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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website 1+ mentions |
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) | SIVIC | software resource, software application | 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. | DICOM MR Spectroscopy Workflows, data processing, data visualization, DICOM MR spectroscopy data, | NCI RO1 CA127612; NCI P01 CA11816; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | 2026-08-12 10:54:17 | 2 | ||||||||
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Purdue University Research Repository (PURR) Resource Report Resource Website |
Purdue University Research Repository (PURR) (RRID:SCR_027877) | PURR | service resource, data repository, storage service resource | Provides online, collaborative working space and data-sharing platform. Provides services with data management planning, boilerplate text for proposal, sample plans and individual consultation. Each dataset gets DOI. PURR publishes and archives digital datasets from researchers across campus and welcomes all kinds of open data from images and videos to spreadsheets and source code. | FAIR, DOI, open data, publishes and archives digital datasets, data-sharing platform, data management planning, boilerplate text for proposal, sample plans, consultation, | Restricted | SCR_027877 | 2026-08-12 10:54:04 | 0 | ||||||||||
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scrattch taxonomy Resource Report Resource Website 1+ mentions |
scrattch taxonomy (RRID:SCR_027910) | software toolkit, software resource, source code | 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 | building cell type taxonomies, single cell RNA-seq data, Allen Institute (AIT) schema, | is related to: Allen Institute | Free, Available for download, Freely available | https://github.com/AllenInstitute/scrattch.taxonomy | SCR_027910 | 2026-08-12 10:54:04 | 1 | |||||||||
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DMRcate Resource Report Resource Website 1+ mentions |
DMRcate (RRID:SCR_028007) | software resource, software application | 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. | de novo identification and extraction, differentially methylated regions, human genome, | Free, Available for download, Freely available | SCR_028007 | 2026-08-12 10:54:18 | 2 | |||||||||||
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Poly Pipeline Resource Report Resource Website |
Poly Pipeline (RRID:SCR_027993) | software resource, software application | Software data analysis pipeline for spatial transcriptomics data tailored to polyploid organisms. | Spatial transcriptomics data, polyploid organisms, data analysis, | Free, Available for download, Freely available | https://zenodo.org/records/18655692 | SCR_027993 | 2026-08-12 10:53:53 | 0 | ||||||||||
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CIMA_BMI_paper Resource Report Resource Website |
CIMA_BMI_paper (RRID:SCR_028241) | software resource, source code | Source analysis and data processing code for article titled "Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk". | analysis and data processing code, Single-Cell Multi-Omics Insights, BMI-Mediated Immune-Related Disease Risk, | Free, Available for download, Freely available | SCR_028241 | 2026-08-12 10:53:56 | 0 | |||||||||||
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somalier Resource Report Resource Website |
somalier (RRID:SCR_028167) | software resource, software application | Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches. | rapid relatedness estimation, cancer and germline studies, efficient genome sketches, quality control, | NHGRI R41HG010126; NHGRI R01HG009141; NCI U24CA209999; NCI R37CA246183; NCI P30CA04014 |
PMID:32664994 | Free, Available for download, Freely available | SCR_028167 | Somalier | 2026-08-12 10:54:07 | 0 | ||||||||
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pod5 Resource Report Resource Website 10+ mentions |
pod5 (RRID:SCR_028166) | software resource, source code | File format for storing nanopore DNA data in an easily accessible way. High performance file format for nanopore reads. | File format, storing nanopore DNA data, DNA data, nanopore reads, | Free, Available for download, Freely available | SCR_028166 | POD5, pod5-file-format | 2026-08-12 10:54:19 | 11 | ||||||||||
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ChatMDV Resource Report Resource Website |
ChatMDV (RRID:SCR_028342) | software resource, software application | Software tool as natural language interface integrated with MDV that allows users to generate high-quality interactive visualisations through natural language commands. ChatMDV employs a retrieval-augmented generation (RAG) pipeline combined with large language models (LLMs) to translate user queries into reproducible Python code and interactive output. Module to add chatbot functionality to query Multi-Dimensional Viewer projects. | add chatbot functionality, query Multi-Dimensional Viewer projects, | DOI:10.1101/2025.08.26.671083 | Free, Available for download, Freely available | https://github.com/Taylor-CCB-Group/MDV | SCR_028342 | 2026-08-12 10:54:20 | 0 | |||||||||
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DAMMIF Resource Report Resource Website |
DAMMIF (RRID:SCR_028444) | software resource, software application | Software tool for rapidly determining the low-resolution three-dimensional shape of biological macromolecules in solution using Small-Angle X-ray Scattering (SAXS) data. Used for rapid ab-initio shape determination in small-angle scattering. | EMBL Hamburg BioSAXS group, determining low-resolution three-dimensional shape of biological macromolecules, macromolecules in solution, Small-Angle X-ray Scattering, | is related to: ATSAS | PMID:27630371 | Free, Available for download | SCR_028444 | Dummy Atom Model Fast | 2026-08-12 10:54:20 | 0 | ||||||||
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HemoGenix Resource Report Resource Website |
HemoGenix (RRID:SCR_028449) | commercial organization, service resource | Specialty contract research laboratory and biotechnology company that provides stem cell testing and in vitro toxicity screening, particularly for the blood-forming (hematopoietic) system. Provides high-throughput hematotoxicity screening and testing with its proprietary HALO®-Tox HT Platform. Provides the expertise to help in predicting toxicity, risk and safety of a drug or other agent. | stem cell testing, in vitro toxicity screening, hematotoxicity screening and testing, predicting toxicity, | SCR_028449 | 2026-08-12 10:54:20 | 0 | ||||||||||||
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GATK VariantFiltration Resource Report Resource Website 1+ mentions |
GATK VariantFiltration (RRID:SCR_028441) | software resource, software application | Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible | hard-filtering variant callsets, annotate low-quality variants, |
is related to: GATK is organization facet of: Broad Institute |
Free, Freely available | https://gatk.broadinstitute.org/hc/en-us | SCR_028441 | 2026-08-12 10:54:09 | 1 | |||||||||
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bedGraphToBigWig Resource Report Resource Website 1+ mentions |
bedGraphToBigWig (RRID:SCR_028439) | software resource, software application | Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser. | Convert bedGraph file to bigWig format, convert text-based bedGraph files, indexed binary bigWig files, transform genome coverage data, |
is related to: BigWig and BigBed works with: UCSC Genome Browser |
DOI:10.1093/bioinformatics/btq351 | Free, Freely available, | SCR_028439 | 2026-08-12 10:54:00 | 3 | |||||||||
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Membrane Protein-Lipid Interaction Database Resource Report Resource Website |
Membrane Protein-Lipid Interaction Database (RRID:SCR_028506) | MPLID | data or information resource, database, software resource, source code | Database for residue-level membrane protein-lipid contact annotations derived from experimentally determined Protein Data Bank structures. Includes automated Python pipeline for identifying lipid-containing PDB structures, calculating all-atom heavy-atom residue-lipid contacts using a 4.0 Angstrom distance cutoff, generating cluster-aware train, validation, and test splits, and producing documented dataset files for machine learning and structural bioinformatics. The dataset is deposited on Zenodo under CC0, while the code is released on GitHub under the MIT license. Contains large-scale experimentally-validated dataset of residue-level protein-lipid contacts from membrane protein structures. | large-scale experimentally-validated dataset, residue-level protein-lipid contacts, membrane protein structures, | Free, Available for download, Freely available | SCR_028506 | MPLID: Membrane Protein-Lipid Interaction Database | 2026-08-12 10:54:01 | 0 | |||||||||
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Modbamtools Resource Report Resource Website |
Modbamtools (RRID:SCR_028809) | software toolkit, software resource, source code | Software tools to visualize methylation data using bam file. Used to manipulate and visualize modified base bam files. | methylation data, bam file, visualize methylation data using bam file, manipulate and visualize modified base bam files, | Free, Available for download, Freely available | SCR_028809 | modbamtools | 2026-08-12 10:54:23 | 0 | ||||||||||
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SCEVAN Resource Report Resource Website |
SCEVAN (RRID:SCR_028766) | software toolkit, software resource, source code | Software R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation. | automatically classify cells, scRNA data, segregating non-malignant cells of tumor microenviroment, malignant cells, copy number profile of malignant cells, identify subclonal structures, | Italian Ministry of Research Grant | PMID:36841879 | Free, Available for download, Freely available | SCR_028766 | Single CEll Variational ANeuploidy | 2026-08-12 10:54:22 | 0 | ||||||||
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Menarini Silicon Biosystems Inc Resource Report Resource Website |
Menarini Silicon Biosystems Inc (RRID:SCR_028704) | commercial organization, service resource | Biotechnology and diagnostics company specializing in "liquid biopsy" technologies to detect and isolate rare cells like circulating tumor cells (CTCs) from blood or tissue samples. They provide precise single-cell analysis tools used in cancer research and personalized medicine. Offers commercial rare-cell laboratory service providing CD138-positive immunomagnetic enrichment of plasma cells from peripheral blood and immunofluorescence-based plasma-cell identification and enumeration, delivering an enriched circulating multiple myeloma cell fraction for downstream analysis. | Biotechnology, diagnostics, company, detect and isolate rare cells, blood, tissue, samples | SCR_028704 | 2026-08-12 10:54:04 | 0 | ||||||||||||
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Stoelting ANY-maze Video Tracking Software Resource Report Resource Website |
Stoelting ANY-maze Video Tracking Software (RRID:SCR_028718) | software resource, software application | Automated platform used in behavioral neuroscience to track and analyze the movements and behaviors of lab animals, such as mice and rats. Standardizes experiments like the Elevated Plus Maze, Open Field, Barnes Maze, and Fear Conditioning. Tracks whole-body movement, distance traveled, freezing/immobility, and zone entries. Connects to external devices like food dispensers, shockers, and lasers to trigger automated responses based on the animal's actions. | behavioral neuroscience, track, analyze, movements and behaviors, lab animals, mice, rats | is used by: Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core Facility | Restricted | SCR_028718 | ANY-maze Video Tracking | 2026-08-12 10:54:22 | 0 | |||||||||
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Bio-Rad: QX600 Droplet Digital PCR System Resource Report Resource Website |
Bio-Rad: QX600 Droplet Digital PCR System (RRID:SCR_028830) | instrument resource | Advanced laboratory instrument used for absolute quantification of DNA and RNA. It partitions samples into 20,000 nanoliter sized droplets and uses 6-color multiplexing to test up to 12 targets per well with high sensitivity. | PCR, absolute quantification, DNA, RNA | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028830.pdf | Model_Number_Bio-Rad_QX600 | SCR_028830 | , Bio-Rad QX600 ddPCR Droplet Digital PCR system | 2026-08-12 10:54:23 | 0 | ||||||||
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Glass Box UMAP Resource Report Resource Website |
Glass Box UMAP (RRID:SCR_028826) | software toolkit, software resource | Software Python package for making UMAP interpretable with exact feature contributions. Used to explain why data points land in specific places on a UMAP map. Augments UMAP by computing exact feature contributions to the UMAP embedding. Standard UMAP produces embeddings but offers no insight into why points land where they do. Glass Box UMAP solves this by using a specially designed neural network that enables exact computation of feature contributions, and does so without approximations. The feature contributions are mathematically exact, validated to near machine precision. | making UMAP interpretable with exact feature contributions, data points land in specific places, UMAP map, | DOI:10.57844/arcadia-4ye8-8tun | Free, Available for download, Freely available | SCR_028826 | 2026-08-12 10:54:07 | 0 |
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