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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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Mayo Clinic Rochehster Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
Mayo Clinic Rochehster Bioinformatics Core Facility (RRID:SCR_017161) | Mayo Clinic Bioinformatics Core | service resource, production service resource, data analysis service, core facility, access service resource, analysis service resource | Core assists in genomics, proteomics and metabolomics data acquisition, management, analyses and interpretation to Mayo investigators. Participates in Basic science research, Clinical trials, Population health, and Translational science to execute analytical workflows and manage large omics data sets. Provides support to Mayo Clinic Center for Individualized Medicine and Mayo Clinic Cancer Center. Has its academic home in Department of Health Sciences Research within Division of Biomedical Statistics and Informatics. | bioinformatics, data, acquisition, management, analysis, genomics, proteomics, metabolomics | has parent organization: Mayo Clinic | Restricted | SCR_017161 | Bioinformatics Core, Division of Biomedical Statistics and Informatics, Rochehster, Mayo Clinic, Core Facility | 2026-08-06 09:29:02 | 2 | ||||||||
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Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility Resource Report Resource Website |
Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility (RRID:SCR_017160) | software resource, service resource, production service resource, data analysis service, core facility, access service resource, analysis service resource | Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing. | bioinformatics, biocomputing, sequencing, data, omics, analysis, visualization, management | has parent organization: Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany | Restricted | SCR_017160 | , Bioinformatics Facility, Core Facility, Bioinformatics Core Facility, Epigenetics, Max Planck Institiute of Immunobiology | 2026-08-06 09:29:01 | 0 | |||||||||
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RaceID Resource Report Resource Website 10+ mentions |
RaceID (RRID:SCR_017045) | software resource, algorithm resource, data analysis software, data processing software, software application | Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows. | inference, cell, type, single, RNAseq, data, sequencing, rare, abundant, transcriptome, marker, gene, organ |
is listed by: OMICtools is related to: R Project for Statistical Computing is related to: CRAN works with: StemID |
European Research Council Advanced grant ; Nederlandse Organisatie voor Wetenschappelijk Onderzoek Vici award |
PMID:26287467 PMID:27345837 |
Free, Available for download, Freely available | OMICS_12591, SCR_017243 | https://rdrr.io/cran/RaceID/, https://github.com/dgrun/RaceID3_StemID2 | SCR_017045 | RaceID3, RaceID2 | 2026-08-06 09:28:57 | 15 | |||||
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University of Michigan School of Medicine Center of Computational Medicine and Bioinformatics Core Facility Resource Report Resource Website |
University of Michigan School of Medicine Center of Computational Medicine and Bioinformatics Core Facility (RRID:SCR_017179) | UM School of Medicine Computational Medicine and Bioinformatics, CCMB, Center of Computational Medicine and Bioinformatics | service resource, data or information resource, core facility, access service resource | University interdisciplinary academic center for bioinformatics, biomedical data science, and translational precision health informatics. Core provides training programs. | Bioinformatics, biomedical, data, translational, informatics | Restricted | SCR_017179 | University of Michigan, CCMB, Computational Medicine and Bioinformatics, UM, School of Medicine | 2026-08-06 09:29:02 | 0 | |||||||||
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Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data analysis software, software application, software resource, data processing software | Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. | Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
PMID:20132535 | Free, Available for download, Freely available | biotools:goseq | https://bio.tools/goseq | SCR_017052 | 2026-08-06 09:29:00 | 354 | |||||||
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University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility Resource Report Resource Website |
University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility (RRID:SCR_017173) | CGAT | training service resource, service resource, production service resource, data analysis service, data or information resource, core facility, access service resource, analysis service resource | Core provides genomics training, as well as assistance in next generation sequencing analyses. | bioinformatics, genomics, next, generation, sequencing, data, analysis | has parent organization: University of Oxford; Oxford; United Kingdom | Restricted | SCR_017173 | Medical Sciences Division, Computational Genomics: Analysis and Training Core Facility, CGAT, University of Oxford, Computational Genomics Analysis and Training Core Facility | 2026-08-06 09:29:02 | 0 | ||||||||
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Montreal Clinical Research Bioinformatics Core Facility Resource Report Resource Website |
Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) | IRCM BIF, BIF | training service resource, service resource, production service resource, data analysis service, data or information resource, core facility, access service resource, analysis service resource | Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses. | bioinformatics, genomic, omics, data, analysis, RNA-Seq, CHIP-Seq, RIP-Seq, DNA, methylation, DNA-Seq, rRNA, microarray | Restricted | SCR_017176 | , Institute of Clinical Research of Montreal, IRCM, Bioinformatics Core Facility, BIF | 2026-08-06 09:29:02 | 0 | |||||||||
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toxprofileR Resource Report Resource Website 1+ mentions |
toxprofileR (RRID:SCR_017027) | software resource, software library, data analysis software, software toolkit, data processing software, software application | Software R package to derive toxicogenomic fingerprints from microarray data. | toxicology, zebrafish, toxicogenomics, transcriptomics, microarray, regression, modelling, fingerprint, data |
is used by: Toxicogenomic Fingerprint Browser is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017027 | 2026-08-06 09:29:00 | 1 | ||||||||||
|
Profinder Resource Report Resource Website 10+ mentions |
Profinder (RRID:SCR_017026) | data analysis software, software application, software resource, data processing software | Software tool as fast, batch processing feature extraction software for differential analysis that supports data from Agilent GC/MSD, GC/Q-TOF, LC/TOF and LC/Q-TOF instruments. Speeds up differential and flux analysis workflows using intuitive user interface. Used to analyze raw mass spectrometry data, choose peaks. | fast, batch, processing, feature, extraction, software, differential, analysis, Agilent, instrument, support, raw, mass, spectrometry, data | Commercially available | SCR_017026 | Profinder 8 | 2026-08-06 09:28:59 | 17 | ||||||||||
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Centre for Genome Regulation Bioinformatics Core Facility Resource Report Resource Website |
Centre for Genome Regulation Bioinformatics Core Facility (RRID:SCR_017145) | Biocore CRG | software resource, service resource, training resource, core facility, access service resource | Provides services of consultation and data analysis, with focus on Next Generation Sequencing and other high throughput experiments, software and database development, and training in basic and advanced bioinformatics techniques. Services provided for fee to support collaborative grant funded investigations. | bioinformatics, NGS, consultation, data, analysis, next, generation, sequencing | has parent organization: Centre for Genomic Regulation; Barcelona; Spain | Restricted | SCR_017145 | Bioinformatics Core, , Core Facility, Centre for Genomic Regulation, Biocore, CRG | 2026-08-06 09:29:02 | 0 | ||||||||
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Bruker WinEPR program Resource Report Resource Website 1+ mentions |
Bruker WinEPR program (RRID:SCR_017023) | data acquisition software, software resource, data analysis software, data processing software, software application | Software tool to operate the EMX series of spectrometers by Bruker. Provides rapid data analysis of 1D and 2D data sets, provides environment for acquisition and processing of CW-EPR and CW-ENDOR spectra with the EMXplus and EMXmicro series of spectrometers. | operate, EMX, serie, spectrophotometer, Bruker, data, analysis, 1D, 2D, dataset, acquisition, processing, CW-EPR, CW-ENDOR | Commercially available | SCR_017023 | 2026-08-06 09:28:59 | 1 | |||||||||||
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OMTools Resource Report Resource Website 1+ mentions |
OMTools (RRID:SCR_017143) | software resource, image analysis software, alignment software, data analysis software, software toolkit, data processing software, data visualization software, software application | Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles. | optical, mapping, data, processing, analysis, visualization, large, scale, profile, phylogenesis | is listed by: SoftCite | Food and Health Bureau of the Hong Kong Special Administrative Region ; Chinese University of Hong Kong ; HKSAR Research Grants Council ; Lo Kwee-Seong Biomedical Research Fund ; Lee Hysan Foundation |
PMID:28505226 | Free, Available for download, Freely available | SCR_017143 | 2026-08-06 09:28:59 | 2 | ||||||||
|
Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | data analysis software, software application, software resource, data processing software | Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias. | quantifying, expression, transcript, RNAseq, data, correct, fragment, GC, content, bias |
is listed by: Debian is listed by: OMICtools has parent organization: Stony Brook University; New York; USA has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: Harvard University; Cambridge; Massachusetts |
Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NHGRI R21 HG006913; NHGRI R01 HG007104; Alfred P. Sloan Research ; NCI T32 CA009337; NHGRI R01 HG005220; NSF BIO-1564917; NSF CCF-1256087; NSF CCF-1053918; NSF EF-0849899 |
PMID:28263959 | Free, Available for download, Freely available | OMICS_09075 | https://github.com/COMBINE-lab/salmon, https://sources.debian.org/src/salmon/ | SCR_017036 | 2026-08-06 09:29:00 | 357 | ||||||
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Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | data analysis software, software application, software resource, data processing software | Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcripto, assembler, RNAseq, data, short, read, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NSFC 61432010; NSFC 61272016; NCRR P20 RR016460; NIGMS P20 GM103429 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | 2026-08-06 09:29:00 | 6 | ||||||
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PCAGO Resource Report Resource Website 1+ mentions |
PCAGO (RRID:SCR_017033) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options. | analysis, RNAseq, read, count, data, principal, component, analysis, PCA, agglomerative, clustering, normalization, filtering, gene, annotation, visualization | is listed by: OMICtools | Deutsche Forschungsgemeinschaft (DFG) ; International Leibniz Research School for Microbial and Biomolecular Interactions |
DOI:10.1101/433078 | Free, Freely available | OMICS_32232 | SCR_017033 | 2026-08-06 09:28:59 | 7 | |||||||
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FateID Resource Report Resource Website 1+ mentions |
FateID (RRID:SCR_017244) | data analysis software, software application, software resource, data processing software | Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations. | inference, cell, fate, bias, single, RNAseq, data, iterative, supervised, learning, algorithm, probabilistic, quantification, progenitor, population, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:29630061 | Free, Available for download, Freely available | biotools:fateid | https://bio.tools/fateid | SCR_017244 | 2026-08-06 09:29:01 | 2 | |||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_017248) | NAT | software resource, data analysis software, 3d visualization software, data processing software, data visualization software, software application | Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons. | 3D, visualization, analysis, data, image, single, neuron, tracing |
is listed by: OMICtools is related to: R Project for Statistical Computing has parent organization: MRC Laboratory of Molecular Biology |
Restricted | OMICS_18884 | http://jefferislab.github.io., https://CRAN.R-project.org/package=nat | SCR_017248 | nat, , NeuroAnatomy Toolbox | 2026-08-06 09:29:01 | 4 | ||||||
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ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | data analysis software, software application, software resource, data processing software | Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. | analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Bioconductor |
PMID:31505654 | Free, Available for download, Freely available | biotools:ascend | https://bio.tools/ascend | SCR_017257 | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-08-06 09:29:04 | 2 | ||||||
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vini: A viewer for fMRI data Resource Report Resource Website |
vini: A viewer for fMRI data (RRID:SCR_017250) | data visualization software, software application, software resource, data processing software | Software Python tool as viewer for MRI data and numpy arrays. | viewer, MRI, data, numpy, array | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | https://github.com/lipsia-fmri/vini | SCR_017250 | 2026-08-06 09:29:02 | 0 | |||||||||
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IQ-TREE Resource Report Resource Website 500+ mentions |
IQ-TREE (RRID:SCR_017254) | data analysis software, software application, software resource, data processing software | Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference. | stochastic, algorithm, estimate, maximum, likelihood, phylogeny, phylogenomic, inference, data, dataset, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Vienna; Vienna; Austria |
Austrian Science Fund ; University of Vienna |
PMID:25371430 | Free, Available for download, Freely available | biotools:ufboot2 | https://bio.tools/ufboot2/ | SCR_017254 | 2026-08-06 09:29:04 | 790 |
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