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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
tidyr Resource Report Resource Website 50+ mentions |
tidyr (RRID:SCR_017102) | data management software, software application, software resource | Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data. | tidy, data, spread, gather, function |
is used by: PlotsOfData is used by: tidyverse is listed by: CRAN is related to: R Project for Statistical Computing works with: dplyr |
Free, Available for download, Freely available | https://github.com/tidyverse/tidyr, https://tidyr.tidyverse.org/ | SCR_017102 | 2026-09-03 04:54:21 | 81 | |||||||||
|
seqNMF Resource Report Resource Website 1+ mentions |
seqNMF (RRID:SCR_017068) | data analysis software, data processing software, software application, software resource | Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers. | sequence, structure, high, dimention, dataset, neuroscience, repeated, sequential, pattern, data | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Department of Energy ; Labor and Economic Growth Computational Science Graduate Fellowship ; G Harold and Leila Y. Mathers Foundation ; NIBIB T32 EB019940; NIDCD R01 DC009183; NIMH R25 MH062204; NINDS U19 NS10 4648; Simons Foundation Simons Collaboration for the Global Brain ; U.S. Department of Defense NDSEG Fellowship program |
PMID:30719973 | Free, Available for download, Freely available | SCR_017068 | 2026-09-03 04:54:25 | 6 | ||||||||
|
iMicrobe Resource Report Resource Website 10+ mentions |
iMicrobe (RRID:SCR_017108) | data or information resource, organism-related portal, portal, topical portal | Portal to provide integrated and federated system that interconnects diverse microbiome data sets, bioinformatics tools, and community resources. Built on guiding principles for FAIR data. Open source, community driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with broader community. Partners with CyVerse and XSEDE. | microbiome, dataset, exchange, discovery, data | has parent organization: University of Arizona; Arizona; USA | Gordon and Betty Moore Fundation ; NSF |
Free, Freely available | SCR_017108 | 2026-09-03 04:54:11 | 20 | |||||||||
|
Ponemah Resource Report Resource Website 10+ mentions |
Ponemah (RRID:SCR_017107) | data acquisition software, data analysis software, data processing software, software application, software resource | 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 | 2026-09-03 04:54:26 | 23 | |||||||||||
|
CDC Diseases & Conditions Resource Report Resource Website 1+ mentions |
CDC Diseases & Conditions (RRID:SCR_017070) | controlled vocabulary, data or information resource | List of diseases and conditions on Centers for Disease Control and Prevention website., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | vocabulary, list, data, condition, center, disease, control, prevention | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017070 | 2026-09-03 04:54:05 | 3 | |||||||||||
|
Data Archive BRAIN Initiative Resource Report Resource Website 10+ mentions |
Data Archive BRAIN Initiative (RRID:SCR_017114) | DABI | data or information resource, data repository, service resource, storage service resource | Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves. | shared, archive, human, invasive, neurophysiology, data, brain, neurotechnology, dataset, BRAIN Initiative |
is recommended by: National Library of Medicine is recommended by: BRAIN Initiative has parent organization: University of Southern California; Los Angeles; USA has parent organization: BRAIN Initiative |
BRAIN Initiative | Restricted | SCR_017114 | Data Archive Brain Initiative, DABI | 2026-09-03 04:54:18 | 17 | |||||||
|
BSA4Yeast Resource Report Resource Website 1+ mentions |
BSA4Yeast (RRID:SCR_017113) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs. | quantitative, trait, loci, mapping, bulk, segregant, analysis, yeast, sequencing, data, processing, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Luxembourg; Luxembourg; Luxembourg |
Fonds Nationale de la Recherche (FNR) Luxembourg | Free, Freely available, Registration required | biotools:BSA4Yeast | https://bio.tools/BSA4Yeast | SCR_017113 | Bulk Segregant Analysis for Yeast | 2026-09-03 04:54:12 | 1 | ||||||
|
shovill Resource Report Resource Website 500+ mentions |
shovill (RRID:SCR_017077) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit. | assembly, bacteria, isolate, genome, Illumina, paired, end, read, data, haploid, organism, bio.tools |
uses: SPAdes is listed by: Debian is listed by: bio.tools is related to: Trimmomatic is related to: SAMTOOLS is related to: BWA is related to: FLASH is related to: Velvet is related to: Pilon |
Free, Available for download, Freely available | , biotools:shovill, BioTools:shovill | https://bio.tools/shovill, https://sources.debian.org/src/shovill/ | SCR_017077 | 2026-09-03 04:54:06 | 587 | ||||||||
|
cwl-metrics Resource Report Resource Website 1+ mentions |
cwl-metrics (RRID:SCR_017076) | CWL-metrics | software library, software resource, software toolkit | Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux. | collect, analyze, computational, resource, usage, workflow, common, language, container, cloud, data, analysis | is listed by: OMICtools | Japan Science and Technology Agency | DOI:10.1101/456756 | Free, Available for download, Freely available | OMICS_32746 | SCR_017076 | Common Workflow Language-metrics, common workflow language metrix | 2026-09-03 04:54:25 | 1 | |||||
|
VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | data analysis software, data processing software, software application, software resource | 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 | 2026-09-03 04:54:14 | 1 | ||||||
|
UMI-tools Resource Report Resource Website 100+ mentions |
UMI-tools (RRID:SCR_017048) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-03 04:54:16 | 145 | |||||
|
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 | 2026-09-03 04:54:22 | 58 | ||||||
|
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 |
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