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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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University of Chicago Human Tissue Resource Center Core Facility Resource Report Resource Website 10+ mentions |
University of Chicago Human Tissue Resource Center Core Facility (RRID:SCR_019199) | access service resource, core facility, service resource | Coordinated, centralized, and dedicated program for procuring, processing, dispersing and assessing all types of biospecimens together with downstream histology services. CAP Accredited. | USEDit, biospecimen procuring, biospecimen processing, biospecimen dispersing, biospecimen assessing, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of Chicago; Illinois; USA |
NCI P30CA014599 | ABRF_1085 | https://coremarketplace.org/?FacilityID=1085 | SCR_019199 | Human Tissue Resource Center | 2026-09-12 01:04:09 | 47 | |||||||
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University of Chicago Integrated Light Microscopy Core Facility Resource Report Resource Website 50+ mentions |
University of Chicago Integrated Light Microscopy Core Facility (RRID:SCR_019197) | access service resource, core facility, service resource | Offers microscopy imaging, including bright field color and DIC, fluorescence multi-dimension,TIRFM including bleaching, ablation, FLIM and high resolution, highspeed, high sensitivity, confocal, and physiologic techniques, STED, GSD3D, lightsheet selective plane illumination and lattice lightsheet structured illumination super resolution microscopy. | USEDit, microscopy, imaging, super resolution microscopy, confocal, fluorescence, physiologic techniques, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of Chicago; Illinois; USA |
NCI P30 CA014599 | ABRF_1083 | https://coremarketplace.org/?FacilityID=1083 | SCR_019197 | Integrated Light Microscopy | 2026-09-12 01:04:09 | 61 | |||||||
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New York University Grossman School of Medicine Langone Health Cytometry and Cell Sorting Laboratory Core Facility Resource Report Resource Website 10+ mentions |
New York University Grossman School of Medicine Langone Health Cytometry and Cell Sorting Laboratory Core Facility (RRID:SCR_019179) | access service resource, core facility, service resource | Provides access to flow cytometry and cell sorting technologies and instruments. If your research requires cytometric analysis, instruments acquire optical measurements using different lasers to detect fluorophores with high level of precision. | flow cytometry, cell sorting, cytometric analysis, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: New York University; New York; USA |
NCI P30CA016087 | ABRF_821 | https://coremarketplace.org/?FacilityID=821 | SCR_019179 | Cytometry and Cell Sorting Laboratory | 2026-09-12 01:04:09 | 22 | |||||||
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University of Nebraska Medical Center Advanced Microscopy Core Facility Resource Report Resource Website 10+ mentions |
University of Nebraska Medical Center Advanced Microscopy Core Facility (RRID:SCR_022467) | access service resource, core facility, service resource | Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options. | USEDit, ABRF, biomedical imaging, microscopy |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Nebraska; Nebraska; USA |
NCI CA036727; NCRR RR027301; NIGMS GM103427; NIGMS GM106397; NIH Office of the Director OD030486 |
open | ABRF_1375 | https://coremarketplace.org/?FacilityID=1375&citation=1 | SCR_022467 | UNMC Advanced Microscopy Core Facility | 2026-09-12 01:04:17 | 23 | ||||||
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MRQy Resource Report Resource Website 1+ mentions |
MRQy (RRID:SCR_025779) | data analysis software, data processing software, software application, software resource | Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data. | quantitative assessment, magnetic resonance imaging, computed tomography, imaging data, | NCI 1F31CA216935; NCI 1U01CA239055; NCI 1U01CA248226; NCI R01CA202752; NCI R01CA208236; NCI R01CA216579; NCI R01CA220581; NCI U24CA199374; NCRR 1C06RR12463; NHLBI R01HL15127701A1; NIBIB 1R43EB028736 |
PMID:33176026 | Free, Available for download, Freely available | SCR_025779 | 2026-09-12 01:04:52 | 1 | |||||||||
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STAR-Fusion Resource Report Resource Website 10+ mentions |
STAR-Fusion (RRID:SCR_025853) | software resource, source code | Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set. | identify candidate fusion transcripts, predict fusions, leverages chimeric and discordant read alignments, chimeric, discordant, read alignment, | Howard Hughes Medical Institute ; Klarman Cell Observatory ; NCI R21CA209940; NCI R50CA211461; NCI U01CA214846; NCI U24CA180922 |
PMID:31639029 | Free, Available for download, Freely available | SCR_025853 | 2026-09-12 01:04:53 | 47 | |||||||||
|
MethylSig Resource Report Resource Website 1+ mentions |
MethylSig (RRID:SCR_025849) | software resource, software toolkit | Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation. | whole genome DNA methylation analysis, whole genome DNA, DNA methylation, testing differentially methylated cytosines, whole-genome bisulfite sequencing, reduced representation bisulfite sequencing, | NCI R01CA158286; NIEHS P30 ES017885 |
PMID:24836530 | Free, Available for download, Freely available | SCR_025849 | 2026-09-12 01:04:53 | 3 | |||||||||
|
Moffitt spatialGE Resource Report Resource Website 1+ mentions |
Moffitt spatialGE (RRID:SCR_025980) | software resource, web application | Web application, a user friendly, point-and-click implementation of spatialGE R package. Contains collection of methods for visualization and spatial statistics analysis of tissue microenvironment and heterogeneity using spatial transcriptomics experiments. Used for user-friendly analysis of spatial transcriptomics data. | Moffitt Cancer Center, spatial transcriptomics data analysis, implementation of spatialGE R package, methods for visualization and spatial statistics analysis, tissue microenvironment and heterogeneity, spatial transcriptomics experiments, | NCI T32 CA23339; NCI U01 CA274489 |
DOI:10.1101/2024.06.27.601050 | Free, Freely available | SCR_025980 | Moffitt Cancer Center spatialGE, spatialGE | 2026-09-12 01:04:55 | 1 | ||||||||
|
ArCH Resource Report Resource Website 1+ mentions |
ArCH (RRID:SCR_025975) | ArCH | software resource, software toolkit | Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants. | sequencing studies analysis, somatic variant calling, detect low variant allele fraction, clonal hematopoiesjsonsis variants, | American Society of Hematology ; Edward P. Evans Foundation ; NCI K08 CA241318; NCI P30 CA008748 |
PMID:38485690 | Free, Available for download, Freely available, | SCR_025975 | , ArCH: Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline, Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline | 2026-09-12 01:04:55 | 1 | |||||||
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TRUST4 Resource Report Resource Website 10+ mentions |
TRUST4 (RRID:SCR_026162) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. Performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length. | analyze TCR and BCR sequences, de novo assembly, unselected RNA sequencing data, fluid and solid tissues, tumors, | NCI U01CA226196; NCI U24CA224316 |
PMID:33986545 | Free, Available for download, Freely available | SCR_026162 | 2026-09-12 01:04:59 | 12 | |||||||||
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TNBCtype Resource Report Resource Website 1+ mentions |
TNBCtype (RRID:SCR_026238) | software resource, web application | Website for predicting the subtype of triple negative breast cancer sample based on its gene expression profile. | predicting subtype, triple negative breast cancer sample, gene expression profile, | American Cancer Society ; Komen Foundation ; NCI CA009385; NCI CA068485; NCI CA070856; NCI CA105436; NCI CA148375; NCI CA95131 |
PMID:22872785 | Free, Freely available | SCR_026238 | 2026-09-12 01:05:00 | 4 | |||||||||
|
scVital Resource Report Resource Website 1+ mentions |
scVital (RRID:SCR_026215) | software application, software resource, source code | Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data. | embed scRNA-seq data, species-agnostic latent space, overcome batch effect, identify cell states shared between species, cross-species integration, scRNA-seq data, | NCI K08 CA267072; NCI P30 CA08748; NCI R01 CA290400; NIA R01 AG054720 |
DOI:10.1101/2024.12.20.629285 | Free, Available for download, Freely available | SCR_026215 | 2026-09-12 01:05:00 | 1 | |||||||||
|
DSigDB Resource Report Resource Website 100+ mentions |
DSigDB (RRID:SCR_026202) | data or information resource, database | Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets. | gene sets, quantitative inhibition, drug induced, gene expression changes, data, drugs, compounds, | NCI P30CA046934; NCI P50CA058187 |
PMID:25990557 | Free, Freely available, | SCR_026202 | , Drug Signatures Database, drug SIGnatures DataBase | 2026-09-12 01:04:59 | 165 | ||||||||
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FACETS Resource Report Resource Website 10+ mentions |
FACETS (RRID:SCR_026264) | data analysis software, data processing software, software application, software resource, source code | Software tool for estimating genome copy numbers from high throughput DNA sequencing data. Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Used to implement Fraction and Copy number Estimate from Tumor/normal Sequencing. | Allele-specific copy number, clonal heterogeneity analysis, estimating genome copy numbers, high throughput DNA sequencing data, Fraction and Copy number Estimate from Tumor/normal Sequencing, | NCI CA124514; NCI CA163251; NCI CA195365; NCI P01 CA129243; NCI P30 CA008748; Susan G. Komen for the Cure |
PMID:27270079 | Free, Available for download, Freely available, | SCR_026264 | 2026-09-12 01:05:01 | 22 | |||||||||
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Eastern Cooperative Oncology Group Performance Status Scale Resource Report Resource Website 1+ mentions |
Eastern Cooperative Oncology Group Performance Status Scale (RRID:SCR_026432) | data or information resource, narrative resource, organization portal, portal, standard specification | ECOG Performance Scale describes patient’s level of functioning in terms of their ability to care for themself, daily activity, and physical ability (walking, working, etc.). Standard criteria for measuring how the disease impacts patient’s daily living abilities. Used to assess the functional status of patient. | ECOG-ACRIN Cancer Research Group, patient’s performance status, assess patient functional status, conduct clinical trials, | NCI | Free, Freely available | SCR_026432 | ECOG Performance Status Scale | 2026-09-12 01:05:04 | 5 | |||||||||
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MeTPeak Resource Report Resource Website 10+ mentions |
MeTPeak (RRID:SCR_026533) | software resource, software toolkit, source code | Software package for finding the location of m6A sites in MeRIP-seq data. | finding location of m6A sites, MeRIP-seq data | Natural Science Foundation of China ; NCI P30CA54174; NCI U54 CA113001; NIGMS R01 GM113245; NSF |
PMID:27307641 | Free, Available for download, Freely available | SCR_026533 | 2026-09-12 01:05:06 | 11 | |||||||||
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HiGlass Resource Report Resource Website 10+ mentions |
HiGlass (RRID:SCR_026687) | software resource, source code, web application | Web-based visual exploration and analysis of genome interaction maps. | visual exploration and analysis, genome interaction maps, | NCI U01CA200059; NHGRI R00 HG007583; NHGRI U54 HG007963 |
PMID:30143029 | Free, Available for download, Freely available | SCR_026687 | 2026-09-12 01:05:09 | 45 | |||||||||
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AMICI Resource Report Resource Website |
AMICI (RRID:SCR_026913) | software resource, software toolkit, source code | Software toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification. Used for high-performance sensitivity analysis for large ordinary differential equation models. | high-performance sensitivity analysis, large ordinary differential equation models, | European Unions Horizon 2020 ; Federal Ministry of Education and Research of Germany ; German Research Foundation ; NCI U54 CA225088 |
PMID:33821950 | Free, Available for download, Freely available | SCR_026913 | Advanced Multilanguage Interface to CVODES and IDAS | 2026-09-12 01:05:14 | 0 | ||||||||
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OpenTOPAS Resource Report Resource Website 1+ mentions |
OpenTOPAS (RRID:SCR_026927) | software application, software resource, source code | Software Monte Carlo tool for particle simulation. Used for simulation of medical applications of ionizing radiation with the Monte Carlo method. Allows to assemble and control library of simulation objects (geometry components, particle sources, scorers, etc.) with no need to write C++ code and without knowledge of underlying Geant4 Simulation Toolkit. | Monte Carlo method, particle simulation, simulation of medical applications, ionizing radiation, | NCI R01 CA140735; NCI U24 CA215123 |
PMID:23127075 PMID:32247964 |
Free, Available for download, Freely available | https://opentopas.github.io/ | SCR_026927 | , TOPAS, TOol for PArticle Simulation | 2026-09-12 01:05:15 | 2 | |||||||
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apeglm Resource Report Resource Website 1+ mentions |
apeglm (RRID:SCR_026951) | software resource, software toolkit | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NCI P01 CA142538; NHGRI R01 HG009125; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-09-12 01:05:15 | 2 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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