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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NiMARE Resource Report Resource Website 10+ mentions |
NiMARE (RRID:SCR_017398) | NiMARE | software application, software resource, data processing software, data analysis software | Software Python package for coordinate and image based meta analysis of neuroimaging data. | Coordinate, image, based, meta, analysis, neuroimaging, data |
uses: PyMARE is used by: Neurosynth Compose |
Free, Available for download, Freely available | https://nimare.readthedocs.io/en/latest/ | SCR_017398 | Neuroimaging Meta Analysis Research Environment, Neuroimaging Meta-Analysis Research Environment | 2026-07-27 09:35:29 | 13 | |||||||
|
NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | data analysis software, simulation software, software resource, software application, data processing software | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-07-27 09:35:23 | 42 | ||||||||
|
ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data visualization software, data analysis software, software resource, software application, data processing software | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
German Cancer Research Center-Heidelberg Center for Personalized Oncology ; BMBF |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap, https://bio.tools/complexheatmap | SCR_017270 | 2026-07-27 09:35:36 | 3266 | ||||||
|
Deltagraph Resource Report Resource Website |
Deltagraph (RRID:SCR_018084) | data visualization software, data analysis software, software resource, software application, data processing software, data analytics software | Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities. | Data, statistic, visualization, chart selection, graph, analysis, Red Rock Software Inc. | Restricted | SCR_018084 | 2026-07-27 09:35:40 | 0 | |||||||||||
|
Hugo Data Resource Report Resource Website |
Hugo Data (RRID:SCR_022763) | patient registry, database, people resource, data or information resource | Platform for individuals who want to make their own data available for research. Used by people to join network with others who wish to contribute to vital research in partnership with and alongside leading scientists. Personal tool for saving and displaying medical information. | Hugo Health, Inc, Hugo Health Kindred, Data, Medicine, own data available for research, join network for people who wish to contribute to research | Free, Freely available | SCR_022763 | 2026-07-27 09:36:47 | 0 | |||||||||||
|
loom-viewer Resource Report Resource Website |
loom-viewer (RRID:SCR_016683) | software application, data visualization software, data processing software, software resource | Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format. | sharing, browsing, visualizing, single, cell, data, stored, Loom, file, format | works with: LoomPy | Free, Available for download, Freely available | SCR_016683 | 2026-07-27 09:35:23 | 0 | ||||||||||
|
MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | software application, data visualization software, data processing software, software resource | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-07-27 09:31:28 | 2194 | |||||
|
Human Tumor Atlas Network Resource Report Resource Website 10+ mentions |
Human Tumor Atlas Network (RRID:SCR_023364) | HTAN | atlas, topical portal, disease-related portal, portal, data or information resource | HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP. | Three dimensional atlases, cancer transitions, diverse set of tumor types, map healthy organs, cancer genomics approaches, bulk sequencing at single point in time, data, precancerous lesions to advanced disease, | cancer | National Cancer Institut Cancer Moonshot Initiative | PMID:32302568 | Free, Freely available | SCR_023364 | 2026-07-27 09:36:55 | 27 | |||||||
|
Charite University and Berlin Institute for Health Research Central Biobank Core Facility Resource Report Resource Website |
Charite University and Berlin Institute for Health Research Central Biobank Core Facility (RRID:SCR_023495) | ZeBanC | material storage repository, service resource, storage service resource, access service resource, core facility, biobank | Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management. | USEDit, ABRF, integrated healthcare biobank, biobank, biospecimens, data, data management, data storage, blood collection, DNA/RNA extraction, virtual microscopy |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
Open | ABRF_563 | https://coremarketplace.org/?FacilityID=563&citation=1 | SCR_023495 | , Charite/BIH (ZeBanC), Charite - Central Biobank Charite/BIH (ZeBanC), Central Biobank of the Charite | 2026-07-27 09:36:57 | 0 | ||||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | web service, service resource, data access protocol, software resource | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-07-27 09:35:55 | 3 | |||||||
|
Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | data analysis software, software resource, software application, data processing software, software toolkit | Software Matlab toolbox to perform representational similarity analysis for neural data. | Representional similarity analysis, data analysis, data, neural data |
is related to: MATLAB has parent organization: University of Cambridge; Cambridge; United Kingdom |
UK Medical Research Council ; European Research Council Starting Grant ; European Research Council Advanced Grant |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | RSA toolbox | 2026-07-27 09:35:56 | 7 | |||||||
|
CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | data analysis software, software resource, software application, data processing software, software toolkit | Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer. | CLIP data, data analysis, raw reads, sequencer data generation, genome assemblies, data | has parent organization: Columbia University; New York; USA | Free, Available for download, Freely available | SCR_019034 | 2026-07-27 09:35:51 | 22 | |||||||||
|
Hetindel Resource Report Resource Website 1+ mentions |
Hetindel (RRID:SCR_018922) | software application, software resource, data processing software, data analysis software | Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels. | Genomic insertions identification, genomic deletions identification, indel, heterozygous sequencing data, alleles, mutation, heterozygous indel, data | has parent organization: Max Planck Institute for Developmental Biology; Tubingen; Germany | Free, Available for download, Freely available | SCR_018922 | 2026-07-27 09:35:51 | 1 | ||||||||||
|
Urinary Stone Disease Research Network Resource Report Resource Website |
Urinary Stone Disease Research Network (RRID:SCR_019059) | USDRN | portal, disease-related portal, topical portal, data or information resource | Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies. | Urinary stone, kidney stone, kidney, treatment, prevention, urologist, nephrologist, pediatrician, clinical trial, data |
is related to: Duke University School of Medicine; North Carolina; USA is related to: University of Pennsylvania; Philadelphia; USA is related to: University of Texas System; Texas; USA is related to: Washington University in St. Louis; Missouri; USA is related to: University of Washington; Seattle; USA |
Kidney stones | NIH ; NIDDK |
Free, Freely available | SCR_019059 | 2026-07-27 09:35:54 | 0 | |||||||
|
COVID-19 Data Repository Resource Report Resource Website 1+ mentions |
COVID-19 Data Repository (RRID:SCR_019105) | service resource, topical portal, storage service resource, disease-related portal, data repository, portal, data or information resource | Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings. | COVID-19, impact data, novel coronavirus global pandemic, novel coronavirus, data |
uses: DataCite is related to: OpenICPSR has parent organization: University of Michigan; Ann Arbor; USA |
COVID-19 | Free, Freely available | https://doi.org/10.3886, https://dx.doi.org/10.3886 | SCR_019105 | 2026-07-27 09:35:51 | 1 | ||||||||
|
Clinical Trials Viewer Resource Report Resource Website |
Clinical Trials Viewer (RRID:SCR_019230) | web service, data access protocol, software resource | Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set. | Drug, clinical data, clinical trial data, data, ClinicalTrials.gov data, FDA submission, FDA documents, FDA dataset |
is related to: ClinicalTrials.gov has parent organization: McGill University; Montreal; Canada |
Free, Available for download, Freely available | SCR_019230 | 2026-07-27 09:35:58 | 0 | ||||||||||
|
Calliope calcium imaging processing package Resource Report Resource Website 1+ mentions |
Calliope calcium imaging processing package (RRID:SCR_021213) | software resource, software application, image processing software, data processing software, software toolkit | Software package for image processing for MATLAB. Used for processing of calcium imaging data. | Image processing, data, calcium imaging data, calcium imaging |
is used by: IRIS two photon acquisition package is related to: MATLAB |
Swiss National Science Foundation ; Novartis Research Foundation |
DOI:10.1016/j.cell.2017.05.023 | Free, Available for download, Freely available | SCR_021213 | 2026-07-27 09:36:17 | 1 | ||||||||
|
Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | software application, software resource, data processing software, data analysis software | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Klarman Cell Observatory ; Manton Foundation ; HHMI ; Ludwig Center at MIT ; Leidos Biomedical Research ; Frederick National Laboratory for Cancer Research ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus, https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst | SCR_021644 | 2026-07-27 09:36:25 | 2 | |||||||
|
Signal Resource Report Resource Website 10+ mentions |
Signal (RRID:SCR_017081) | data analysis software, software resource, data acquisition software, software application, data processing software | Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS. | sweep, based, data, acquisition, analysis, time, based, waveform, data, CED, transient, capture, patch, voltage, clamp, LTP study, evoked, response | Available for purchase | SCR_017081 | Signal Version 6, CED Signal, Cambridge Electronic Design Signal | 2026-07-27 09:35:29 | 13 | ||||||||||
|
ImmuneDB Resource Report Resource Website 1+ mentions |
ImmuneDB (RRID:SCR_017125) | service resource, data analysis service, database, analysis service resource, production service resource, data or information resource | Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features. | collect, store, analysis, B cell, T cell, immune, receptor, sequencing, data, process, raw, read | is used by: AIRR Data Commons | NIAID P01 AI106697; NIAID P30 AI0450080; NIDDK UC4 DK112217; NCI P30 CA016520 |
PMID:30298069 | Free, Available for download, Freely available | https://github.com/arosenfeld/immunedb | SCR_017125 | 2026-07-27 09:35:25 | 8 |
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