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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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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | software application, software resource, data analysis software, data processing software | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-07-28 09:42:56 | 24583 | ||||||
|
pClamp Resource Report Resource Website 5000+ mentions |
pClamp (RRID:SCR_011323) | software application, data analysis software, software resource, data processing software, data acquisition software | Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis. | electrophysiology, data, acquisition, analysis, Molecular Device, voltage, clamp, | is listed by: SoftCite | Commercially available | rid_000085 | https://www.moleculardevices.com/products/axon-patch-clamp-system/acquisition-and-analysis-software/pclamp-software-suite#gref | SCR_011323 | patch clamp, Axon™pCLAMP™ 10 Electrophysiology Data Acquisition and Analysis Software, patch CLAMP, pCLAMP 11, pCLAMP 10, patch Clamp | 2026-07-28 09:43:00 | 9678 | |||||||
|
HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
NURSA consortium grant ; NIH HC088093; NIDDK DK063491; NCI CA52599; NIGMS P50 GM081892; Foundation Leducq Transatlantic Network Grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-07-28 09:42:59 | 5370 | |||||
|
TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | software application, data analysis software, sequence analysis software, software resource, data processing software, alignment software, image analysis software | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ | http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-07-28 09:43:10 | 9575 | ||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | software application, software resource, data analysis software, data processing software | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-07-28 09:43:18 | 2996 | ||||
|
edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | software application, software resource, data analysis software, data processing software | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
NHMRC 406657; Independent Research Institutes Infrastructure Support Scheme 361646; Victorian State Government OIS grant ; Melbourne International Research Scholarship ; Harris and IBS Honours scholarships |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-07-28 09:43:10 | 21899 | ||||
|
University of Southern California School of Pharmacy Translational Research Laboratory Resource Report Resource Website |
University of Southern California School of Pharmacy Translational Research Laboratory (RRID:SCR_012253) | USC, School of Pharmacy, TRLab, Translational Research Lab, University of Southern California, School of Pharmacy | access service resource, service resource, core facility | Core is equipped with a wide variety of technologically advanced instruments essential for cutting edge biomedical discovery and therapeutic development research. TRLab is composed of two major units. The Computational Bioinformatics Unit houses graphic workstations and modeling programs that enable in silico virtual screening and rational drug design applications. The Therapeutic Screening Unit houses a number of specialized instruments that enable a broad range of automated and multiplexed biological analyses in a throughput manner. The core mission of the TRLab has been to provide investigators with a state-of-the-art technological platform and technical expertise to advance translational research endeavors in the School of Pharmacy and at USC. | immunobiology, Molecular biology, analysis, imaging, |
is listed by: ScienceExchange has parent organization: University of Southern California; Los Angeles; USA |
Available to external user | SciEx_11044 | http://www.scienceexchange.com/facilities/the-translational-research-laboratory | SCR_012253 | USC, Translational Research Lab, Translational Research Laboratory, TRLab, University of Southern California, School of Pharmacy | 2026-07-28 09:43:02 | 0 | ||||||
|
University of Southern California Epigenome Center Data Production Facility Resource Report Resource Website |
University of Southern California Epigenome Center Data Production Facility (RRID:SCR_012476) | USC Epigenome Center, | access service resource, service resource, core facility | Core conducts genome-scale epigenetic and genetic data production and analysis, technology development, and epigenomic and population-based genomic research. | genome-scale epigenetic, genetic data production, analysis, technology development, epigenomic, population-based genomic research |
is listed by: ScienceExchange is related to: University of Southern California Labs and Facilities has parent organization: University of Southern California; Los Angeles; USA |
Available to external user | SciEx_206 | SCR_012476 | University of Southern California Epigenome Center Data Production Facility | 2026-07-28 09:43:06 | 0 | |||||||
|
Vancouver Prostate Centre Laboratory for Advanced Genome Analysis Resource Report Resource Website 1+ mentions |
Vancouver Prostate Centre Laboratory for Advanced Genome Analysis (RRID:SCR_012394) | VPC LAGA, LAGA | access service resource, service resource, core facility | Core offers sequencing and microarray services, solutions for the profiling of FFPE tissues, and complete, project-tailored downstream bioinformatics analysis. The core's structure enables the management of research projects from experimental design to analysis and interpretation of data as well as support for grant applications and publications. The LAGA provides open fee-for-service access as a core facility (intra-institutional services to its researchers) and as regional, national and international facility (inter-institutional services). | Microarray, Profiling of FFPE, Analysis |
is listed by: ScienceExchange is related to: Vancouver Prostate Centre Labs and Facilities has parent organization: University of British Columbia; British Columbia; Canada |
Available to external user | SciEx_13 | https://www.prostatecentre.com/our-research/core-facilities/LAGA | https://www.scienceexchange.com/labs/laboratory-for-advanced-genome-analysis | SCR_012394 | , Laboratory for Advanced Genome Analysis, PC-TRiADD, VPC | 2026-07-28 09:43:06 | 1 | |||||
|
Sanford Burnham Prebys Medical Discovery Institute Cheminformatics Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Cheminformatics Core (RRID:SCR_014875) | access service resource, service resource, core facility | Core facility that supports assay development, high throughput (HTS), ultra-high throughput (uHTS), and high-content screening (HCS) activities performed at the Conrad Prebys Center for Chemical Genomics by providing databases and tools for compound registration and inventory, HTS plate formatting and tracking, HTS and HCS bioassay data processing as well as related data and information handling. Data mining and reporting are also facilitated with a user-friendly database interface. The Cheminformatics core also supports the design and obtaining of appropriate compound collections, as well as SAR follow-up of hits, hit-to-lead optimization and in silico screening through docking and other molecular modeling approaches. | facility, la jolla, cheminformatics, analysis, assay, throughput, database | Commercially available | SCR_014875 | SBP Cheminformatics Core, SBP Medical Discovery Institute Cheminformatics Core | 2026-07-28 09:43:56 | 0 | ||||||||||
|
JP Sulzberger Columbia Genome Center Resource Report Resource Website 1+ mentions |
JP Sulzberger Columbia Genome Center (RRID:SCR_012650) | Columbia Genome Center | access service resource, service resource, core facility | Core sells sequencing data and bioinformatic analytics services to the scientific community. Core aims to permit the development of research on sequencing protocols and encourage collaboration with clinicians to develop the next generation genomic DNA testing. | analysis, sequencing, screening |
is listed by: ScienceExchange is related to: Columbia University Labs and Facilities has parent organization: Columbia University; New York; USA |
Available to external user | SciEx_608 | http://www.scienceexchange.com/facilities/columbia-genome-center-columbia | SCR_012650 | Columbia University Genome Center | 2026-07-28 09:43:14 | 1 | ||||||
|
Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) Resource Report Resource Website 500+ mentions |
Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) | SALK IGC, IGC | access service resource, service resource, core facility | 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 | NCI CA014195; Helmsley Trust ; Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility |
Open | SCR_014842 | , Integrative Genomics, Salk, Core Facility, Institute, Razavi Newman, UCSD, Bioinformatics | 2026-07-28 09:43:37 | 940 | ||||||||
|
Gamess Resource Report Resource Website 100+ mentions |
Gamess (RRID:SCR_014896) | source code, software resource | Software program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Capabilities include using nuclear gradients for automatic geometry optimization, modeling of solvent effects, computation of the energy hessian for prediction of vibrational frequencies, as well as computation of nuclear wavefunctions. The program can also compute variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities. | molecular quantum chemistry, molecular properties, computation, analysis, visualization | SCR_014896 | The General Atomic and Molecular Electronic Structure System | 2026-07-28 09:43:37 | 263 | |||||||||||
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Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility Resource Report Resource Website |
Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility (RRID:SCR_014877) | TSRI CBS | access service resource, service resource, core facility | Core facility that provides access to genome-wide collections of cDNAs and siRNAs that can be used to interrogate cellular models of signal transduction pathways and phenotypes. Services include cell lines, hit-picking clones and various screening sets, and access to equipment.Provides instruments:Analyst Molecular Devices,Embla Molecular Devices, Envision Perkin Elmer, Platemate Matrix, Tecan M200, Wellmate Matrix. | USEDit, ABRF, Cell, high, throughput, screening, genome, collection, cDNA, siRNA, cellular, model, signal, transduction, pathway, phenotype, analysis, service, core, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Scripps Research Institute |
SCR_017832, ABRF_618 | https://coremarketplace.org/?FacilityID=618 | SCR_014877 | The Scripps Research Institute (CBS) Core, The Scripps Research Institute Cell-Based Screening (CBS) Core, Scripps Research Institute Cell-Based Screening Core, Cell-Based High-Throughput Screening Core | 2026-07-28 09:43:34 | 0 | |||||||
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Chicago Center for Diabetes Translation Research Quantitative Analysis Core Resource Report Resource Website |
Chicago Center for Diabetes Translation Research Quantitative Analysis Core (RRID:SCR_015208) | access service resource, service resource, resource, core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30,2023. Core facility that provides analytic support for a wide range of projects in diabetes translation research ranging from program evaluation to cost-effectiveness analysis. | diabetes, translation, diabetes research, chicago, analytic, program evaluation, analysis |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Chicago; Illinois; USA has parent organization: Chicago Center for Diabetes Translation Research is organization facet of: Chicago Center for Diabetes Translation Research |
Diabetes | NIDDK P30DK092949 | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_015208 | 2026-07-28 09:43:42 | 0 | ||||||||
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University of Washington Genomics Core Cystic Fibrosis Research Translation Center and Research Development Program Resource Report Resource Website 1+ mentions |
University of Washington Genomics Core Cystic Fibrosis Research Translation Center and Research Development Program (RRID:SCR_015404) | CF Research Translation Center and Research Development Program, CFRTC | access service resource, service resource, resource, core facility | Core provides genomics-based tools, data management and analysis tools, and creates platforms that integrate data from the Clinical and Immunology Cores for human samples and bacterial isolates. Services include consultation and experimental design assistance for using new-generation sequencing technology, data analysis, bioinformatic support, data access and storage, high throughput and new-generation whole-genome sequencing, and RNA-seq analysis of transcriptomes. | genomics core, sequencing technology, cystic fibrosis genomics, RNA sequencing, analysis |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Washington; Seattle; USA has parent organization: Cystic Fibrosis Center - University of Washington is organization facet of: Cystic Fibrosis Center - University of Washington |
Cystic Fibrosis | NIDDK P30 DK89507 | Available to external user | SCR_015404 | Genomics Core, Cystic Fibrosis Research Translation Center, CFRTC, Research Development Program, University of Washington | 2026-07-28 09:43:48 | 1 | ||||||
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SPIKE Resource Report Resource Website 100+ mentions |
SPIKE (RRID:SCR_010466) | SPIKE | data or information resource, service resource, database | Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways | visualization, analysis, cellular, signaling pathway, regulatory network, function, genomic, proteomic, cell cycle, dna damage, cell death, stress, transcription factor, mitogen, protein kinase, pathway, immune response, signaling, hearing, dna damage response, programmed cell death, development, ear, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: ConsensusPathDB has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Cancer | A-T Children's Project ; Wolfson Foundation ; European Union FP7 ; Israel Science Foundation |
PMID:21097778 PMID:18289391 |
biotools:spike, nlx_157705 | https://bio.tools/spike | SCR_010466 | Signaling Pathway Integrated Knowledge Engine | 2026-07-28 09:42:51 | 128 | ||||
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Phenotypes and Mutant Alleles Resource Report Resource Website 10+ mentions |
Phenotypes and Mutant Alleles (RRID:SCR_017523) | data or information resource, service resource, database | Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes. | MGI, phenotype, human, disease, analysis, model, genetically, engineered, mutation, strain, specific, phenotype, data | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017523 | Phenotypes, Alleles & Disease Models | 2026-07-28 09:44:30 | 11 | |||||||||
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C. elegans RNAi Collection (Ahringer) Resource Report Resource Website 10+ mentions |
C. elegans RNAi Collection (Ahringer) (RRID:SCR_017064) | data or information resource, database | C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies. | Source BioScience Ltd, data, collection, bacterial, strain, Caenorhabditis elegans, RNA, interference, RNAi, gene, function, analysis, feeding, library | has parent organization: University of Cambridge; Cambridge; United Kingdom | Howard Hughes Medical Institute Predoctoral Fellow- ship ; Wellcome Trust Senior Research Fellowship |
PMID:12828945 | Available for purchase | SCR_017064 | 2026-07-28 09:44:28 | 14 | ||||||||
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University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility Resource Report Resource Website |
University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) | MidSouth Bioinformatics Center, MBC | access service resource, service resource, software resource, core facility | Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice. | bioinformatics, assistance, consulting, training, analysis, omic, data | has parent organization: University of Arkansas; Arkansas; USA | Open | SCR_017168 | Bioinformatics Center, , University of Arkansas, UA, Core Facility, MBC, UALR, MidSouth, Little Rock | 2026-07-28 09:44:31 | 0 |
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