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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ragu Resource Report Resource Website 1+ mentions |
Ragu (RRID:SCR_016851) | Ragu | data analysis software, data processing software, software application, software resource | 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 | 2026-09-19 12:53:29 | 3 | |||||||||
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Polyman Resource Report Resource Website 1+ mentions |
Polyman (RRID:SCR_016850) | data analysis software, data processing software, software application, software resource | Software tool as an European Data Format EDF/EDF+ viewer and manual sleep scoring program. Used in EEG and Sleep investigations, but can be used for almost any (also non-medical) sequential time series and event lists. | European, data, format, viewer, manual, sleep, scoring, program, electroencephalography, EEG, EDF, neurophysiology | Free, Available for download, Freely available | SCR_016850 | 2026-09-19 12:53:29 | 3 | |||||||||||
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Sashimiplot Resource Report Resource Website |
Sashimiplot (RRID:SCR_016861) | sashimiplot | data processing software, data visualization software, software application, software resource | Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. | quantitative, visualization, aligned, RNA-Seq, read, data, compare, exon, usage, sample, experiment, condition, MISO | is related to: MISO | Alfred P. Sloan research fellowship ; NCI R01 CA157304; NCI U01 CA184897; NHGRI R01 HG002439; NIGMS R01 GM085319; NIGMS R01 GM096193; NSF IIS 1149662; Starr Cancer Consortium |
PMID:25617416 DOI:10.1093/bioinformatics/btv034 |
Free, Available for download, Freely available | http://miso.readthedocs.org/en/fastmiso/sashimi.html | SCR_016861 | sashimi_plot | 2026-09-19 12:53:29 | 0 | |||||
|
NetworkX Resource Report Resource Website 100+ mentions |
NetworkX (RRID:SCR_016864) | data analysis software, data processing software, network analysis software, software application, software resource | 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 | 2026-09-19 12:53:29 | 132 | |||||||||
|
Bulked segregation analysis tools for outbreeding species Resource Report Resource Website 1+ mentions |
Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) | BSATOS | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data. | next, generation, sequencing, bulked, segregation, analysis, outbreeting, specie, gene, mapping, data | Free, Available for download, Freely available | SCR_017009 | Bulked segregation analysis tools for outbreeding species, Bulked Segregation Analysis Tools for Outbreeding Species, BSATOS | 2026-09-19 12:53:32 | 2 | |||||||||
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Allen Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Brain Atlas (RRID:SCR_017001) | atlas, data or information resource, portal, project portal | Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases. | genomic, data, neuroanatomy, gene, expression, map, mouse, human, brain, atlas, neurobiology |
is related to: Allen Software Development Kit is related to: Common Cell Type Nomenclature has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas expression map of Cre and other drivers provides: ABA Mouse Brain: Atlas works with: Transcriptomics Explorer works with: Kinase Associated Neural Phospho Signaling |
Free, Freely available | SCR_017530 | SCR_017001 | Allen Brain Atlas, Brain Atlases, Allen Mouse Brain Atlas, The Allen Brain Atlas, Allen Human Brain Atlas | 2026-09-19 12:53:32 | 237 | ||||||||
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mzStudio Resource Report Resource Website 1+ mentions |
mzStudio (RRID:SCR_017088) | data analysis software, data processing software, data visualization software, software application, 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 |
Barr Program in Basic Research ; Dana-Farber Strategic Research Initiative ; Honorable Tina Brozman Foundation for Ovarian Cancer Research ; Michael J. Fox Foundation ; NCI CA042368; NCI CA178860; NCI CA188881 |
PMID:28763045 | Free, Available for download, Freely available | OMICS_26946 | https://omictools.com/mzstudio-tool | SCR_017088 | 2026-09-19 12:53:34 | 1 | ||||||
|
GenomeScope Resource Report Resource Website 500+ mentions |
GenomeScope (RRID:SCR_017014) | Genomescope | data analysis software, data processing software, service resource, software application, software resource | Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach. | genome, unassembled, sequenced, data, short, read, analysis, heterozygosity, repeat, content, size, kmer | is related to: Cold Spring Harbor Laboratory | NHGRI R01 HG006677; NSF DBI 1350041; NSF IOS 1237880 |
PMID:28369201 | Free, Freely available, | http://qb.cshl.edu/genomescope/ | SCR_017014 | 2026-09-19 12:53:32 | 800 | ||||||
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OmicsSIMLA Resource Report Resource Website 1+ mentions |
OmicsSIMLA (RRID:SCR_017011) | simulation software, software application, software resource, software toolkit | Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version. | multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNA | is listed by: OMICtools | Ministry of Science and Technology in Taiwan | DOI:10.1101/426510 | Freely available, Available to download, Free | OMICS_31363 | SCR_017011 | 2026-09-19 12:53:32 | 1 | |||||||
|
miRTarVisPlus Resource Report Resource Website 1+ mentions |
miRTarVisPlus (RRID:SCR_017103) | miRTarVis+ | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | 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 | Hankuk University of Foreign Studies Research Fund ; National Research Foundation of Korea |
PMID:28600227 | Free, Freely available | http://hcil.snu.ac.kr/research/mirtarvisplus | SCR_017103 | mirtarvisplus | 2026-09-19 12:53:34 | 3 | |||||
|
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 | 2026-09-19 12:53:34 | 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 | 2026-09-19 12:53:33 | 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 | 2026-09-19 12:53:34 | 20 | |||||||||
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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 | 2026-09-19 12:53:34 | 23 | |||||||||||
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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 | 2026-09-19 12:53:33 | 3 | |||||||||||
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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 | 2026-09-19 12:53:34 | 17 | |||||||
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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 | 2026-09-19 12:53:34 | 1 | ||||||
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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 | 2026-09-19 12:53:33 | 587 | ||||||||
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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 | 2026-09-19 12:53:33 | 1 | |||||
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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 | 2026-09-19 12:53:32 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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