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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | software resource, data processing software, software application, data analysis software | Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections. | variant, antigen, profiling, data, genome, transcriptome, proteome, gene, expression, infection, Trypanosoma, bio.tools |
is listed by: Debian is listed by: bio.tools requires: Python Programming Language |
Free, Available for download, Freely available | biotools:VAPPER | https://bio.tools/VAPPER | SCR_016993 | VAP, VariantAntigenProfilingPER | 2026-08-05 10:46:47 | 1 | ||||||
|
UMI-tools Resource Report Resource Website 100+ mentions |
UMI-tools (RRID:SCR_017048) | software resource, data processing software, software application, data analysis software | Open source software package for handling Unique Molecular Identifiers in NGS data sets. | unique, molecular, identifier, NGS, data, dataset, random, oligonucleotide, barcode, sequencing, copy, molecule, PCR, amplification, bio.tools |
is listed by: Debian is listed by: bio.tools |
Medical Research Council | PMID:28100584 | Free, Available for download, Freely available | biotools:umi-tools | https://bio.tools/umi-tools | SCR_017048 | Unique Molecular Identifiers tools | 2026-08-05 10:46:42 | 126 | |||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data processing software, software application, sequence analysis software, data analysis software, 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 | 2026-08-05 10:46:47 | 53 | ||||||
|
RaceID Resource Report Resource Website 10+ mentions |
RaceID (RRID:SCR_017045) | data processing software, algorithm resource, software application, data analysis software, 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 | 2026-08-05 10:46:42 | 15 | |||||
|
Growth Profiling Toolbox Resource Report Resource Website |
Growth Profiling Toolbox (RRID:SCR_016878) | data processing software, software application, data analysis software, software toolkit, software resource | 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 | 2026-08-05 10:46:45 | 0 | |||||||||||
|
sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | software resource, data processing software, software application, 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 | 2026-08-05 10:46:40 | 24 | ||||||
|
ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | software resource, data processing software, software application, 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 | 2026-08-05 10:46:40 | 12 | ||||||
|
ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 1+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | data or information resource, project portal, portal, catalog, database | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIH ; NIDDK |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-08-05 10:46:46 | 9 | ||||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | software resource, data processing software, software application, data analysis 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 | 2026-08-05 10:46:48 | 354 | |||||||
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toxprofileR Resource Report Resource Website 1+ mentions |
toxprofileR (RRID:SCR_017027) | data processing software, software library, software application, data analysis software, software toolkit, software resource | 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 | 2026-08-05 10:46:42 | 1 | ||||||||||
|
Profinder Resource Report Resource Website 10+ mentions |
Profinder (RRID:SCR_017026) | software resource, data processing software, software application, data analysis 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 | 2026-08-05 10:46:47 | 17 | ||||||||||
|
Bruker WinEPR program Resource Report Resource Website 1+ mentions |
Bruker WinEPR program (RRID:SCR_017023) | data processing software, data acquisition software, software application, data analysis software, 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 | 2026-08-05 10:46:48 | 1 | |||||||||||
|
Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | software resource, data processing software, software application, data analysis 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 | 2026-08-05 10:46:47 | 357 | ||||||
|
Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | software resource, data processing software, software application, data analysis 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 | 2026-08-05 10:46:47 | 6 | ||||||
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PCAGO Resource Report Resource Website 1+ mentions |
PCAGO (RRID:SCR_017033) | web service, data access protocol, software resource, production service resource, service resource, 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 | 2026-08-05 10:46:47 | 7 | |||||||
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FateID Resource Report Resource Website 1+ mentions |
FateID (RRID:SCR_017244) | software resource, data processing software, software application, data analysis 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 | 2026-08-05 10:46:45 | 2 | |||||||
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CellCycleTRACER Resource Report Resource Website Rating or validation data |
CellCycleTRACER (RRID:SCR_017128) | data processing software, data access protocol, software application, data analysis software, 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 | SNSF ; European Research Council ; NIDDK UC4 DK108132; SystemsX MetastasiX grant |
PMID:29434325 | Free, Restricted | SCR_017128 | 2026-08-05 10:46:50 | 0 | |||||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_017248) | NAT | data processing software, 3d visualization software, software application, data visualization software, data analysis software, 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 | 2026-08-05 10:46:49 | 4 | ||||||
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mzStudio Resource Report Resource Website 1+ mentions |
mzStudio (RRID:SCR_017088) | data processing software, software application, data visualization software, data analysis software, software resource | 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 | 2026-08-05 10:46:49 | 1 | ||||||
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PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data or information resource, data repository, data access protocol, software resource, storage service resource, 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 |
NIGMS R01 GM103551; NIGMS R01 GM121696; NHGRI U54 HG008097; 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 | 2026-08-05 10:46:50 | 0 |
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