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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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Research-tested Intervention Programs (RTIPs) Resource Report Resource Website 10+ mentions |
Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) | RTIPs | data or information resource, database | Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials. | cancer, control, intervention, prevention, diagnosis, planning, research, program, public, health, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
cancer | NCI | Freely available, Public | biotools:rtips | https://bio.tools/rtips | SCR_016042 | SciCrunch Registry | Research-tested Intervention Programs | 2026-10-17 01:33:39 | 25 | ||||
|
ClinGen Resource Report Resource Website 1000+ mentions |
ClinGen (RRID:SCR_014968) | CGR | data or information resource, database | Genomics knowledgebase for clinical relevance of genes and variants for use in research. ClinGen's primary function is to store and share information for the benefit of the scientific community. Laboratory scientists, clinicians, and patients can share and access data. | database, knowledgebase, genomics, healthcare, clinical, FASEB list | is related to: CivicDb | Eunice Kennedy Schriver NICHD ; NHGRI U41 HG006834-01A1; NHGRI U01 HG007437-01; NHGRI U01 HG007436-01; NCI HHSN261200800001E; NCI contract HHSN261200800001E |
PMID:26014595 | Free, Available to the scientific community | SCR_014968 | SciCrunch Registry | Clinical Genome Resource (ClinGen), Clinical Genome Resource | 2026-10-17 01:33:36 | 1153 | ||||||
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Pancreatlas Resource Report Resource Website 10+ mentions |
Pancreatlas (RRID:SCR_018567) | atlas, data or information resource | Collection of human pancreas data and images. Platform to share data from human pancreas samples. Houses reference datasets from human pancreas samples, achieved through generosity of organ donors and their families. | Human pancreas data, pancreas image, reference dataset, human pancreas sample, organ donor pancreas data |
lists: Exeter Archival Diabetes Biobank (EADB) is related to: Vanderbilt University; Tennessee; USA is related to: Human Islet Research Network (HIRN) works with: Exeter Archival Diabetes Biobank (EADB) |
Type 1 diabetes, Diabetes, Type 2 diabetes, Cystic Fibrosis-Related Diabetes | Leona M. and Harry B. Helmsley Charitable Trust ; NCI CA68485; NEI EY08126; NIDDK DK104211; NIDDK DK106755; NIDDK DK108120; NIDDK DK112232; NIDDK DK20593; NIDDK DK58404; NIDDK DK59637 |
Free, Freely available | SCR_018567 | SciCrunch Registry | 2026-10-17 01:33:39 | 13 | ||||||||
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Robot Reviewer Resource Report Resource Website 1+ mentions |
Robot Reviewer (RRID:SCR_018961) | software application, software resource, text extraction software | Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments. | Automated review, data mining, manuscript screening, artificial intelligence, automatic evidence synthesis, evidence synthesis, trial conduct information, data trial, bias, bias assessement | NCI UH2 CA203711; NLM R01 LM012086; UK Medical Research Council |
PMID:26104742 | Free, Freely available | SCR_018961 | SciCrunch Registry | 2026-10-17 01:33:39 | 7 | |||||||||
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SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. | scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories | NCI K99 CA252020; NIMH U19 MH114831; UCSD School of Medicine |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | SciCrunch Registry | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-10-17 01:31:48 | 23 | |||||||
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RobotReviewer Resource Report Resource Website 1+ mentions |
RobotReviewer (RRID:SCR_021064) | software application, software resource, text-mining software, web application | Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials. | Data automatic extraction, clinical trial reports, automatically extract key data, Evidence Based Medicine, text journal articles processing, randomized controlled trials |
is related to: Northeastern University; Massachusetts; USA is related to: University of Texas at Austin; Texas; USA |
Medical Research Council UK ; NCI UH2 CA203711; NLM R01 LM012086 |
PMID:29093610 DOI:10.1093/jamia/ocv044 |
Free, Available for download, Freely available | https://github.com/ijmarshall/robotreviewer, https://robotreviewer.vortext.systems/ | SCR_021064 | SciCrunch Registry | Automating Biomedical Evidence Synthesis | 2026-10-17 01:31:51 | 1 | ||||||
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Exemplar Microscopy Images of Tissues Resource Report Resource Website 1+ mentions |
Exemplar Microscopy Images of Tissues (RRID:SCR_021052) | EMIT | 2d spatial image, data or information resource, data repository, data set, experimental protocol, image, image collection, image repository, immuno detection protocol, immunofluorescence, narrative resource, service resource, storage service resource | Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets. | Reference dataset, multiplexed immunofluorescence microscopy images, tissue microarray, cyclic immunofluorescence, tissues images, tumors images |
is related to: Synapse is related to: Harvard Medical School; Massachusetts; USA |
glioblastoma, lung adenocarcinoma, prostate adenocarcinoma, seminoma, meningioma, mesothelioma, GI stromal tumor, liver cirrhosis, leiomyosarcoma, high-grade serous ovarian cancer, diverticulitis, acute appendicitis, metastatic melanoma, dedifferentiated liposarcoma | Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation ; NCI U2C CA233262; NCI U2C CA233280; NIH U54 CA225088 |
DOI:10.1101/2021.03.15.435473 | Restricted | SCR_021052 | SciCrunch Registry | Exemplar Microscopy Images of Tissues ( and Tumors) | 2026-10-17 01:30:33 | 3 | |||||
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Appyters Resource Report Resource Website 10+ mentions |
Appyters (RRID:SCR_021245) | software resource, web application | Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms. | Jupyter Notebooks, data-driven web apps collection, Jupyter Notebook results report |
is used by: Hypothesis Center has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24 CA224260; NHLBI U54 HL127624; NIH Office of the Director OT2 OD030160 |
DOI:10.1016/j.patter.2021.100213 | Free, Available for download, Freely available | https://github.com/MaayanLab/appyter, https://github.com/MaayanLab/appyter-catalog | SCR_021245 | SciCrunch Registry | 2026-10-17 01:30:39 | 16 | |||||||
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Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility (RRID:SCR_014873) | access service resource, core facility, service resource | Facility that aims to investigate role of metabolism in cancer on cellular and organismal level, combining in vitro and in vivo analysis. Comprehensive metabolic facility, including stable isotope tracing and flux analysis. Provides analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All instruments and approaches are available on fee-for-service basis to Cancer Center scientists, but alsoto outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis. | Cancer metabolism, cellular metabolism, metabolism analysis, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Sanford Burnham Prebys Medical Discovery Institute |
NCI P30CA030199 | Open | ABRF_565 | https://coremarketplace.org/?FacilityID=565 | http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_CancerMetabolism.aspx | SCR_014873 | SciCrunch Registry | SBP Cancer Metabolism Core, Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core, SBP Medical Discovery Institute Cancer Metabolism Core | 2026-10-17 01:36:19 | 0 | |||||
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Sanford Burnham Prebys Medical Discovery Institute Flow Cytometry Core Resource Report Resource Website 1+ mentions |
Sanford Burnham Prebys Medical Discovery Institute Flow Cytometry Core (RRID:SCR_014854) | access service resource, core facility, service resource | Facility that provides access to high-speed cell sorting, analytical flow cytometry, imaging flow cytometry, and validated immune profiling spectral antibody panels. Core staff provide technical expertise in experiment design, data analysis, hardware and software training, operate the facility cell sorters, and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist. | ABRF, cell sorting, analytical flow cytometry, spectral, full spectrum, FACS, imaging flow cytometry, immune profiling, antibody panel |
is listed by: ABRF CoreMarketplace has parent organization: Sanford Burnham Prebys Medical Discovery Institute |
NCI P30CA030199; NIH Office of the Director S10OD032325; NIH Office of the Director S10OD040289 |
ABRF_446 | https://coremarketplace.org/?FacilityID=446&citation=1 | SCR_014854 | SciCrunch Registry | SBP Flow Cytometry Core, SBP Flow Cytometry Facility, Sanford Burnham Prebys Medical Discovery Institute Flow Cytometry Core, Sanford Burnham Prebys Medical Discovery Institute Flow Cytometry Shared Resource, SBP Medical Discovery Institute Flow Cytometry Facility | 2026-10-17 01:36:18 | 2 | |||||||
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Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) Resource Report Resource Website 10+ mentions |
Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) | SALK IGC, IGC | access service resource, core facility, service resource | Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications. | core facility, gene, genomic, genomic data, analysis, consultation, applications | Helmsley Trust ; NCI CA014195; Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility |
Open | SCR_014842 | SciCrunch Registry | , Integrative Genomics, Salk, Core Facility, Institute, Razavi Newman, UCSD, Bioinformatics | 2026-10-17 01:37:18 | 38 | ||||||||
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SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software resource, software toolkit | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | American Cancer Society Research Scholar Grant ; NCI U24CA143835; NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950 |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SciCrunch Registry | SYstems Genetic Network AnaLysis | 2026-10-17 01:35:06 | 1 | ||||||||
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mtradeR Resource Report Resource Website 1+ mentions |
mtradeR (RRID:SCR_022977) | software resource, software toolkit | Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually. | test association between taxa and disease risk, correlated taxa screening, taxa and disease risk | American Lebanese Syrian Associated Charities ; NCI CA21765; NIDDK U24DK097771 |
PMID:36123651 | Free, Available for download, Freely available | SCR_022977 | SciCrunch Registry | Metagenomic TRajectory Analysis with Disease Endpoint and Risk factors | 2026-10-17 01:34:33 | 1 | ||||||||
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SCRuB Resource Report Resource Website 1+ mentions |
SCRuB (RRID:SCR_023518) | software resource, software toolkit | Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program. | Source tracking, contamination removal, microBiomes, MiSeq decontamination, contamination in microbial studies, | CIFAR Azrieli Global Scholarship ; Columbia University ; NCI R01CA245894; NICHD R01HD106017; Rockefeller University |
PMID:36928429 | Free, Available for download, Freely available | SCR_023518 | SciCrunch Registry | Source-tracking for Contamination Removal in microBiomes, Source tracking for Contamination Removal in microBiomes | 2026-10-17 01:34:36 | 2 | ||||||||
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bam readcount Resource Report Resource Website 10+ mentions |
bam readcount (RRID:SCR_023653) | software application, software resource | Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads. | BAM file, CRAM file, sequencing data, nucleotide positions, | Edward P. Evans Foundation ; NCI 1U01CA209936; NCI K22CA188163; NCI P01CA101937; NCI R50CA211782; NCI U24CA237719; NHGRI R00 HG007940 |
PMID:34341766 | Free, Available for download, Freely available | SCR_023653 | SciCrunch Registry | bam-readcount | 2026-10-17 01:36:14 | 38 | ||||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, software resource, source code | Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer. | Cancer Genes, SNV, indel, gene-specific probabilistic estimates, strength of negative and positive selection, cancer | NCI U54 CA143874; NIGMS R01 GM078598; NIMH R01 MH101244 |
PMID:29106416 | Free, Available for download, Freely available | https://github.com/weghornlab/CBaSE, http://genetics.bwh.harvard.edu/cbase | SCR_027765 | SciCrunch Registry | Cancer Bayesian SElection estimation | 2026-10-17 01:39:20 | 0 | |||||||
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T Cell ExTRECT Resource Report Resource Website 1+ mentions |
T Cell ExTRECT (RRID:SCR_027742) | software resource, software toolkit, source code | 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, | NCATS UL1TR000100; NCI P30CA023100; NCI R21CA177519; NCI U01CA196406; NHLBI U54HL108460; NIH Office of the Director DP5OD017937; NLM T15LM011271; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | SciCrunch Registry | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-10-17 01:37:52 | 1 | ||||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, software resource, software toolkit, source code | 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, | NCI R01 CA227388; NCI R37 CA222574; NCI U01 CA233100; NIGMS T32 GM008313; NSF |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | SciCrunch Registry | 2026-10-17 01:38:25 | 4 | |||||||||
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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 application, software resource | 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 P01 CA11816; NCI RO1 CA127612; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | SciCrunch Registry | 2026-10-17 01:39:21 | 2 | ||||||||
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tximeta Resource Report Resource Website 1+ mentions |
tximeta (RRID:SCR_028005) | software resource, software toolkit | Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility. | reference sequence checksums, provenance identification in RNA-seq, numerous annotation, metadata gathering, | NCI P01 CA142538; NHGRI R01 HG009937; NHGRI U41 HG004059; NIEHS P30 ES010126; NIMH R01 MH118349 |
PMID:32097405 | Free, Available for download, Freely available | SCR_028005 | SciCrunch Registry | Tximeta | 2026-10-17 01:37:56 | 1 |
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