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https://github.com/tomcatsmith19/ArucoDetection

Automated rodent behavioral scoring system, complete with 3D design files and code/software. System monitors behavioral engagement using open-source software. 3D design files and necessary software has been made available, as well as code that can be used for data analysis.

Proper citation: ArUco (RRID:SCR_026572) Copy   

•   Source: SciCrunch Registry

https://github.com/Washington-University/HCPpipelines

Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space.

Proper citation: HCP Pipelines (RRID:SCR_026575) Copy   

•   Source: SciCrunch Registry

https://medresearch.umich.edu/office-research/about-office-research/biomedical-research-core-facilities/vector-core

Vector Core produces gene transfer vectors that facilitate transfer of specific genes into either normal or aberrant cells. Provides intellectual and technical advice to researchers regarding the optimal use of these systems.

Proper citation: University of Michigan Medical School BRCF Vector Core Facility (RRID:SCR_026696) Copy   

•   Source: SciCrunch Registry

https://www.mdanderson.org/research/research-resources/core-facilities/advanced-microscopy-core.html

Core provides microscopy services to departments at MD Anderson in high resolution and multispectral fluorescence microscopy for users from divisions including Basic Research, Cancer Medicine, Diagnostic Imaging, Surgery, Internal Medicine Pediatrics and Radiation Oncology, among others. Offers microscopy resources and expertise in fluorescence imaging to spatially and dynamically assess cells, tissues and their requisite contents across scales.

Proper citation: University of Texas MD Anderson Cancer Center Advanced Microscopy Core Facility (RRID:SCR_026611) Copy   

•   Source: SciCrunch Registry

https://endomap.hms.harvard.edu/

Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes.

Proper citation: EndoMap (RRID:SCR_026690) Copy   

•   Source: SciCrunch Registry

https://archive.ics.uci.edu/

Collection of databases, domain theories, and data generators that are used by machine learning community for empirical analysis of machine learning algorithms. Datasets approved to be in the repository will be assigned Digital Object Identifier (DOI) if they do not already possess one. Datasets will be licensed under a Creative Commons Attribution 4.0 International license (CC BY 4.0) which allows for the sharing and adaptation of the datasets for any purpose, provided that the appropriate credit is given

Proper citation: UCI Machine Learning Repository (RRID:SCR_026571) Copy   

•   Source: SciCrunch Registry

https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2

Software tool to call somatic short mutations via local assembly of haplotypes. Somatic variant caller that uses local assembly and realignment to detect SNVs and indels.

Proper citation: Mutect2 (RRID:SCR_026692) Copy   

•   Source: SciCrunch Registry

https://cores.research.umich.edu/core/proteomics-resource-facility/

Core is dedicated to protein analysis and applying mass spectrometry-based proteomic approaches to varied biological questions.

Proper citation: University of Michigan Medical School BRCF Proteomics Resource Core Facility (RRID:SCR_026723) Copy   

•   Source: SciCrunch Registry

https://www.liverpool.ac.uk/research/facilities/centre-for-preclinical-imaging/

Provides access to imaging systems. Offers researchers technologies for multi-modality, non-invasive approaches to imaging on small, live animals, or tissues and organs extracted from animals . Our equipment can be used for pre-clinical models and non-biological samples.

Proper citation: University of Liverpool Centre for Preclinical Imaging Core Facility (RRID:SCR_026605) Copy   

•   Source: SciCrunch Registry

https://www.liverpool.ac.uk/research/facilities/histology/

Facility offers preparation of samples from fresh or fixed tissue through to scanned images. Provides training to prepare and use equipment to embed, section and hand stain tissues as required. Offers three different types of wax for embedding and sectioning as required. Fully equipped for methyl methacrylate and glycol methacrylate embedding and sectioning (including larger samples), freeze microtomy and high throughput slide imaging using our Zeiss Axioscan Z1.

Proper citation: University of Liverpool Shared Research Histology Core Facility (RRID:SCR_026606) Copy   

•   Source: SciCrunch Registry

https://github.com/kaizhang/SnapATAC2

Software Python/Rust package for single-cell epigenomics analysis.

Proper citation: SnapATAC2 (RRID:SCR_026622) Copy   

•   Source: SciCrunch Registry

https://obc.bio.uci.edu/

Shared resource facility to provide researchers access to resources, including state of the art instrumentation and technical support, to conduct biomedical research. Provides access to light microscopes (confocal, mesoscale lightsheet, and Super Resolution), as well as software for 3D and 4D analysis.

Proper citation: University of California at Irvine Optical Biology Core Facility (RRID:SCR_026614) Copy   

•   Source: SciCrunch Registry

https://www.countyhealthrankings.org/

Program of University of Wisconsin Population Health Institute, highlights policies and practices that can help everyone be as healthy as possible. Aims to grow shared understanding of health, equity and power of communities to improve health for all.

Proper citation: County Health Rankings and Roadmaps (RRID:SCR_026613) Copy   

•   Source: SciCrunch Registry

https://genomics.uci.edu/about-us/

Core provides services ranging from DNA/RNA QC analysis, library construction and sequencing on various platforms. Offers several sequencing platforms from Illumina’s MiSeq and NovaSeq to PacBio’s Sequel II System.

Proper citation: University of California at Irvine Genomics Research and Technology Hub Core Facility (RRID:SCR_026615) Copy   

•   Source: SciCrunch Registry

https://github.com/Breeding-Insight/BIGapp

Species-agnostic web-based application for processing genotypic data in no-code RShiny user-friendly interface. Allows users without coding experience to process genetic data in all genome ploidy ranges and for multiallelic data, starting from number of input formats (including VCF). Also allows to perform downstream QC analyses (e.g., PCA) and run genomic analysis (e.g., Linkage mapping, QTL analysis, genome-wide association studies (GWAS), and genomic selection (GS).

Proper citation: BIGapp (RRID:SCR_026676) Copy   

•   Source: SciCrunch Registry

https://github.com/Breeding-Insight/bi-web

Breeding-Insight/bi-web development.

Proper citation: bi-web (RRID:SCR_026678) Copy   

•   Source: SciCrunch Registry

https://github.com/jmschrei/tfmodisco-lite

Software tool as lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments. Rewrite of the original TF-MoDISCo code.

Proper citation: tfmodisco-lite (RRID:SCR_026709) Copy   

•   Source: SciCrunch Registry

https://github.com/aertslab/scenicplus

Software Python package to build gene regulatory networks using combined or separate single-cell gene expression and single-cell chromatin accessibility (scATAC-seq) data. Used for inferring and analyzing enhancer-driven gene regulatory networks using single-cell multiomic data.

Proper citation: SCENIC+ (RRID:SCR_026702) Copy   

•   Source: SciCrunch Registry

https://www.augusta.edu/scimath/analysis-facility.php

Core focused on metabolomics, lipidomics, medicinal chemistry, and small molecule analysis. Offers services, expertise, and collaboration for the research community. Instrumentation includes high field nuclear magnetic resonance (NMR), liquid chromatography–mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), high-performance liquid chromatography (HPLC), circular dichroism spectrometer (CD), inductively coupled plasma optical emission spectrometry (ICP-OES), and fluorimeter. Consulting is available to assist with experimental design and data interpretation.

Proper citation: Augusta University Chemical and Biomolecular Analysis Core Facility (RRID:SCR_026668) Copy   

•   Source: SciCrunch Registry

https://github.com/YuningHao/FARDEEP

Software R tool for enumerating immune cell subsets from whole tumor tissue samples. Utilizes adaptive least trimmed square to automatically detect and remove outliers before estimating cell compositions.

Proper citation: FARDEEP (RRID:SCR_026704) Copy   

•   Source: SciCrunch Registry