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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NetworkAnalyst Resource Report Resource Website 500+ mentions |
NetworkAnalyst (RRID:SCR_016909) | data analysis service, data processing software, data analysis software, analysis service resource, web service, software resource, software application, data access protocol, production service resource, service resource, network analysis software | Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data. | gene, expression, profiling, meta, data, analysis, statistical, visual, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:25950236 | Free, Freely available, Tutorial available | biotools:networkanalyst | https://bio.tools/networkanalyst | SCR_016909 | 2026-08-04 09:44:00 | 635 | |||||||
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National Resource for Translational and Developmental Proteomics Resource Report Resource Website |
National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) | NRTDP | portal, training resource, organization portal, service resource, data or information resource | Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists. | protein, mass, spectrometry, proteomics, measurement, targeted, untargeted, analysis |
has parent organization: Northwestern University; Illinois; USA provides: ProSight Lite |
NIGMS P41 GM108569 | SCR_016907 | The National Resource for Translational and Developmental Proteomics, NRTDP | 2026-08-04 09:44:02 | 0 | ||||||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
NINDS 1U54NS093793; NIH Office of the Director R24 OD022005; The Robert and Janice McNair Foundation ; Baylor College of Medicine Medical Scientist Training Program ; NINDS U54 NS093793; NIGMS R01 GM067858; NIGMS R01 GM120033; NSF DMS 1263932; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; Belfer Foundation ; T T Chao Family Foundation ; NIGMS R01 GM067761; NIGMS R01 GM084947; NCRR R24 RR032668; NIH Office of the Director R24 OD021997; NCI P30 CA06516; NHGRI U01 HG007709; Simons Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-08-04 09:44:00 | 22 | ||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | 2026-08-04 09:44:04 | 53 | ||||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data processing software, software application, software resource, data analysis software | Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | NIDDK R24 DK096518; NHLBI R24 HL123482; NIDDK R01 DK115791; Fraternal Order of Eagles Diabetes Research Center ; University of Iowa Center for Gene Therapy ; Carver Chair in Molecular Medicine ; NIGMS T32 GM082729 |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-08-04 09:44:02 | 5 | |||||||||
|
PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | data processing software, data analysis software, software resource, software application, network analysis software | Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome. | mapping, omics, data, pathways, network, analysis, proteoform, generate, Reactome, database, match, bio.tools |
is listed by: Galaxy is listed by: OMICtools is listed by: Debian is listed by: bio.tools works with: Reactome |
European Research Council ; Research Council of Norway ; Bergen Research Foundation ; NIGMS U54 GM114833; NHGRI U41 HG003751 |
DOI:10.1101/375097 | Free, Available for download, Freely available | BioTools:PathwayMatcher, biotools:PathwayMatcher | https://anaconda.org/bioconda/pathwaymatcher, https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher | SCR_016759 | 2026-08-04 09:43:59 | 1 | ||||||
|
Growth Profiling Toolbox Resource Report Resource Website |
Growth Profiling Toolbox (RRID:SCR_016878) | data processing software, data analysis software, software resource, software application, software toolkit | Software package as a growth curve automatic processing pipeline in Matlab. | growth, curve, automatic, pipeline, analysis, process, data | Free, Available for download, Freely available | SCR_016878 | 2026-08-04 09:44:00 | 0 | |||||||||||
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sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | data processing software, software application, software resource, data analysis software | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NIDDK R01 DK094699; NHGRI R01 HG006129 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth, https://bio.tools/sleuth, https://bio.tools/sleuth | SCR_016883 | 2026-08-04 09:44:00 | 24 | ||||||
|
ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | data processing software, software application, software resource, data analysis software | Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. | multivariate, analysis, feature, selection, omics, data, visualization, regression, classification, variable, exceedes, number, sample, multicollinearity, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | BioTools:ropls, biotools:ropls | https://bio.tools/ropls, https://bio.tools/ropls, https://bio.tools/ropls | SCR_016888 | R Orthogonal Partial Least Squares | 2026-08-04 09:44:01 | 12 | ||||||
|
Ragu Resource Report Resource Website 1+ mentions |
Ragu (RRID:SCR_016851) | Ragu | data processing software, software application, software resource, data analysis software | Software tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics. | statistical, analysis, EEG, MEG, electromagnetic, data, scalp, field | DOI:doi/10.1155/2011/938925 | SCR_016851 | Randomization Graphical User interface, Randomization Graphical User | 2026-08-04 09:44:00 | 3 | |||||||||
|
Nuclear Hormone Receptor Scan Resource Report Resource Website 1+ mentions |
Nuclear Hormone Receptor Scan (RRID:SCR_016975) | NHR-scan | analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications. | prediction, nuclear, hormone, receptor, binding, site, genomic, sequence, parameter, modification, analysis | is listed by: OMICtools | Pharmacia Corporation to the Center for Genomics and Bioinformatics ; Canadian Institutes of Health Research |
PMID:15563547 | Free, Available, Acknowledgement requested | OMICS_14042 | SCR_016975 | NHR-scan, NHR Scan, NHRScan, Nuclear Hormoe Receptor Scan | 2026-08-04 09:44:03 | 5 | |||||
|
NetworkX Resource Report Resource Website 100+ mentions |
NetworkX (RRID:SCR_016864) | data processing software, data analysis software, software resource, software application, network analysis software | Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | create, analysis, structure, dynamic, function, complex, network, data | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/networkx/networkx | SCR_016864 | 2026-08-04 09:44:00 | 111 | |||||||||
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Good Calculators Resource Report Resource Website |
Good Calculators (RRID:SCR_017123) | analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web service as calculator for statistics and analysis. Used on variety of browsers as well as mobile and tablet devices.They include Z-score, sample size, t value, One Way ANOVA Calculator, Percentile Calculator, Chi Square, p Value, and more. | statistics, analysis, calculator | Free, Freely available | SCR_017123 | 2026-08-04 09:44:06 | 0 | |||||||||||
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mzStudio Resource Report Resource Website 1+ mentions |
mzStudio (RRID:SCR_017088) | data processing software, data analysis software, software resource, software application, data visualization software | Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows. | proteomic, data, analysis, visualization, notebooking, mass, spectrometry, modification, gas, phase, fragmentation, behavior |
is listed by: OMICtools is related to: Python Programming Language |
NCI CA188881; NCI CA178860; NCI CA042368; Dana-Farber Strategic Research Initiative ; Barr Program in Basic Research ; Honorable Tina Brozman Foundation for Ovarian Cancer Research ; Michael J. Fox Foundation |
PMID:28763045 | Free, Available for download, Freely available | OMICS_26946 | https://omictools.com/mzstudio-tool | SCR_017088 | 2026-08-04 09:44:06 | 1 | ||||||
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BRASS Resource Report Resource Website 10+ mentions |
BRASS (RRID:SCR_017091) | data processing software, software application, software resource, data analysis software | Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements. | analysis, BAM, file, paired, end, sequencing, determine, rearrangement, breakpoint, assemble |
is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | SCR_017091 | 2026-08-04 09:44:06 | 42 | ||||||||||
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CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | portal, topical portal, disease-related portal, consortium, organization portal, data or information resource | Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies. | identify, protein, alteration, cancer, genome, clinical, study, proteome, proteogenomic, tumor, data, analysis, consortium, reproducibility | has parent organization: National Cancer Institute | cancer | SCR_017135 | Clinical Proteomic Tumor Analysis Consortium | 2026-08-04 09:44:05 | 131 | |||||||||
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miRTarVisPlus Resource Report Resource Website 1+ mentions |
miRTarVisPlus (RRID:SCR_017103) | miRTarVis+ | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web based interactive visual analytics tool for miRNA target predictions and integrative analyses of multiple prediction results. Used for sequence based miRNA target prediction by exploiting miRNA-mRNA expression profile data. | interactive, visual, analytical, miRNA, target, prediction, analysis, mRNA, expression, data | has parent organization: Seoul National University; Seoul; South Korea | National Research Foundation of Korea ; Hankuk University of Foreign Studies Research Fund |
PMID:28600227 | Free, Freely available | http://hcil.snu.ac.kr/research/mirtarvisplus | SCR_017103 | mirtarvisplus | 2026-08-04 09:44:05 | 3 | |||||
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University of Gothenburg Bioinformatics Core Facility Resource Report Resource Website |
University of Gothenburg Bioinformatics Core Facility (RRID:SCR_017189) | GU Bioinformatics Core Facility | data analysis service, analysis service resource, access service resource, core facility, production service resource, service resource | Core assists with statistical and bioinformatics consultation and data analysis. | bioinformatics, data, analysis, consulting, statistical | has parent organization: University of Gothenburg; Gothenburg; Sweden | Open | SCR_017189 | University of Gothenburg, GU, Bioinformatics Core Facility | 2026-08-04 09:44:06 | 0 | ||||||||
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Ponemah Resource Report Resource Website 10+ mentions |
Ponemah (RRID:SCR_017107) | data processing software, data analysis software, software resource, software application, data acquisition software | Software tool for complete physiologic data acquisition and analysis used by physiologists, pharmacologists, and toxicologists to collect, analyze, and summarize preclinical study data. Allows to custom design configuration based on needs, budget and convenience without need for any programming. | Data Sciences International, Inc., physiologic, data, acquisition, analysis, collect, summerize, preclinical, custom, design | Available for purchase | SCR_017107 | 2026-08-04 09:44:06 | 20 | |||||||||||
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ot-tools Resource Report Resource Website 1+ mentions |
ot-tools (RRID:SCR_017191) | data processing software, software application, software resource, data analysis software | Software tools for analysis of cellular cryo-ET data. | analysis, cellular, cryo-ET, data | Free, Available for download, Freely available | SCR_017191 | 2026-08-04 09:44:06 | 5 |
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