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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
RaceID Resource Report Resource Website 10+ mentions |
RaceID (RRID:SCR_017045) | algorithm resource, data analysis software, data processing software, software application, software resource | 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 | 2026-09-03 04:54:04 | 15 | |||||
|
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 | 2026-09-03 04:54:04 | 382 | |||||||
|
toxprofileR Resource Report Resource Website 1+ mentions |
toxprofileR (RRID:SCR_017027) | data analysis software, data processing software, software application, software library, software resource, software toolkit | 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 | 2026-09-03 04:54:23 | 1 | ||||||||||
|
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 | 2026-09-03 04:54:11 | 19 | ||||||||||
|
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 | 2026-09-03 04:54:07 | 1 | |||||||||||
|
Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | data analysis software, data processing software, software application, software resource | 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 |
Alfred P. Sloan Research ; Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NCI T32 CA009337; NHGRI R01 HG005220; NHGRI R01 HG007104; NHGRI R21 HG006913; NSF BIO-1564917; NSF CCF-1053918; NSF CCF-1256087; 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 | 2026-09-03 04:54:16 | 439 | ||||||
|
Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | data analysis software, data processing software, software application, software resource | 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 |
NCRR P20 RR016460; NIGMS P20 GM103429; NSFC 61272016; NSFC 61432010 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | 2026-09-03 04:54:07 | 6 | ||||||
|
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 | 2026-09-03 04:54:13 | 10 | |||||||
|
FateID Resource Report Resource Website 1+ mentions |
FateID (RRID:SCR_017244) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-03 04:54:24 | 2 | |||||||
|
CellCycleTRACER Resource Report Resource Website Rating or validation data |
CellCycleTRACER (RRID:SCR_017128) | data access protocol, data analysis software, data processing software, software application, software resource, web service | Software tool as supervised machine learning algorithm that classifies and sorts single cell mass cytometry data according to their cell cycle, which allows to correct for cell cycle state and cell volume heterogeneity. Reveals signaling relationships and cell heterogeneity that were otherwise masked. Computational method to quantify cell cycle and cell volume variability. | classify, sort, single, cell, mass, cytometry, data, cycle, state, volume, heterogeneity, quantify, volume, variability | European Research Council ; NIDDK UC4 DK108132; SNSF ; SystemsX MetastasiX grant |
PMID:29434325 | Free, Restricted | SCR_017128 | 2026-09-03 04:54:19 | 0 | |||||||||
|
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 | 2026-09-03 04:54:26 | 4 | ||||||
|
PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data access protocol, data or information resource, data repository, service resource, software resource, storage service resource, web service | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NHGRI U54 HG008097; NIGMS R01 GM103551; NIGMS R01 GM121696; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-09-03 04:54:19 | 0 | ||||||
|
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 | 2026-09-03 04:54:25 | 2 | ||||||
|
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 | 2026-09-03 04:54:14 | 213 | |||||||||
|
vini: A viewer for fMRI data Resource Report Resource Website |
vini: A viewer for fMRI data (RRID:SCR_017250) | data processing software, data visualization software, software application, software resource | 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 | 2026-09-03 04:54:15 | 0 | |||||||||
|
IQ-TREE Resource Report Resource Website 1000+ mentions |
IQ-TREE (RRID:SCR_017254) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-03 04:54:27 | 1007 | ||||||
|
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 | 2026-09-03 04:54:24 | 1 | |||||||
|
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 | 2026-09-03 04:54:10 | 0 | ||||||||
|
MeshView Resource Report Resource Website 10+ mentions |
MeshView (RRID:SCR_017222) | data access protocol, software resource, web service | Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases. | real, time, 3D, display, surface, mesh, data, structural, parcellation, generation, defined, cut, plane, volumetric, atlas, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain works with: Allen Mouse Brain Reference Atlas works with: Waxholm Space |
European Union Horizon 2020 Human brain project | DOI:10.1371/journal.pone.0216796 | Free, Freely available | https://localiview.apps.ebrains.eu/, https://meshview-for-brain-atlases.readthedocs.io, https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases | SCR_017222 | MeshView for brain atlases | 2026-09-03 04:54:25 | 11 | ||||||
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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 | 2026-09-03 04:54:14 | 119 |
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