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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Magee-Womens Research Institute Magee Obstetric Medical and Infant Database and Biobank Core Facility Resource Report Resource Website 1+ mentions |
Magee-Womens Research Institute Magee Obstetric Medical and Infant Database and Biobank Core Facility (RRID:SCR_025230) | MOMI | service resource, access service resource, core facility | Core provides collection of obstetric biological materials from prenatal visits through delivery along with annotated clinical information. In addition to specimen access, MOMI staff can provide study design assistance as needed. | ABRF, infant, obstetric biological materials, prenatal visits through delivery samples, specimen access, | is listed by: ABRF CoreMarketplace | ABRF_2714 | https://coremarketplace.org/?FacilityID=2714&citation=1 | SCR_025230 | Magee Obstetric Medical and Infant Database and Biobank | 2026-08-14 09:29:32 | 1 | |||||||
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NextPolish Resource Report Resource Website 100+ mentions |
NextPolish (RRID:SCR_025232) | data processing software, software application, data analysis software, source code, software resource | Software tool to fix base errors SNV/Indel in genome generated by noisy reads. Used to correct error bases in reference genome. | fix base errors, SNV/Indel, genome, noisy reads, correct error bases, reference genome, | Free, Available for download, Freely available | SCR_025232 | 2026-08-14 09:28:58 | 105 | |||||||||||
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cuteSV Resource Report Resource Website 10+ mentions |
cuteSV (RRID:SCR_025233) | data processing software, software application, data analysis software, source code, software resource | Software tool for long read based human genomic structural variation detection. Collects signatures of various types of SVs and employs clustering-and-refinement method to analyze signatures to implement sensitive SV detection.cuteSV2 is upgraded version of cuteSV. | long-read-based SV detection, structural variation, SV detection, structural variation detection, long read based human genomic structural variation detection, | NSF of China | DOI:10.1101/2022.08.29.505534 PMID:35751813 |
Free, Available for download, Freely available | SCR_025233 | cuteSV2 | 2026-08-14 09:29:33 | 20 | ||||||||
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m6anet Resource Report Resource Website 1+ mentions |
m6anet (RRID:SCR_025234) | data processing software, software application, data analysis software, source code, software resource | Software Python tool for detection of m6A from direct RNA-Seq data. Leverages multiple instance learning framework to detect m6a modifications from Nanopore Direct RNA Sequencing data. | Nanopore Direct RNA Sequencing data, detection of m6A, RNA-Seq data, | PMID:36357692 | Free, Available for download, Freely available | SCR_025234 | 2026-08-14 09:29:11 | 7 | ||||||||||
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University of Pittsburgh Hillman Cancer Center Biostatistics Core Facility Resource Report Resource Website 1+ mentions |
University of Pittsburgh Hillman Cancer Center Biostatistics Core Facility (RRID:SCR_025355) | service resource, access service resource, core facility | Provides statistical and computational methods for design, execution, analysis, and reporting of cancer-related research studies and trials including biomarker analysis and grant development. | ABRF, statistical services, cancer-related research studies and trials, biomarker analysis, |
is listed by: ABRF CoreMarketplace has parent organization: University of Pittsburgh; Pennsylvania; USA |
ABRF_2778 | https://coremarketplace.org/?FacilityID=2778&citation=1 | SCR_025355 | UPMC Hillman Cancer Center Biostatistics Facility (BF), Biostatistics Facility (BF) | 2026-08-14 09:29:35 | 1 | ||||||||
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StereoSiTE Resource Report Resource Website 1+ mentions |
StereoSiTE (RRID:SCR_025236) | data processing software, software application, data analysis software, source code, software resource, data visualization software | Software Python package for analysis and visualization of spatial transcriptomics data. Framework to spatially and quantitatively profile the cellular neighborhood organized iTME. | Spatial Transcriptomics, Spatial Transcriptome Analysis, Python | DOI:10.1101/2022.12.31.522366 | Free, Available for download, Freely available | SCR_025236 | 2026-08-14 09:29:33 | 2 | ||||||||||
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University of Pittsburgh Hillman Cancer Center Cancer Genomics Core Facility Resource Report Resource Website 1+ mentions |
University of Pittsburgh Hillman Cancer Center Cancer Genomics Core Facility (RRID:SCR_025357) | service resource, access service resource, core facility | Supports genomics and transcriptomics platforms including nucleic acid extraction, sample QC, next-generation library preparation and sequencing. Specializes in paraffin-embedded tissue samples. | ABRF, genomics, transcriptomics, nucleic acid extraction, sample QC, next-generation library preparation, sequencing |
is listed by: ABRF CoreMarketplace has parent organization: University of Pittsburgh; Pennsylvania; USA |
ABRF_2781 | https://coremarketplace.org/?FacilityID=2781&citation=1 | SCR_025357 | , Cancer Genome Facility (CGF), UPMC Hillman Cancer Center Cancer Genome Facility (CGF) | 2026-08-14 09:29:00 | 2 | ||||||||
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MCMCtreeR Resource Report Resource Website 10+ mentions |
MCMCtreeR (RRID:SCR_025348) | software toolkit, source code, software resource | Software R package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree. Helps users choose parameters to reflect age information for prior age distributions, visualise time priors, and produce output files ready to be used in MCMCtree. Used to prepare MCMCtree analyses and visualize posterior ages on trees. | estimate distribution values, temporal node constraints, prepare input files for MCMCtree, | PMID:31292621 | Free, Available for download, Freely available | SCR_025348 | 2026-08-14 09:29:00 | 17 | ||||||||||
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yEd Resource Report Resource Website 1+ mentions |
yEd (RRID:SCR_025325) | software application, software resource | Software desktop application as general purpose diagramming program with multi-document interface. Cross-platform Java application to generate high-quality diagrams. Runs on Windows, Linux, Mac OS, and other platforms that support Java Virtual Machine. | yWorks, Java, general purpose diagramming program, diagrams, | Restricted | SCR_025325 | yWorks yEd Graph Editor | 2026-08-14 09:28:59 | 7 | ||||||||||
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LIFEx Resource Report Resource Website 100+ mentions |
LIFEx (RRID:SCR_025284) | data processing software, software application, software resource, image analysis software | Software for calculation of radiomic features for medical images. Enables calculation of conventional, histogram based, textural, and shape features from PET, SPECT, MR, CT, and US images, or from any combination of imaging modalities. Dedicated to researchers, radiologists, nuclear medicine physicians and oncologists to give access to 306 histogram, textural and shape indices in addition to conventional indices and where users can change calculation options. | radiomic features calculation, medical images, histogram, textural, shape features, PET, SPECT, MR, CT, US, images, | IDEX Paris-Saclay University ; European Commission |
PMID:29959149 | Restricted | SCR_025284 | 2026-08-14 09:29:34 | 116 | |||||||||
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TooManyCellsInteractive Resource Report Resource Website 1+ mentions |
TooManyCellsInteractive (RRID:SCR_025315) | TMCI | software resource, web application, source code | Web browser-based JavaScript application for visualizing hierarchical cellular populations as interactive radial tree. Allows users to explore, filter, and manipulate hierarchical data structures through intuitive interface while also enabling batch export of high-quality custom graphics. | Single-Cell Analysis, Data Visualization, hierarchical data structures, visualizing hierarchical cellular populations, interactive radial tree, custom graphics, |
is related to: too-many-cells-python is related to: TooManyCells |
Free, Available for download, Freely available | https://schwartzlab-methods.github.io/too-many-cells-interactive/ | SCR_025315 | 2026-08-14 09:28:59 | 1 | ||||||||
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GBMatch_CNN - GBMPredictor Resource Report Resource Website 1+ mentions |
GBMatch_CNN - GBMPredictor (RRID:SCR_025316) | source code, software application, software resource | Software tool for predicting TS and risk from glioblastoma whole slide images. Used to predict risk scores and transcriptional subtypes from whole slide images of glioblastomas. | Histology, predicting TS, glioblastoma whole slide images, predict risk scores, predict transcriptional subtypes, whole slide images, glioblastomas, | Free, Available for download, Freely available | SCR_025316 | 2026-08-14 09:29:34 | 1 | |||||||||||
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FusionGDB2 Resource Report Resource Website 1+ mentions |
FusionGDB2 (RRID:SCR_025299) | database, data or information resource | Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level. | Functional annotation database, human fusion genes, fusion gene breakage tendency score, | NIGMS R35GM138184; University of Texas |
PMID:34755868 | Free, Freely available | SCR_025299 | FusionGDB 2.0 | 2026-08-14 09:29:34 | 4 | ||||||||
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gNOMO2 Resource Report Resource Website 1+ mentions |
gNOMO2 (RRID:SCR_025293) | software toolkit, source code, software resource | Software as comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes. Enables integration of taxonomic and functional analyses in microbiome multi-omics data. | microbiome, multi-omics, data integration, amplicon sequencing, metagenomics, metatranscriptomics, metaproteomics | TUBITAK | DOI:10.1101/2023.12.03.569767 | Free, Available for download, Freely available | SCR_025293 | 2026-08-14 09:29:34 | 1 | |||||||||
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ParaVision 360 Resource Report Resource Website 1+ mentions |
ParaVision 360 (RRID:SCR_025295) | software application, software resource | Software for preclinical imaging integrated with Bruker MRI spectrometers. Used with Bruker MRI, PET/MR, and PET/CT instruments. Enables easy and high throughput imaging. All images, protocols, and subjects are in one location with inherent co-registration, image fusion, data processing, and analysis. | preclinical imaging integrated with Bruker MRI spectrometers, preclinical imaging, Bruker MRI spectrometers, data processing, data analysis, | Restricted | SCR_025295 | 2026-08-14 09:28:59 | 2 | |||||||||||
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Purdue University Cryo-Electron Microscopy Core Facility Resource Report Resource Website 1+ mentions |
Purdue University Cryo-Electron Microscopy Core Facility (RRID:SCR_025545) | service resource, access service resource, core facility | Facility provides access to instrumentation enabling users to collect data for high-resolution single particle reconstructions and tomographic studies of cells and larger complexes. | ABRF, single particle reconstructions, tomographic studies, cells and larger complexes, |
is listed by: ABRF CoreMarketplace has parent organization: Purdue University; West Lafayette; Indiana |
ABRF_2835 | https://indianactsi.org/servicecores/core/63/, https://coremarketplace.org/?FacilityID=2835&citation=1 | SCR_025545 | Cryo-Electron Microscopy, Purdue Cryo-EM Facility | 2026-08-14 09:29:15 | 5 | ||||||||
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VolcaNoseR Resource Report Resource Website 100+ mentions |
VolcaNoseR (RRID:SCR_025419) | data access protocol, software resource, web application, web service | Web app for creating, exploring, labeling and sharing volcano plots . The plot can be annotated to show genes/proteins based on their top ranking or based on user input. | Plot, creating, exploring, labeling, sharing, volcano plots | DOI:10.1038/s41598-020-76603-3 | Free, Freely available, | SCR_025419 | 2026-08-14 09:29:01 | 111 | ||||||||||
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University of Nebraska-Lincoln Methodology and Evaluation Research Core Facility Resource Report Resource Website 1+ mentions |
University of Nebraska-Lincoln Methodology and Evaluation Research Core Facility (RRID:SCR_025551) | MERC | service resource, access service resource, core facility | Provides range of evaluation and data services to support client needs.Through consulting, evaluation, methodology, and training, we work to fill gaps and improve and empower data driven decision making.At the proposal stage of grants, we can design evaluation plans to meet your project needs, with the associated narrative text, budget, and letter of collaboration, as needed. We can also fill gaps post-award, or provide support with internal funding. We can assist with logic models, Broader Impacts, methodologies, needs assessments, survey design and implementation, support with Institutional Review Board applications, and trainings in our areas of expertise. | evaluation and data services, consulting, evaluation, methodology, training, |
is listed by: ABRF CoreMarketplace has parent organization: University of Nebraska; Nebraska; USA |
Open | ABRF_2871 | https://coremarketplace.org/?FacilityID=2871&citation=1 | SCR_025551 | Methodology and Evaluation Research Core Facility | 2026-08-14 09:29:03 | 1 | ||||||
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Notre Dame Freimann Life Science Center Core Facility Resource Report Resource Website 1+ mentions |
Notre Dame Freimann Life Science Center Core Facility (RRID:SCR_025552) | FLSC | service resource, access service resource, core facility | Home to virtually all laboratory animals. Services include Procurement, Animal care, Breeding, Training,Limited procedures for research. | ABRF, laboratory animals, procurement, animal care, breeding, training, procedures |
is listed by: ABRF CoreMarketplace has parent organization: University of Notre Dame; Indiana; USA |
Restricted | ABRF_2872 | https://indianactsi.org/servicecores/core/26/, https://coremarketplace.org/?FacilityID=2872&citation=1 | SCR_025552 | Freimann Life Sciences Center (FLSC) | 2026-08-14 09:29:39 | 1 | ||||||
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V-pipe Resource Report Resource Website 1+ mentions |
V-pipe (RRID:SCR_025399) | data processing software, workflow, software application, data analysis software, training material, data or information resource, software resource, source code, sequence analysis software, narrative resource | Software pipeline for analysis of next-generation sequencing data derived from intra-host and environmental viral populations. Designed for analysing NGS data of short viral genomes. Used for assessing viral genetic diversity from high-throughput data. | viral sequencing data, next-generation sequencing data, viral populations, analysing NGS data, short viral genomes. | Swiss Institute of Bioinformatics | PMID:33471068 | Free, Available for download, Freely available | SCR_025399 | 2026-08-14 09:29:00 | 1 |
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