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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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Bismark Resource Report Resource Website 1000+ mentions |
Bismark (RRID:SCR_005604) | Bismark | software resource | Software tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step. | Map bisulfite treated sequence reads, determine cytosine methylation states, genome, sequence reads, perform methylation calls, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
PMID:21493656 DOI:10.1093/bioinformatics/btr167 |
Free, Available for download, Freely available | biotools:bismark, OMICS_00575 | https://github.com/FelixKrueger/Bismark, https://bio.tools/bismark | https://sources.debian.org/src/bismark/ | SCR_005604 | 2026-08-01 12:02:55 | 1123 | |||||
|
jMHC Resource Report Resource Website 10+ mentions |
jMHC (RRID:SCR_005605) | jMHC | software resource | Software for analyzing and visualization of the results of deep amplicon sequencing. | matlab |
is listed by: OMICtools has parent organization: Google Code |
PMID:21676201 | GNU General Public License, v3, Acknowledgement requested | OMICS_00300 | SCR_005605 | jmhc - software for analyzing and visualization of the results of deep amplicon sequencing | 2026-08-01 12:02:56 | 10 | ||||||
|
TMA-Combiner Resource Report Resource Website 1+ mentions |
TMA-Combiner (RRID:SCR_005600) | TMA-Combiner | software resource | A Simple Software Tool to Permit Analysis of Replicate Cores on Tissue Microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tissue microarray |
is listed by: OMICtools is related to: Stanford TMA Software has parent organization: Stanford University; Stanford; California |
PMID:16258508 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00822 | SCR_005600 | 2026-08-01 12:03:00 | 1 | |||||||
|
TMAJ Resource Report Resource Website 10+ mentions |
TMAJ (RRID:SCR_005601) | TMAJ | software resource | Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. | tissue microarray, java, java swing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA has parent organization: SourceForge |
GNU General Public License, v3 | biotools:tmaj, OMICS_00823 | https://bio.tools/tmaj | SCR_005601 | TMAJ Software Project | 2026-08-01 12:02:55 | 10 | ||||||
|
GOProfiler Resource Report Resource Website 1+ mentions |
GOProfiler (RRID:SCR_005683) | GOProfiler | service resource | Service that provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided. | ontology or annotation browser, annotation, protein, gene ontology |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
PMID:16961921 | Free for academic use | OMICS_02269, nlx_149127 | SCR_005683 | 2026-08-01 12:03:01 | 2 | |||||||
|
National Hellenic Research Foundation Resource Report Resource Website 1+ mentions |
National Hellenic Research Foundation (RRID:SCR_005719) | NHRF | institution | The National Hellenic Research Foundation (NHRF) is a multidisciplinary Research Centre established by Royal Decree on 9th October 1958. Its purpose is the organisation, finance and support of high-level research projects in the humanities and the natural sciences. The Humanities Institute cover a wide spectrum of study and research fields in Greek history and culture, contributing substantially and critically to the knowledge and promotion of Greek identity. The Natural Sciences Institutes perform basic and applied research in leading edge areas of science such as health, pharmaceuticals, environment, biotechnology and new materials. They develop innovative methods for solving complex problems facing Greek industry and they provide specialised services and know-how both to the public and private sector. The NHRF is governed by the Board of Directors and the Central Administration under the Director/Chairman of the Board. | humanities, natural sciences | is parent organization of: StRAnGER | ISNI: 0000 0001 2232 6894, grid.22459.38, Wikidata: Q1248816, nlx_149177 | https://ror.org/033m02g29 | SCR_005719 | National Hellenic Research Foundation | 2026-08-01 12:03:01 | 4 | |||||||
|
Stanford TMA Software Resource Report Resource Website 1+ mentions |
Stanford TMA Software (RRID:SCR_005598) | Stanford TMA | software resource | Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays. | tissue microarray |
is listed by: OMICtools is related to: TMA-Combiner has parent organization: Stanford University; Stanford; California |
PMID:12414504 | OMICS_00819 | SCR_005598 | Stanford TMA Software website, Stanford Tissue Microarray Software | 2026-08-01 12:02:56 | 1 | |||||||
|
OXBench Resource Report Resource Website 1+ mentions |
OXBench (RRID:SCR_005591) | OXBench | software resource | A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure. | alignment, linux, protein, sequence alignment |
is listed by: OMICtools has parent organization: University of Dundee; Scotland; United Kingdom |
PMID:14552658 | Acknowledgement requested | OMICS_00983 | http://www.compbio.dundee.ac.uk/Software/Oxbench/oxbench.html Alt. URL: http://www.compbio.dundee.ac.uk/software.html | SCR_005591 | 2026-08-01 12:02:55 | 2 | ||||||
|
Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden, https://sources.debian.org/src/staden/ | SCR_005629 | Staden Package | 2026-08-01 12:02:57 | 79 | ||||||
|
Chromaseq Resource Report Resource Website 1+ mentions |
Chromaseq (RRID:SCR_005587) | Chromaseq | software resource | A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap. | chromatogram, sequence, mesquite |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF EF-0531754 | Acknowledgement required | OMICS_01017 | SCR_005587 | Chromaseq: a package for processing chromatograms and sequence data in Mesquite | 2026-08-01 12:02:55 | 7 | ||||||
|
snp-search Resource Report Resource Website |
snp-search (RRID:SCR_005618) | snp-search | software resource | A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses. | is listed by: OMICtools | PMID:24246037 | OMICS_00303 | SCR_005618 | 2026-08-01 12:02:55 | 0 | |||||||||
|
Burroughs Wellcome Fund Resource Report Resource Website 100+ mentions |
Burroughs Wellcome Fund (RRID:SCR_005772) | BWF | institution | The Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation. | biomedical sciences, research, science, education | Wellcome Trust | nlx_149371, grid.427464.7, Wikidata: Q5000488, ISNI: 0000 0000 8727 8697, Crossref funder ID: 100000861 | https://ror.org/01d35cw23 | SCR_005772 | 2026-08-01 12:02:59 | 103 | ||||||||
|
CSIBS Resource Report Resource Website |
CSIBS (RRID:SCR_005889) | CSIBS | software resource | A software tool designed to aid researchers in browsing through scientific literature. As one reads an online article and encounters a citation that looks important, CSIBS creates a preview summary of the cited document. The key innovation is the contextual tailoring of the automatically generated summaries using the citation and its surrounding text. As this context changes, so too does the citation-specific summary portion of the preview, which contains contextually-relevant sentences extracted from the cited document. The CSIBS preview presents relevant information required to appraise the citation, containing meta-data about the reference, the abstract and the citation-specific summary. Thus, CSIBS, alleviates information overload by enabling the reader to determine whether or not to invest time in exploring the cited article further. Reference, http://www.sciencedirect.com/science/article/pii/S1570826810000181 | elsevier grand challenge, natural language processing, text summarization, document browsing aid, contextual summary, computational linguistics, text mining, metadata |
is listed by: FORCE11 has parent organization: ICT Centre has parent organization: Macquarie University; Sydney; Australia |
Prototype | nlx_149460 | http://www.force11.org/node/4689 | SCR_005889 | CSIBS: The Citation-Sensitive In-Browser Summarizer, Citation-Sensitive In-Browser Summarizer | 2026-08-01 12:03:03 | 0 | ||||||
|
University of California at San Francisco; California; USA Resource Report Resource Website 1+ mentions |
University of California at San Francisco; California; USA (RRID:SCR_010605) | UCSF | university | Public research university in San Francisco, California. Part of University of California system. Dedicated entirely to health sciences. Major center of medical and biological research and teaching. Ranked as one of top universities in biomedical field in USA and around world. | institution, university, health science, medical, biological, teaching, center, biomedical |
is affiliated with: Diabetes Research Centers is related to: NCIRE is related to: ONE Study is related to: Alzheimers Disease Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is related to: Diabetic Foot Consortium has parent organization: University of California; California; USA is parent organization of: DOCK is parent organization of: MochiView is parent organization of: Kravitz Dataset 2 is parent organization of: uManager is parent organization of: UCSF Brain Tumor Tissue Bank is parent organization of: CryptoBase is parent organization of: Resource for Biocomputing Visualization and Informatics is parent organization of: Hyperpolarized MRI Technology Resource Center is parent organization of: Sherlock is parent organization of: Center for Imaging of Neurodegenerative Diseases is parent organization of: WikiPathways is parent organization of: International Gene Trap Consortium is parent organization of: Microstructural correlation toolbox is parent organization of: NUTMEG is parent organization of: AltAnalyze - Alternative Splicing Analysis Tool is parent organization of: Integrative Modeling Platform is parent organization of: UCSF Spot is parent organization of: Allelic Variations of The XP Genes is parent organization of: Edinburgh Postnatal Depression Scale is parent organization of: AIDS and Cancer Specimen Resource is parent organization of: UCSF DNA Bank is parent organization of: Babel is parent organization of: UCSF DataShare is parent organization of: Scientific Data Sharing Project is parent organization of: ModBase is parent organization of: UCSF Laboratory for Visual Neuroscience is parent organization of: UCSF AIDS Specimen Bank is parent organization of: Gene Map Annotator and Pathway Profiler is parent organization of: ExPANdS is parent organization of: UCSF Center for AIDS Prevention Studies (CAPS) is parent organization of: HOLLOW is parent organization of: MAPPFinder is parent organization of: iBioSeminars is parent organization of: Bioelectromagnetism Matlab Toolbox is parent organization of: UCSF Brain Tumor Tissue Bank is parent organization of: Krogan Lab Interactome Database is parent organization of: BayGenomics is parent organization of: CanPredict is parent organization of: MODELLER is parent organization of: DeRisi Lab is parent organization of: CTSpedia is parent organization of: Kravitz Dataset1 is parent organization of: UCSF Helen Diller Family Comprehensive Cancer Center is parent organization of: Clinical Research Resource HUB is parent organization of: National Bio-Organic Biomedical Mass Spectrometry Resource Center is parent organization of: Program to Reduce Incontinence by Diet and Exercise is parent organization of: Brain Health Registry is parent organization of: The Li Lab at UCSF is parent organization of: UCSF Nikon Imaging Center is parent organization of: UCSF School of Medicine; California; USA is parent organization of: Microarrays.org is parent organization of: University of California, San Francisco School of Pharmacy is parent organization of: PRICE is parent organization of: HMMSplicer is parent organization of: ArrayOligoSelector is parent organization of: stepNorm is parent organization of: National Center for X-ray Tomography is parent organization of: SURPI is parent organization of: Research Network in Early Experience and Brain Development is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging is parent organization of: PSCBS is parent organization of: Sparky is parent organization of: Cytokine Registry is parent organization of: Protein Prospector is parent organization of: University of California San Francisco Diabetes Research Center Mouse Genetics Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Islet Production Core Facility is parent organization of: University of California San Francisco Parnassus Flow Cytometry Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Lentiviral RNAi Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Microscopy Core Facility is parent organization of: University of California San Francisco Diabetes Research Center is parent organization of: University of California San Francisco Diabetes Research Center Mouse Metabolism Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Mouse Metabolism and Imaging Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Human Metabolism Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Genetics and Genomics Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center is parent organization of: Cystic Fibrosis Center - University of California San Francisco is parent organization of: UCSF ChimeraX is parent organization of: MotionCor2 is parent organization of: Clonotator is parent organization of: FoXS is parent organization of: covidcounties.org is parent organization of: DoubletFinder is parent organization of: syndRomics is parent organization of: PhotometryBox is parent organization of: University of California at San Francisco Immunology Lab Core Facility is parent organization of: Similarity Ensemble Approach is parent organization of: University of California at San Francisco Advanced Microscopy Core Facility is parent organization of: University of California San Francisco Clinical Cancer Genomics Laboratory Core Facility is parent organization of: UCSF Helen Diller Family Comprehensive Cancer Center Flow and Cell Sorting Core Facility |
nlx_57854, GRID grid.266102.1; ISNI 0000 0001 2297 6811; Crossref Funder ID 100008069; Wikidata Q1061104 | https://ror.org/043mz5j54 | SCR_010605 | UC San Francisco, The University of California, San Francisco, University of California San Francisco, University of California at San Francisco | 2026-08-01 12:04:14 | 9 | |||||||
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vipR Resource Report Resource Website 50+ mentions |
vipR (RRID:SCR_010685) | vipR | software resource | A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00081 | SCR_010685 | 2026-08-01 12:04:16 | 58 | ||||||||||
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MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-08-01 12:03:55 | 463 | |||||||
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Life Extension Foundation Resource Report Resource Website |
Life Extension Foundation (RRID:SCR_010574) | institution | Established in 1980, the Life Extension Foundation is a nonprofit organization, whose long-range goal is to radically extend the healthy human lifespan by discovering scientific methods to control aging and eradicate disease. The largest organization of its kind in the world, the Life Extension Foundation has always been at the forefront of discovering new scientific breakthroughs for use in developing novel disease prevention and treatment protocols to improve the quality and length of human life. Through its private funding of research programs aimed at identifying and developing new therapies to slow and even reverse the aging process, the Life Extension Foundation seeks to reduce, and ultimately eliminate, such age-related killers as heart disease, stroke, cancer and Alzheimer''s disease. Long-time members are keenly aware of the scientific research that Life Extension Foundation funds to develop validated methods to slow and reverse the aging process. Less known is Life Extension''s multi-prong program to develop safer and more effective cancer therapies. One reason we focus so heavily on cancer research is that this dreaded disease represents a roadblock in our ability to develop effective means to combat aging. | is parent organization of: Life Extension | Aging | ISNI: 0000 0001 0300 2958, nlx_41735, grid.490868.b | https://ror.org/02vzd2x77 | SCR_010574 | 2026-08-01 12:04:14 | 0 | |||||||||
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Gossamer Resource Report Resource Website 1+ mentions |
Gossamer (RRID:SCR_010612) | Gossamer | software resource | A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability. | is listed by: OMICtools | OMICS_00017 | SCR_010612 | Gossamer: A Space-Efficient Genome Assembler | 2026-08-01 12:04:16 | 1 | |||||||||
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Meraculous Resource Report Resource Website 10+ mentions |
Meraculous (RRID:SCR_010700) | Meraculous | software resource | An algorithm for de novo genome assembly with short paired-end reads. | is listed by: OMICtools | OMICS_00021 | SCR_010700 | Meraculous: De Novo Genome Assembly with Short Paired-End Reads | 2026-08-01 12:03:55 | 39 | |||||||||
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Matrix2png Resource Report Resource Website 100+ mentions |
Matrix2png (RRID:SCR_010669) | software resource | An open visualization tool for the display of matrix data. It is available for download or interactive web use. It is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data. | dna microarray, matrix | has parent organization: University of British Columbia; British Columbia; Canada | nlx_74565 | SCR_010669 | 2026-08-01 12:04:15 | 126 |
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