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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Porechop Resource Report Resource Website 1000+ mentions |
Porechop (RRID:SCR_016967) | software resource, data processing software, software application | Software tool for finding and removing adapters from Oxford Nanopore reads. | finding, removing, adapter, Oxford Nanopore, read, sequencing, data |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_17306 | https://sources.debian.org/src/porechop/ | SCR_016967 | 2026-02-14 02:05:34 | 1100 | ||||||||
|
PopMedNet Resource Report Resource Website 1+ mentions |
PopMedNet (RRID:SCR_016456) | PopMedNet | data or information resource, portal | Software as an open source informatics platform to facilitate the implementation and operation of distributed health data networks. Consists of a web-based portal for distributing requests and administering the network, and the DataMart Client. Designed by the Therapeutics Research and Infectious Disease Epidemiology (TIDE) group at the Department of Population Medicine (DPM) of the Harvard Pilgrim Health Care Institute (HPHCI) to enable creation, operation, and governance of distributed health data networks. | implement, distribute, health, data, network, research, coordinate, center, governance, | has parent organization: Harvard Medical School; Massachusetts; USA | The National Institutes of Health ; the HHS Assistant Secretary for Planning and Evaluation ; NIH DRN |
PMID:27141522 | Free, Available for download, Freely available | https://github.com/PopMedNet-Team/popmednet | SCR_016456 | Population Medicine Network | 2026-02-14 02:05:36 | 3 | |||||
|
glmmADMB Resource Report Resource Website 1+ mentions |
glmmADMB (RRID:SCR_016859) | software resource, data processing software, software application | Software R package for fitting generalized linear mixed models (GLMMs) using AD Model Builder. Fits mixed-effects models to count data using Poisson or negative binomial response distributions. | generalized, linear, mixed, model, ADMB, count, data, Poisson, negative, binominal, distribution |
uses: AD Model Builder is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | http://r-forge.r-project.org/projects/glmmadmb/ | SCR_016859 | glmm AD Model Builder, generalized linear mixed models using AD Model Builder, generalized linear mixed models using ADMB | 2026-02-14 02:05:15 | 3 | ||||||||
|
cryoSPARC Resource Report Resource Website 1000+ mentions |
cryoSPARC (RRID:SCR_016501) | software resource, image analysis software, data processing software, software application | Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery. | Structura Biotechnology Inc., data, processing, analysis, image, single, particle, cryo-EM, structure, discovery, automated, protein, virus, molecular, complex | is related to: University of Toronto; Ontario; Canada | PMID:28165473 | Available free of charge for academic users with a valid institutional email address, Trail available | SCR_016501 | 2026-02-14 02:05:34 | 2480 | |||||||||
|
MaRe Resource Report Resource Website 1+ mentions |
MaRe (RRID:SCR_018069) | data processing software, software resource, software toolkit, software application | Software tool to leverage power of Docker and Spark to run and scale your serial tools in MapReduce fashion. | Docker, Spark, run and scale serial tools, data, MapReduce fashion | Free, Available for download, Freely available | SCR_018069 | EasyMapReduce | 2026-02-14 02:05:40 | 3 | ||||||||||
|
Whole Tale Resource Report Resource Website 1+ mentions |
Whole Tale (RRID:SCR_017537) | data or information resource, portal, project portal | Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility. | Reproducible, data, merging, science, cyberinfrastructure, pathway, tale, capture, code, finding, analysis | NSF 1541450 | DOI:10.1016/j.future.2017.12.029 | Free, Freely available | https://github.com/whole-tale/wt-design-docs//blob/stable/README.rst | SCR_017537 | 2026-02-14 02:05:39 | 1 | ||||||||
|
Clarivate Analytics Resource Report Resource Website 50+ mentions |
Clarivate Analytics (RRID:SCR_017657) | data or information resource, organization portal, portal | Data analytics company that operates a collection of services: Web of Science (EndNote, InCites, Journal Citation Reports, Publons, Kopernio), Cortellis, Derwent, Derwent World Patents Index, CompuMark, MarkMonitor, Techstreet, Publons, EndNote, Kopernio, and ScholarOne. Deliver critical data, information, workflow solutions and deep domain expertise to innovators everywhere. | Data, analytics, Web of Science, Cortellis, Derwent, Derwent World Patents Index, CompuMark, MarkMonitor, Techstreet, Publons, EndNote, Kopernio, ScholarOne. | SCR_017657 | 2026-02-14 02:05:43 | 57 | ||||||||||||
|
Nonhuman Primate Reference Transcriptome Resource Resource Report Resource Website 10+ mentions |
Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) | NHPRTR | data or information resource, portal, project portal | Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species. | Nonhuman, primate, reference, transcriptome, deep, sequencing, RNAseq, data, species | NIH | Free, Freely available | SCR_017534 | Nonhuman Primate Reference Transcriptome Resource | 2026-02-14 02:05:35 | 10 | ||||||||
|
DiffuserCam Resource Report Resource Website |
DiffuserCam (RRID:SCR_017466) | software resource, data processing software, software application | Software tool as processing code. Alternating direction method of multipliers (ADMM) algorithm for recovering 3D volumes from 2D raw data captured with DiffuserCam. | Processing, code, multiplier, algorithm, recovering, 3D, volume, 2D, raw, data, capture, BRAIN Initiative | is recommended by: BRAIN Initiative | NEI EY027597 | Free, Freely available | SCR_017466 | 2026-02-14 02:05:35 | 0 | |||||||||
|
FateID Resource Report Resource Website 1+ mentions |
FateID (RRID:SCR_017244) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:25 | 2 | |||||||
|
CellCycleTRACER Resource Report Resource Website Rating or validation data |
CellCycleTRACER (RRID:SCR_017128) | web service, data processing software, data analysis software, software application, data access protocol, software resource | 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 | 2026-02-14 02:03:23 | 0 | |||||||||
|
NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_017248) | NAT | data visualization software, data processing software, data analysis software, 3d 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 | 2026-02-14 02:03:10 | 4 | ||||||
|
PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data repository, storage service resource, web service, data or information resource, service resource, data access protocol, software resource | 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 | 2026-02-14 02:03:21 | 0 | ||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:25 | 2 | ||||||
|
CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | portal, consortium, data or information resource, organization portal, disease-related 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 | 2026-02-14 02:03:08 | 131 | |||||||||
|
vini: A viewer for fMRI data Resource Report Resource Website |
vini: A viewer for fMRI data (RRID:SCR_017250) | data visualization software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:22 | 0 | |||||||||
|
IQ-TREE Resource Report Resource Website 500+ mentions |
IQ-TREE (RRID:SCR_017254) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:22 | 790 | ||||||
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proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | data analysis software, software resource, data processing software, software application | 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; NIA R01 AG046170; NIAID U19 AI118610 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-02-14 02:03:16 | 1 | |||||||
|
University of Gothenburg Bioinformatics Core Facility Resource Report Resource Website |
University of Gothenburg Bioinformatics Core Facility (RRID:SCR_017189) | GU Bioinformatics Core Facility | data analysis service, core facility, analysis service resource, production service resource, service resource, access 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 | 2026-02-14 02:03:16 | 0 | ||||||||
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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://meshview-for-brain-atlases.readthedocs.io https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases |
SCR_017222 | MeshView for brain atlases | 2026-02-14 02:03:22 | 11 |
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