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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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spdep Resource Report Resource Website 1+ mentions |
spdep (RRID:SCR_019294) | software toolkit, data processing software, software application, data analysis software, software resource | Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree. | Spatial weights matrix objects, spatial dependence, weighting schemes, spatial weights, matrix objects | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/r-spatial/spdep/ | SCR_019294 | Spatial Dependence: Weighting Schemes and Statistics, spatial dependence | 2026-08-14 09:28:16 | 2 | ||||||||
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MesKit Resource Report Resource Website 1+ mentions |
MesKit (RRID:SCR_020959) | software toolkit, data processing software, software application, data analysis software, software resource, data visualization software, sequence analysis software | Software R package for dissecting cancer evolution from multi region derived tumor biopsies via somatic mutations. Used for characterizing cancer genomic ITH and inferring history of tumor evolution via implementation of well established computational and statistical methods. | Dissecting cancer evolution, region derived tumor biopsies, somatic mutations, cancer genomic ITH, tumor evolution | has parent organization: Sun Yat-sen University; Guangdong; China | Free, Available for download, Freely available | https://bioconductor.org/packages/MesKit/ | SCR_020959 | Multi region exome sequencing analysis tool Kit | 2026-08-14 09:28:30 | 4 | ||||||||
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scales Resource Report Resource Website 10+ mentions |
scales (RRID:SCR_019295) | software toolkit, data processing software, software application, software resource, data visualization software | Software R package as scale functions for visualization. Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends. | Scale functions, visualization, graphical scales, map data, axes, determining breaks, legend, determining labels | Free, Available for download, Freely available | https://github.com/r-lib/scales | SCR_019295 | 2026-08-14 09:28:08 | 18 | ||||||||||
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trRosetta Resource Report Resource Website 100+ mentions |
trRosetta (RRID:SCR_021181) | software application, service resource, simulation software, software resource | Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets. | protein structure, restraint-guided structure generation, protein structure prediction | uses: Rosetta | National Natural Science Foundation of China ; Fok Ying-Tong Education Foundation ; Key Laboratory for Medical Data Analysis and Statistical Research of Tianjin ; Thousand Youth Talents Plan of China ; China Scholarship Council ; NIGMS R01 GM092802; NIH Office of the Director DP5 OD026389 |
PMID:31896580 | Free, Freely available | https://github.com/gjoni/trRosetta | SCR_021181 | transformed restrained Rosetta | 2026-08-14 09:28:21 | 100 | ||||||
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Neurodata Extensions Catalog Resource Report Resource Website 1+ mentions |
Neurodata Extensions Catalog (RRID:SCR_021340) | NDX Catalog | database, data or information resource, software application, software resource, catalog | Community led catalog of extensions to Neurodata Without Borders data standard. | Extensions catalog, NWB, Neurodata Without Borders, data standard, Neurodata Without Borders data standard, software tools catalog |
is related to: Neurodata Without Borders is related to: PyNWB is related to: Hierarchical Data Modeling Framework |
NIH | Free, Available for download, Freely Available | https://github.com/nwb-extensions | SCR_021340 | 2026-08-14 09:28:33 | 1 | |||||||
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HDMF Documentation Utilities Resource Report Resource Website |
HDMF Documentation Utilities (RRID:SCR_021341) | software toolkit, software library, standard specification, data or information resource, software resource, narrative resource | Software tool for generating documentation for data standard schema defined using HDMF specification language. Collection of CLIs, scripts and modules useful to generate NWB documentation. | Data standard schema, documentation utilitites, HDMF specification language, NWB documentation generation |
is related to: Hierarchical Data Modeling Framework is related to: Neurodata Without Borders |
Free, Available for download, Freely Available | SCR_021341 | 2026-08-14 09:28:23 | 0 | ||||||||||
|
RobotReviewer Resource Report Resource Website 1+ mentions |
RobotReviewer (RRID:SCR_021064) | software application, text-mining software, web application, software resource | Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials. | Data automatic extraction, clinical trial reports, automatically extract key data, Evidence Based Medicine, text journal articles processing, randomized controlled trials |
is related to: Northeastern University; Massachusetts; USA is related to: University of Texas at Austin; Texas; USA |
NLM R01 LM012086; Medical Research Council UK ; NCI UH2 CA203711 |
PMID:29093610 DOI:10.1093/jamia/ocv044 |
Free, Available for download, Freely available | https://github.com/ijmarshall/robotreviewer, https://robotreviewer.vortext.systems/ | SCR_021064 | Automating Biomedical Evidence Synthesis | 2026-08-14 09:28:19 | 1 | ||||||
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RNAProt Resource Report Resource Website 1+ mentions |
RNAProt (RRID:SCR_021218) | software application, simulation software, software resource | Software tool for modelling RNA binding protein binding preferences. Used to predict RPB binding sites. Computational RBP binding site prediction framework based on recurrent neural networks. Includes functionalities from dataset generation over model training to evaluation of binding preferences and binding site prediction. | RBP, RNA Binding Protein, RNA sequences, protein binding preferences, predict RPB binding sites, neural networks |
is related to: Conda is related to: BioConda |
Free, Available for download, Freely available | SCR_021218 | 2026-08-14 09:28:32 | 1 | ||||||||||
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Panda3D Resource Report Resource Website 1+ mentions |
Panda3D (RRID:SCR_021216) | software development environment, data processing software, software development tool, software application, software resource, data visualization software, 3d visualization software | Open source game engine and framework for 3D rendering and game development for Python and C++ programs. Graphics engine and programming environment to support everything from real time graphics applications to development of high end virtual reality theme park attractions or video games. | Disney VR Studio, game engine, 3D rendering, game development, Python, graphics engine, programming environment |
is related to: Two photon Calcium Imaging in Mice Navigating Virtual Reality Environment has parent organization: Carnegie Mellon University; Pennsylvania; USA |
DOI:10.1109/MC.2004.180 | Free, Available for download, Freely available | https://github.com/panda3d/panda3d | SCR_021216 | Platform agnostic networked display architecture 3D | 2026-08-14 09:28:21 | 7 | |||||||
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Friedrich Miescher Institute data repository Resource Report Resource Website 1+ mentions |
Friedrich Miescher Institute data repository (RRID:SCR_021214) | data or information resource, storage service resource, service resource, data repository | Data repository for Friedrich Miescher Institute for Biomedical Research in areas of epigenetics, quantitative biology, and neurobiology. | Friedrich Miescher Institute for Biomedical Research, epigenetics data, quantitative biology data, neurobiology data | has parent organization: Friedrich Miescher Institute | Data is freely available | SCR_021214 | FMI data repository | 2026-08-14 09:28:14 | 3 | |||||||||
|
PROMIS 2 MY Health Resource Report Resource Website 1+ mentions |
PROMIS 2 MY Health (RRID:SCR_021215) | data or information resource, portal, disease-related portal, topical portal | Portal for cross sectional study where population based sample of adult cancer patients were recruited for mailed survey (with telephone follow-up of non-responders) to evaluate equivalence of PROMIS measures across socio-demographic and clinical sub-groups. | PROMIS, cross sectional study, adult cancer patients, mailed survey, |
is related to: Harvard University; Cambridge; United States is related to: Dataverse Network Project |
female breast cancer, uterine and cervical cancers, prostate cancer, colorectal cancer, non- small cell lung cancer (NSCLC) and non-Hodgkin’s Lymphoma, | Restricted | SCR_021215 | 2026-08-14 09:28:32 | 1 | |||||||||
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IRIS two photon acquisition package Resource Report Resource Website 1+ mentions |
IRIS two photon acquisition package (RRID:SCR_021212) | software toolkit, data processing software, software application, software resource, image acquisition software, data acquisition software | Software LabView package for two-photon calcium imaging acquisition. Used for controlling two-photon microscope and preprocessing of calcium imaging data. | LabView, Two-photon calcium imaging, 2-photon microscope, photon acquisition, calcium imaging acquisition | uses: Calliope calcium imaging processing package | Novartis Research Foundation ; Swiss National Science Foundation |
DOI:10.1016/j.cell.2017.05.023 | Free, Available for download, Freely available | SCR_021212 | IRIS two-photon acquisition package | 2026-08-14 09:28:32 | 7 | |||||||
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Calliope calcium imaging processing package Resource Report Resource Website 1+ mentions |
Calliope calcium imaging processing package (RRID:SCR_021213) | software toolkit, image processing software, data processing software, software application, software resource | 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 | 2026-08-14 09:28:21 | 1 | ||||||||
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DepthSizer Resource Report Resource Website 1+ mentions |
DepthSizer (RRID:SCR_021232) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool for read-depth based genome size prediction. Wrapper for genome size estimate methods of Diploidocus.Uses long read depth of coverage and BUSCO single copy orthologue prediction to estimate genome size. | Genome size prediction, genome size estimate wrapper, estimate genome size | is used by: Diploidocus | Free, Available for download, Freely available | SCR_021232 | 2026-08-14 09:28:22 | 2 | ||||||||||
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seqpac Resource Report Resource Website 1+ mentions |
seqpac (RRID:SCR_021079) | software toolkit, data processing software, software application, data analysis software, software resource | Software R package for analysis of short sequenced reads. Framework for small RNA analysis in R using Sequence Based Counts.Can be applied on any type of data generated by large scale nucleotide sequencing, where user wish to maintain sequence integrity during whole analysis. | sRNA-seq data analysis, RNA-seq, small RNA, short sequence reads analysis, sequence based counts, nucleotide sequencing data | is related to: R Project for Statistical Computing | The Swedish Research Council 2015-03141; Knut and Alice Wallenberg Stiftelse ; 2015.0165; Ragnar Söderberg ; Formas - Swedish Research Council for Sustainable Development 2020-01042 |
DOI:10.1101/2021.03.19.436151 | Free, Available for download, Freely available | SCR_021079 | 2026-08-14 09:28:31 | 1 | ||||||||
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Lung Disease Knowledge Portal Resource Report Resource Website 1+ mentions |
Lung Disease Knowledge Portal (RRID:SCR_021352) | LDKP | topical portal, disease-related portal, data repository, storage service resource, portal, data or information resource, service resource | Portal enables browsing, searching, and analysis of human genetic information linked to lung diseases and related traits, while protecting integrity and confidentiality of underlying data. | Human genetic information, lung diseases, data searching, data analysis | Free, Freely available | SCR_021352 | 2026-08-14 09:28:23 | 2 | ||||||||||
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Hifiasm Resource Report Resource Website 500+ mentions |
Hifiasm (RRID:SCR_021069) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool as haplotype resolved de novo assembler for PacBio Hifi reads. Can assemble human genome in several hours.Introduces new graph binning algorithm and achieves haplotype resolved assembly given trio data. Takes advantage of long high fidelity sequence reads to represent haplotype information in phased assembly graph. Preserves contiguity of all haplotypes. | PacBio Hifi reads, haplotype resolved de novo assembler, trio data, long high fidelity sequence reads, | NHGRI R01 HG010040; NHGRI U01 HG010961; NHGRI U41HG010972 |
PMID:33526886 | Free, Available for download, Freely available | SCR_021069 | 2026-08-14 09:28:31 | 584 | |||||||||
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GenAlEx Resource Report Resource Website 50+ mentions Issue |
GenAlEx (RRID:SCR_021102) | software toolkit, data processing software, software application, data analysis software, software resource | Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level. | population genetic analyses, Microsoft Excel, diploid codominant analysis, haploid genetic loci, binary genetic loci, DNA sequences analysis | PMID:22820204 | Free, Available for download, Freely available | SCR_021102 | GenAlEx 6.5, Genetic Analysis in Excel | 2026-08-14 09:28:31 | 79 | |||||||||
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ploidyNGS Resource Report Resource Website 1+ mentions |
ploidyNGS (RRID:SCR_021320) | data processing software, software application, data analysis software, software resource, data visualization software | Open source software tool for visually exploring ploidy with Next Generation Sequencing data.Used to visualize and explore ploidy levels in newly sequenced genome, exploiting short read data. Allows identification of ploidy level of newly sequenced genome in visual way. Implemented in Python and R. | Visually exploring ploidy, Next Generation Sequencing, newly sequenced genome, exploiting short read data | Sao Paulo Research Foundation | PMID:28383704 | Free, Available for download, Freely available | SCR_021320 | 2026-08-14 09:28:33 | 8 | |||||||||
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PiDose project Resource Report Resource Website |
PiDose project (RRID:SCR_021441) | project portal, data or information resource, portal, instrument resource | Project related to oral drug administration to group housed mice. Provides open source system for oral drug administration to group housed mice. System includes home cage attached device that weighs individual animals and administers daily dosage of drug solution based on each animal bodyweight through their drinking water. Group housed mice are identified through use of RFID tagging and receive both regular water and drug solution drops by licking at spout within PiDose module. | Oral drug administration, group housed mice, OpenBehavior, Instrument | is listed by: OpenBehavior | DOI:10.1038/s41598-020-68477-2 | Free, Freely available | SCR_021441 | PiDose | 2026-08-14 09:28:17 | 0 |
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