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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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almondcv2 Resource Report Resource Website 1+ mentions |
almondcv2 (RRID:SCR_027064) | source code, software application, software resource | Software repository provides open-source implementation of RGB imaging workflow for morphological and morphometric analysis of fruits and seeds. | RGB imaging workflow, morphological and morphometric analysis, fruits and seeds, | DOI:10.1101/2025.05.05.652179 | Free, Available for download, Freely available | SCR_027064 | 2026-08-14 09:29:28 | 1 | ||||||||||
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vcf2maf Resource Report Resource Website 10+ mentions |
vcf2maf (RRID:SCR_027063) | source code, software application, software resource | Software tool to convert Virtual Contact File into Mutation Annotation Format, where each variant is annotated to only one of all possible gene isoforms. | Virtual Contact File, Mutation Annotation Format, convert VCF into MAF, gene isoforms, genomics, aggregate mutation data, storing genetic variation data, variant annotation, one gene isoform, | Free, Available for download, Freely available | SCR_027063 | 2026-08-14 09:29:37 | 25 | |||||||||||
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Meshlab Resource Report Resource Website 50+ mentions |
Meshlab (RRID:SCR_027065) | source code, software application, software resource | Software application used for processing and editing 3D triangular meshes. Provides tools for editing, cleaning, repairing, inspecting, rendering, texturing, and converting meshes. This makes it suitable for variety of tasks related to 3D data, including preparing models for 3D printing. | processing and editing 3D triangular meshes, editing, cleaning, repairing, inspecting, rendering, texturing, converting, meshes | Free, Available for download, Freely available | https://github.com/cnr-isti-vclab/meshlab | SCR_027065 | 2026-08-14 09:29:51 | 80 | ||||||||||
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clusterCrit Resource Report Resource Website 1+ mentions |
clusterCrit (RRID:SCR_027219) | software toolkit, source code, software resource | Software package for computing collection of clustering validation or quality criteria and partition comparison indices. | clustering validation, quality criteria, partition comparison indices, | Free, Available for download, Freely available | SCR_027219 | 2026-08-14 09:29:31 | 2 | |||||||||||
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TinkerHap Resource Report Resource Website 1+ mentions |
TinkerHap (RRID:SCR_027235) | source code, software application, algorithm resource, software resource | Software accurate read-based phasing tool that integrates multiple methodologies to enhance phasing accuracy. Used to efficiently phase genomic data by linking sequencing reads across heterozygous sites, extending haplotype blocks, and incorporating pre-phased data when available. Read-based phasing algorithm with integrated multi-method support for enhanced accuracy. | genomic analyses, estimation of haplotypes, phasing, read-based phasing, read-aware phasing, Assembly Based ReAligner | DOI:10.1101/2025.02.16.638517 | Free, Available for download, Freely available | SCR_027235 | 2026-08-14 09:29:39 | 1 | ||||||||||
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Palantir Resource Report Resource Website 1+ mentions |
Palantir (RRID:SCR_027194) | source code, algorithm resource, software resource | Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state. | Trajectory, align cells along differentiation trajectories, | NICHD DP1-HD084071; NCI R01CA164729; NCI P30 CA008748 |
PMID:30899105 | Free, Available for download, Freely available | SCR_027194 | 2026-08-14 09:29:39 | 5 | |||||||||
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BioDare2 Resource Report Resource Website 50+ mentions |
BioDare2 (RRID:SCR_027193) | production service resource, data repository, time sampled measurement data set, data processing software, storage service resource, numeric dataset, data analysis service, data set, data or information resource, software application, software resource, data visualization software, service resource, analysis service resource | Data analysis resource and repository for biological data related to circadian rhythms, sharing public data from over 10,000 experiments (in 2025). The main features of BioDare2 are: fast analysis of rhythmic data (rhythm detection and period, phase, amplitude), timeseries processing, attractive visualizations, simple data description, data sharing with permalinks, easy data uploads and a modern UI. | circadian rhythms data, biological data related to circadian rhythms, analysis of rhythmic data, timeseries processing, attractive visualizations, simple data description, data sharing with permalinks, | UKRI-BBSRC BB/Y006194/1; EU European Commission FP7 Collaborative Project TiMet (award 245143); UKRI-BBSRC BB/M018040/1 |
PMID:34674164 | Restricted | SCR_027193 | 2026-08-14 09:29:52 | 72 | |||||||||
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ProteinCartography Resource Report Resource Website 1+ mentions |
ProteinCartography (RRID:SCR_027230) | software toolkit, source code, software resource | Software pipeline to build similarity maps of protein space. Identifies proteins related to query protein using sequence- and structure-based searches, compares all protein structures, and creates navigable map that can be used to look at protein relationships and make hypotheses about function. | Identifies proteins, build similarity maps, protein space, protein relationships, | DOI:10.57844/arcadia-a5a6-1068 | Free, Available for download, Freely available | SCR_027230 | 2026-08-14 09:29:39 | 1 | ||||||||||
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TEProf3 Resource Report Resource Website 1+ mentions |
TEProf3 (RRID:SCR_027288) | software toolkit, source code, software resource | Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data. | Transposable Elements, Transposable Elements transcripts, detect TE transcripts, transcriptomic data, short-read RNA-seq data, long-read RNA-seq data, single cell RNA-seq data, | NHGRI R01HG007175; NIA R01AG078958; NINDS U24NS132103; NHGRI U01HG013227 |
PMID:40360186 | Free, Available for download, Freely available, | SCR_027288 | , TE-derived Promoter Finder 3 | 2026-08-14 09:29:53 | 1 | ||||||||
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EMImR Resource Report Resource Website 1+ mentions |
EMImR (RRID:SCR_027327) | data processing software, software application, data analysis software, time-series analysis software, software resource, source code, 1d time-series analysis software | Software application for identifying transcriptomic and epigenomic changes. | identifying transcriptomic and epigenomic changes, transcriptomic changes, epigenomic changes, | is related to: Shiny | Free, Available for download, Freely available | SCR_027327 | 2026-08-14 09:29:33 | 1 | ||||||||||
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EC-LMGraph Resource Report Resource Website 1+ mentions |
EC-LMGraph (RRID:SCR_027317) | source code, software application, simulation software, software resource | Software tool, which combine graph deep learning and protein language model, for accurate enzyme function and catalytic site prediction. | accurate enzyme function, catalytic site prediction, | Free, Available for download, Freely available | SCR_027317 | EC-LMGraph: Enzyme function and Catalytic Site | 2026-08-14 09:29:53 | 1 | ||||||||||
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University of Michigan Human Organoid Core Facility Resource Report Resource Website 1+ mentions |
University of Michigan Human Organoid Core Facility (RRID:SCR_027333) | service resource, access service resource, core facility | Core enables the use of primary human organoids as tissue models for discovery, translation and regenerative medicine by providing:access to high-quality, well-characterized neonatal through adult human organoid lines from multiple organs for investigators studying human development and disease; access to detailed protocols; access to specialized, quality controlled and batch-tested reagents; expertise, guidance and training; help obtaining data;help establishing organoid lines;letters of support for grant submissions. | organoid, NAMs, primary human tissue models, drug discovery, translation, regenerative medicine, development, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of Michigan; Ann Arbor; USA |
ABRF_4094 | https://coremarketplace.org/RRID:SCR_027333/?citation=1 | SCR_027333 | Human Organoid Multi-organ Biosample Repository, University of Michigan Human Organoid Core (UM-HOC, formerly the Translational Tissue Modeling Laboratory), University of Michigan Translational Tissue Modeling Laboratory Core Facility | 2026-08-14 09:29:53 | 4 | ||||||||
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MRanalysis Resource Report Resource Website 1+ mentions |
MRanalysis (RRID:SCR_027338) | production service resource, data analysis service, web application, software resource, service resource, analysis service resource | Web-based platform providing integrated and standardized Mendelian Randomization analysis workflow. This includes GWAS data quality assessment, power/ sample size estimation, MR analysis, SNP-to-gene enrichment analysis, and data visualization. Interactive R Shiny application designed for Mendelian randomization analysis. | Mendelian Randomization, Mendelian randomization analysis, | Free, Freely available | https://github.com/xingabao/MRanalysis | SCR_027338 | 2026-08-14 09:29:33 | 2 | ||||||||||
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BTE-RAG Resource Report Resource Website 1+ mentions |
BTE-RAG (RRID:SCR_027297) | software application, software resource, source code | Software application for BTE RAG implementation for DMDB QA datasets. Provides implementation of BTE-RAG framework, designed specifically for retrieval-augmented question answering (QA) in biomedical contexts. BTE-RAG leverages explicit mechanistic knowledge retrieval from BioThings Explorer (BTE) to significantly enhance the accuracy and reliability of large language models (LLMs) on biomedical benchmarks. | retrieval-augmented question answering in biomedical contexts, retrieval-augmented question answering, BTE RAG implementation, DMDB QA datasets, | Free, Available for download, Freely available, | SCR_027297 | 2026-08-14 09:29:40 | 1 | |||||||||||
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MarketScan by Merative Resource Report Resource Website 1+ mentions |
MarketScan by Merative (RRID:SCR_027329) | database, data or information resource | Employer-sourced medical and drugs claims database of the under-65 working population and their dependents, as well as 65+ with Medicare supplemental insurance paid by employers. | medical and drugs claims database, under-65 working population, Medicare, supplemental insurance population, | Restricted | SCR_027329 | 2026-08-14 09:29:41 | 1 | |||||||||||
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Howard Hughes Medical Institute at Janelia Research Campus Janelia Experimental Technology jET Core Facility Resource Report Resource Website 1+ mentions |
Howard Hughes Medical Institute at Janelia Research Campus Janelia Experimental Technology jET Core Facility (RRID:SCR_027301) | jET | service resource, access service resource, core facility | Core team designs, builds and tests instruments, tools, and software that enable novel scientific investigation. Offers expertise in Data acquisition and analysis; Machine vision and image processing; Precision machining; Embedded systems design and programming; Laser, microscopy, and optical imaging systems engineering; Custom circuit design; Novel sensor systems; Lab automation, robotics and motion control; Mechanical design, machined and/or fabricated components and assemblies; Process automation. | ABRF, process automation, systems design and programming, lab automation, robotics, design, build, test, instruments and software, |
is listed by: ABRF CoreMarketplace has parent organization: Howard Hughes Medical Institute |
ABRF_4084 | https://coremarketplace.org/RRID:SCR_027301/?citation=1 | SCR_027301 | , HHMI's Janelia Research Campus Janelia Experimental Technology, Janelia Experimental Technology (jET) | 2026-08-14 09:29:32 | 1 | |||||||
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State University of Campinas LIAFQ-IQ Laboratory of Physicochemical Analysis Core Facility Resource Report Resource Website 1+ mentions |
State University of Campinas LIAFQ-IQ Laboratory of Physicochemical Analysis Core Facility (RRID:SCR_027389) | service resource, access service resource, core facility | Laboratory for Physicochemical Analysis of IQ-UNICAMP houses equipment for a range of analytical techniques:Thermal Analysis comprises techniques that measure the physical or chemical properties of a substance, or its reaction products, under controlled temperature variation;Atomic Spectrometry enables multi-element determination in solution samples;Elemental Analysis is used to determine the Carbon, Hydrogen, and Nitrogen content in solid and viscous samples.Nitrogen Physisorption is a technique used to determine the surface area and pore size of solid materials. | ABRF, Physicochemical Analysis, Thermal Analysis, Atomic Spectrometry, Elemental Analysis, Nitrogen Physisorption, |
is listed by: ABRF CoreMarketplace has parent organization: State University of Campinas; São Paulo; Brazil |
ABRF_4607 | https://coremarketplace.org/?FacilityID=4607&citation=1 | SCR_027389 | , LIAFQ-IQ - Laboratory of Physicochemical Analysis, Universidade Estadual de Campinas (UNICAMP) LIAFQ-IQ - Laboratory of Physicochemical Analysis | 2026-08-14 09:29:34 | 1 | ||||||||
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DELAY Resource Report Resource Website 1+ mentions |
DELAY (RRID:SCR_027302) | source code, software application, software resource | Software application as convolutional neural network for inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. Used for depicting pseudotime-lagged causality for accurate gene-regulatory inference. | convolutional neural network, inference of gene-regulatory relationships, pseudotime-ordered single-cell trajectories, accurate gene-regulatory inference, | is organization facet of: BRAIN Initiative Cell Atlas Network | National Science Foundation Graduate Research Fellowship Grant ; Howard Hughes Medical Institute |
PMID:37113980 | Free, Available for download, Freely available, | SCR_027302 | DEpicting LAgged causalitY | 2026-08-14 09:29:53 | 2 | |||||||
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MCWorkflow Resource Report Resource Website 1+ mentions |
MCWorkflow (RRID:SCR_027305) | workflow, training material, data or information resource, source code, software resource, narrative resource | Software application as computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and procaryotic reference genomes. | workflow, metagenomics, contamination detection, | Knut and Alice Wallenberg Foundation ; Swedish Research Council ; SciLifeLab |
DOI:10.1101/2025.03.19.644176 | Free, Available for download, Freely available | SCR_027305 | Microbial Contamination Workflow | 2026-08-14 09:29:32 | 1 | ||||||||
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Transformers Resource Report Resource Website 1+ mentions |
Transformers (RRID:SCR_027381) | source code, software application, software resource | Software framework for machine learning models in text, computer vision, audio, video, and multimodal model, for both inference and training. | model-definition framework, | Free, Available for download, Freely available, | https://github.com/huggingface/transformers | SCR_027381 | 2026-08-14 09:29:54 | 8 |
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