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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Brain Score Resource Report Resource Website 1+ mentions |
Brain Score (RRID:SCR_027769) | data or information resource, storage service resource, service resource, data repository | Platform provides accurate, machine-executable computational models of how the brain gives rise to the mind. Enables researchers to quickly get a sense of the alignment of their model(s) to neural and behavioral measurements, and provides these models to experimentalists to prototype new experiments and make sense of biological data. All code is open-source and community members may choose to make their data or model weights fully public. | Benchmark, benchmarking, modeling, experimental data, computational models, neural and behavioral measurements, | Free, Freely available | https://github.com/brain-score | SCR_027769 | 2026-08-14 09:29:58 | 4 | ||||||||||
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Memorial Sloan Kettering Cancer Center Integrated Genomics Operation Core Facility Resource Report Resource Website 1+ mentions |
Memorial Sloan Kettering Cancer Center Integrated Genomics Operation Core Facility (RRID:SCR_027801) | service resource, access service resource, core facility | Core provides services and expertise to Center investigators interested in evaluating gene expression, chromosome structure, and nucleotide sequence on a broad scale. Enables basic, clinical, and translational research projects across the Center. Through its production group, the Core enables genomic and transcriptomic analyses and has the expertise to process challenging samples from all origins (tissue, dissociated single cells and cell pellets, paraffin curls, blood, serum, etc.). Bulk DNA/RNA assays operate in highly automated environment, from sample reception to sequencing library preparation. | ABRF, gene expression, chromosome structure, nucleotide sequence, services, genomic and transcriptomic analyses, expertise to process samples, |
is listed by: ABRF CoreMarketplace has parent organization: Memorial Sloan Kettering Cancer Center |
ABRF_5702 | https://coremarketplace.org/RRID:SCR_027801/?citation=1 | SCR_027801 | 2026-08-14 09:29:58 | 5 | |||||||||
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T Cell ExTRECT Resource Report Resource Website 1+ mentions |
T Cell ExTRECT (RRID:SCR_027742) | software toolkit, source code, software resource | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NHLBI U54HL108460; NCATS UL1TR000100; NCI R21CA177519; NCI P30CA023100; NCI U01CA196406; NLM T15LM011271; NIH Office of the Director DP5OD017937; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-08-14 09:29:57 | 1 | ||||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software toolkit, software resource, source code, software library | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NSF ; NIGMS T32 GM008313; NCI R37 CA222574; NCI R01 CA227388; NCI U01 CA233100 |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | 2026-08-14 09:29:49 | 4 | |||||||||
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Telomerecat Resource Report Resource Website 1+ mentions |
Telomerecat (RRID:SCR_027747) | software toolkit, source code, software resource | Software R package for estimating average telomere length (TL) for paired end, whole genome sequencing (WGS) sample.Telomere computational analysis tool. | telomere, estimating average telomere length, paired end, whole genome sequencing sample, | PMID:29358629 | Free, Available for download, Freely available | SCR_027747 | 2026-08-14 09:29:38 | 1 | ||||||||||
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CancerMine Resource Report Resource Website 1+ mentions |
CancerMine (RRID:SCR_027748) | database, data or information resource | Text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. | Cancer genes, literature-mined database, drivers, oncogenes, tumor suppressors, cancer | BC Cancer Foundation and Genome British Columbia ; Vanier Canada Graduate Scholarship |
PMID:31110280 | Free, Freely available | SCR_027748 | 2026-08-14 09:29:57 | 6 | |||||||||
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Semi-Automated MEA Spike Sorting (SAMS) Resource Report Resource Website 1+ mentions |
Semi-Automated MEA Spike Sorting (SAMS) (RRID:SCR_027843) | software toolkit, source code, software resource | Software MATLAB-based application for spike sorting multi-electrode array (MEA) recordings. Used for efficient, reproducible spike sorting in high-throughput neuronal culture experiments. SAMS performs batched automated spike sorting processes and also allows the users to review and correct any clusters or spike assignments. | spike sorting, spike sorting multi-electrode array recordings, review and correct, clusters, spike assignments, | PMID:39975344 | Free, Available for download, Freely available | SCR_027843 | Semi-Automated MEA Spike Sorting | 2026-08-14 09:29:39 | 1 | |||||||||
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Canvas Copy Number Variant Caller Resource Report Resource Website 1+ mentions |
Canvas Copy Number Variant Caller (RRID:SCR_027970) | canvas | source code, software application, software resource | Software tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome. | detection of copy number variants, copy number variants, human DNA sequencing data, | PMID:27153601 PMID:29028893 |
SCR_027970 | Illumina Canvas, Canvas | 2026-08-14 09:30:00 | 1 | |||||||||
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Phy Resource Report Resource Website 50+ mentions |
Phy (RRID:SCR_027975) | software toolkit, software resource, source code, software library | Software open-source Python library providing graphical user interface for visualization and manual curation of large-scale electrophysiological data. It is optimized for high-density multielectrode arrays containing hundreds to thousands of recording sites. | multielectrode arrays recording sites, data visualization and manual curation, large-scale electrophysiological data, | Free, Available for download, Freely available | SCR_027975 | 2026-08-14 09:29:40 | 54 | |||||||||||
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Tracker Resource Report Resource Website 1+ mentions |
Tracker (RRID:SCR_027845) | software application, software resource | Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing. | frame-by-frame tracking, anatomical landmarks and articulated structures, video recordings, extraction of time-dependent kinematic variables, | Free, Available for download, Freely available | SCR_027845 | Tracker Video Analysis and Modeling | 2026-08-14 09:29:51 | 6 | ||||||||||
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Developmental Human Brain Atlas Ontology (DHBA) Resource Report Resource Website 1+ mentions |
Developmental Human Brain Atlas Ontology (DHBA) (RRID:SCR_027940) | controlled vocabulary, ontology, data or information resource, software resource, source code | Machine-readable framework designed to standardize, organize, and annotate the anatomical structures, developmental stages, and spatial relationships of the human brain during development. It is primarily derived from the Allen Developing Human Brain Atlas (BrainSpan) to provide a structured, hierarchical taxonomy for researchers. Application ontology built by combining ontologised versions of the Allen Institute Developing Human Brain Atlas (DHBA) StructureGraph mapped to Uberon. | Allen Developing Human Brain Atlas, hierarchical taxonomy, standardize, organize, annotate, anatomical structures, developmental stages, spatial relationships, human brain, brain during development, Uberon, | is related to: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) | Free, Available for download, Freely available | SCR_027940 | 2026-08-14 09:29:39 | 1 | ||||||||||
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piecewiseSEM Resource Report Resource Website 1+ mentions |
piecewiseSEM (RRID:SCR_027935) | software toolkit, source code, software resource | Software R package for performing Piecewise Structural Equation Modeling, designed to fit complex causal networks by breaking them into smaller, manageable "pieces" (individual regressions) rather than using global covariance estimation. Used to analyze complex, direct/indirect ecological and evolutionary data. | Structural Equation Modeling, fit complex causal networks, analyze complex data, direct, indirect, ecological data, evolutionary data, | Free, Available for download, Freely available | https://github.com/jslefche/piecewiseSEM | SCR_027935 | , piecewise Structural Equation Modeling, piecewiseSEM: Piecewise Structural Equation Modeling | 2026-08-14 09:29:59 | 3 | |||||||||
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SCIPI Resource Report Resource Website 1+ mentions |
SCIPI (RRID:SCR_027939) | software toolkit, source code, software resource | Software hepatocyte ploidy identification pipeline on the stereo-cell platform for accurate liver polyploidy classification via fluorescence staining and deep learning tools. | hepatocyte ploidy identification, liver polyploidy classification, fluorescence staining, deep learning tools, | Free, Available for download, Freely available | SCR_027939 | 2026-08-14 09:29:53 | 2 | |||||||||||
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CellNEST Resource Report Resource Website 1+ mentions |
CellNEST (RRID:SCR_027883) | CellNEST | source code, software application, software resource | Software tool to decipher patterns of communication. Used to relay-network communication detection that identifies putative ligand–receptor–ligand–receptor communication. Detects T cell homing signals in human lymph nodes, identifies aggressive cancer communication in lung adenocarcinoma and colorectal cancer, and predicts new patterns of communication that may act as relay networks in pancreatic cancer. | ABRF, decipher patterns of communication, relay-network communication detection, identifies putative ligand–receptor–ligand–receptor communication, spatial transcriptomics data, | PMID:40481363 | Free, Available for download, Freely available | SCR_027883 | Cell Neural Networks on Spatial Transcriptomics (CellNEST) | 2026-08-14 09:29:59 | 1 | ||||||||
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4D-BioReconX Resource Report Resource Website 1+ mentions |
4D-BioReconX (RRID:SCR_027919) | data processing software, software application, data analysis software, time-series analysis software, software resource, 1d time-series analysis software | Software bioinformatic framework for reconstructing 4D spatial transcriptomics atlas and spatiotemporal analyses+. | spatial atlas, reconstructing 4D spatial transcriptomics atlas, spatiotemporal analyses, | Free, Available for download, Freely available | SCR_027919 | 2026-08-14 09:29:52 | 1 | |||||||||||
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Photoline Resource Report Resource Website 1+ mentions |
Photoline (RRID:SCR_027878) | data processing software, software application, software resource, data visualization software, 3d visualization software | Software versatile all-purpose image and graphics editor for Windows, macOS, and Linux (via Wine) that combines raster (bitmap) and vector editing, making it a strong, affordable alternative to Adobe Photoshop, with features like layers, masks, color management (CMYK, Lab, 16-bit), batch processing, and web tools, presented in a comprehensive yet sometimes retro-looking interface . You can edit images or optimize them for the web, but you can also prepare print-ready PDF data. | image and graphics editor, edit images, print-ready PDF data, | Restricted | SCR_027878 | PhotoLine | 2026-08-14 09:29:39 | 5 | ||||||||||
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ABC-Enhancer-Gene-Prediction Resource Report Resource Website 10+ mentions |
ABC-Enhancer-Gene-Prediction (RRID:SCR_027918) | source code, software application, software resource | Software tool for cell type specific enhancer-gene predictions using ABC model. | cell type specific enhancer-gene predictions, ABC model, | DOI:s41588-019-0538-0 | Free, Available for download, Freely available, | SCR_027918 | 2026-08-14 09:29:59 | 14 | ||||||||||
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Fit-Hi-C Resource Report Resource Website 1+ mentions |
Fit-Hi-C (RRID:SCR_027917) | source code, software application, software resource | Software tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C. | assigning statistical confidence estimates, chromosomal contact maps, genome-wide, genome architecture assays, Hi-C | Free, Available for download, Freely available | SCR_027917 | 2026-08-14 09:29:39 | 4 | |||||||||||
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Collection of Alternative Methods for Regulatory Application (CAMERA) Resource Report Resource Website 1+ mentions |
Collection of Alternative Methods for Regulatory Application (CAMERA) (RRID:SCR_027893) | CAMERA | database, data or information resource | Interactive database and user interface providing online access to validated alternative methods for U.S. regulatory and other contexts of use. Central hub and unified resource of validated alternative methods that enhances accessibility to validation study reports, data, protocols / SOPs, and information on regulatory guidance.Users can filter searches by alternative method types, defined approaches, Test Method Endpoint, and regulatory guidance. | NAMSD, validated alternative methods, U.S. regulatory, validation study reports, data, protocols, SOPs, regulatory guidance, | Free, Freely available | SCR_027893 | Collection of Alternative Methods for Regulatory Application | 2026-08-14 09:29:39 | 1 | |||||||||
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Paris Brain Institute iPSC Core Facility Resource Report Resource Website 10+ mentions |
Paris Brain Institute iPSC Core Facility (RRID:SCR_027891) | training service resource, service resource, access service resource, core facility | As part of the cellular engineering and vectorology core facility (ICV), the iPSC core facility (ICV-iPS) proposes the generation and the genetic engineering of human induced pluripotent stem cells to internal research teams, external academic teams, and industrial partners. Services include generation of human iPSc with Sendai virus, full molecular and functional characterization of iPSc clones, genetic engineering of human iPSc with CRISPR/Cas9 system and theoretical and practical learning sessions on human iPSc culture. The core facility provides also access to L2 cell culture box dedicated to human iPSc culture. | Human induced pluripotent stem cell, IPSC, Reprogramming, Sendai, CRISPR/Cas9 |
is listed by: ABRF CoreMarketplace has parent organization: Paris Brain Institute |
Open | ABRF_5739 | https://coremarketplace.org/RRID:SCR_027891/?citation=1 | SCR_027891 | ICV-iPS platform at the Paris Brain Institute (ICM), CELIS-iPS core facility, ICV-iPS core facility, iPS cell culture facility of the Paris Brain Institute | 2026-08-14 09:29:52 | 11 |
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