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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-05 06:28:16 | 58 | ||||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data analysis software, data processing software, software application, software resource | 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 | Carver Chair in Molecular Medicine ; Fraternal Order of Eagles Diabetes Research Center ; NHLBI R24 HL123482; NIDDK R01 DK115791; NIDDK R24 DK096518; NIGMS T32 GM082729; University of Iowa Center for Gene Therapy |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-09-05 06:28:16 | 5 | |||||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:28:17 | 382 | |||||||
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Profinder Resource Report Resource Website 10+ mentions |
Profinder (RRID:SCR_017026) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:28:17 | 19 | ||||||||||
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Nuclear Hormone Receptor Scan Resource Report Resource Website 1+ mentions |
Nuclear Hormone Receptor Scan (RRID:SCR_016975) | NHR-scan | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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 | Canadian Institutes of Health Research ; Pharmacia Corporation to the Center for Genomics and Bioinformatics |
PMID:15563547 | Free, Available, Acknowledgement requested | OMICS_14042 | SCR_016975 | NHR-scan, NHR Scan, NHRScan, Nuclear Hormoe Receptor Scan | 2026-09-05 06:28:16 | 5 | |||||
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Bruker WinEPR program Resource Report Resource Website 1+ mentions |
Bruker WinEPR program (RRID:SCR_017023) | data acquisition software, data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:28:17 | 1 | |||||||||||
|
TransRate Resource Report Resource Website 50+ mentions |
TransRate (RRID:SCR_017034) | data analysis software, data processing software, software application, software resource | Open source software tool for de novo transcriptome assembly reference free quality analysis. Used to examine assembly in detail and compare it to sequencing reads, reporting quality scores for contigs and assemblies to allow to choose between assemblers and parameters, filter out bad contigs from an assembly, and help decide when to stop trying to improve assembly. | de novo, transcriptome, assembly, reference, free, quality, analysis, sequencing, read, contig, parameter | BBSRC ; Bill & Melinda Gates Foundation ; European Union Horizon 2020 research and innovation program ; Millennium Seed Bank ; Royal Society University Research |
PMID:27252236 | Free, Available for download, Freely available | https://github.com/Blahah/transrate | SCR_017034 | 2026-09-05 06:28:17 | 51 | ||||||||
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PCAGO Resource Report Resource Website 10+ mentions |
PCAGO (RRID:SCR_017033) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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 | 2026-09-05 06:28:17 | 10 | |||||||
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nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | JDRF ; NCI R33 CA225248; NIBIB R21 EB020976; NIDDK DP3 DK110844; NIDDK UC4 DK104167; NIGMS P41 GM103493; NIH Office Of The Director S10 OD016350 |
PMID:29491378 | SCR_017129 | 2026-09-05 06:28:19 | 1 | |||||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_017248) | NAT | 3d visualization software, data analysis software, data processing software, data visualization software, software application, software resource | 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 | 2026-09-05 06:28:21 | 4 | ||||||
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ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:28:21 | 2 | ||||||
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CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | consortium, data or information resource, disease-related portal, organization portal, portal, topical portal | 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 | 2026-09-05 06:28:19 | 213 | |||||||||
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pKiss Resource Report Resource Website 1+ mentions |
pKiss (RRID:SCR_017256) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for folding RNA secondary structures, including two limited classes of pseudoknots. Performs abstract shape analysis for structures holding pseudoknots up to complexity of kissing hairpin motifs. Successor of pknotsRG. Used for secondary structure prediction including kissing hairpin motifs. | folding, RNA, secondary, structure, pseudoknot, abstract, shape, analysis, hairpin, motif | is listed by: OMICtools | PMID:25273103 | Free, Available for download, Freely available | SCR_017256 | pKISS | 2026-09-05 06:28:21 | 4 | ||||||||
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proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | data analysis software, data processing software, software application, software resource | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIAID U19 AI118610; NIA R01 AG046170 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-09-05 06:28:20 | 1 | |||||||
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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 | access service resource, analysis service resource, core facility, data analysis service, 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 | 2026-09-05 06:28:20 | 0 | ||||||||
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Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | data analysis software, data processing software, software application, software resource | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | Cancer Prevention Research Institute of Texas ; Google Research Award ; IBM University Challenge Award ; McNair Medical Institute Scholar Award ; NHGRI HG003067; NHGRI HG006193; NHLBI U01 HL130010; NIH Office of the Director DP2 OD008540; NSF PHY-1427654; NVIDIA Research Center Award ; PD Soros Fellowship ; President Early Career Award in Science and Engineering ; Welch Foundation |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-09-05 06:28:20 | 119 | ||||||||
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ot-tools Resource Report Resource Website 1+ mentions |
ot-tools (RRID:SCR_017191) | data analysis software, data processing software, software application, software resource | Software tools for analysis of cellular cryo-ET data. | analysis, cellular, cryo-ET, data | Free, Available for download, Freely available | SCR_017191 | 2026-09-05 06:28:20 | 5 | |||||||||||
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Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility Resource Report Resource Website |
Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility (RRID:SCR_017190) | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource, training service resource | IGC Core in Oeiras, Portugal, promotes use of computational methods in biological research, through training and development of resources and materials, supports biological data analysis using computational methods, conducts research and development in bioinformatics, in particular in data flows, data warehousing and data analyses. | bioinformatics, consulting, data, analysis, management, repository | Open | SCR_017190 | Bioinformatics and Computational Unit, IGC, core facility, Instituto Gulbenkian de Ciencia, Gulbenkian Institute of Science | 2026-09-05 06:28:20 | 0 | ||||||||||
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University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility Resource Report Resource Website |
University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility (RRID:SCR_017194) | MRC Institute of Genetics and Molecular Medicine BAC | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource, software resource, training service resource | Core provides advice, training, provision of computational tools and collaborative expertise to all IGMM researchers. | bioinformatics, data, analysis, sequencing | has parent organization: University of Edinburgh; Scotland; United Kingdom | Restricted | SCR_017194 | The University of Edinburgh, Bioinformatics Analysis, College of Medicine and Veterinary Medicine, College of Medicine & Veterinary Medicine, Core Facility, Institute of Genetics and Molecular Medicine, IGMM, MRC | 2026-09-05 06:28:20 | 0 | ||||||||
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Genome Institute of Singapore Scientific and Research Computing Core Facility Resource Report Resource Website |
Genome Institute of Singapore Scientific and Research Computing Core Facility (RRID:SCR_017193) | GIS Scientific and Research Computing | access service resource, analysis service resource, core facility, data analysis service, production service resource, service resource, software resource | Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers. | bioinformatics, genomic, data, management, next, generation, sequencing, genotyping, analysis | Open | SCR_017193 | Core Facility, GIS, Scientific & Research Computing, Scientific and Research Computing, Genome Institute of Singapore | 2026-09-05 06:28:20 | 0 |
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