.edu.et/

Ethiopia's oldest and largest public research university, founded in 1950 and located in the capital, Addis Ababa. It is the premier higher education institution in the country, featuring multiple campuses, extensive postgraduate programs, and ranking high among East African universities.

Proper citation: Addis Ababa University; Addis Ababa; Ethiopia (RRID:SCR_028147) Copy   

•   Source: SciCrunch Registry