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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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con/duct Resource Report Resource Website |
con/duct (RRID:SCR_025436) | source code, software resource | Software application as helper to run command, capture stdout/stderr and details about running. | run command helper, capture stdout/stderr, | Free, Available for download, Freely available | SCR_025436 | duct | 2026-08-09 09:09:13 | 0 | ||||||||||
|
ColabFold Resource Report Resource Website 100+ mentions |
ColabFold (RRID:SCR_025453) | source code, software resource | Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding. | prediction of protein structures and complexes, protein folding, protein structure prediction, | Max Planck Society ; University of Göttingen ; National Research Foundation of Korea ; Seoul National University ; NIH Office of the Director DP5OD026389; NIAID R21AI156595; NSF |
PMID:35637307 | Free, Available for download, Freely available | https://github.com/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb | SCR_025453 | 2026-08-09 09:09:14 | 493 | ||||||||
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GenBiomApps Resource Report Resource Website 1+ mentions |
GenBiomApps (RRID:SCR_025542) | software toolkit, software resource | Software R package as collection of functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution.Enhanced model for burn-in studies, where failures are tackled by countermeasures. | Clopper-Pearson Confidence Interval, Generalized Binomial Distribution, distribution function, quantile function, random generation | Free, Available for download, Freely available | SCR_025542 | 2026-08-09 09:09:17 | 1 | |||||||||||
|
km.ci Resource Report Resource Website |
km.ci (RRID:SCR_025543) | software toolkit, software resource | Software R package to compute various confidence intervals for the Kaplan-Meier estimator, namely: Peto's CI, Rothman CI, CI's based on Greenwood's variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner. | Confidence intervals, Kaplan-Meier estimator, | Free, Available for download, Freely available | SCR_025543 | 2026-08-09 09:08:46 | 0 | |||||||||||
|
3D Developmental Mouse Brain Common Coordinate Framework Resource Report Resource Website 1+ mentions |
3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) | data or information resource, atlas | Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain. | multimodal 3D atlases, developing mouse brain, mouse brain data, |
is related to: Allen Mouse Brain Common Coordinate Framework is organization facet of: BRAIN Initiative |
NIMH RF1MH12460501; NINDS R01NS108407; NIMH R01MH116176; NIBIB R01EB031722 |
PMID:37745386 | Free, Freely available | SCR_025544 | DevCCF | 2026-08-09 09:09:15 | 2 | |||||||
|
pbmm2 Resource Report Resource Website 1+ mentions |
pbmm2 (RRID:SCR_025549) | source code, software resource | Software application as minimap2 frontend for PacBio native data formats. SMRT C++ wrapper for minimap2's C API. | minimap2, PacBio, native data formats, SMRT C++ wrapper, minimap2 C API, | Free, Available for download, Freely available, | SCR_025549 | 2026-08-09 09:09:17 | 7 | |||||||||||
|
signed ks test Resource Report Resource Website 1+ mentions |
signed ks test (RRID:SCR_025636) | source code, software resource | Software tool as modified R ks.test to obtain sign and force exact p-value. | modified R ks.test, obtain sign and force exact p-value, p-value, | Free, Available for download, Freely available, | SCR_025636 | 2026-08-09 09:08:49 | 1 | |||||||||||
|
2s-LCA Resource Report Resource Website 1+ mentions |
2s-LCA (RRID:SCR_025613) | software application, software resource | Software for multi-omic data integration. Used to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition. | multi-omic data integration, two-stage linked component analysis, jointly decompose biologically related experimental data sets, decomposition, | PMID:35358296 | https://github.com/CHuanSite/SJD | SCR_025613 | two-stage Linked Component Analysis | 2026-08-09 09:08:48 | 1 | |||||||||
|
GRNBoost2 Resource Report Resource Website 10+ mentions |
GRNBoost2 (RRID:SCR_025614) | software application, software resource | Algorithm for regulatory network inference using gradient boosting, based on GENIE3 architecture. Used for inference of gene regulatory networks. | GRN, Gene Regulatory Network, inference of gene regulatory networks, | PMID:30445495 | Free, Freely available | https://arboreto.readthedocs.io/en/latest/, https://github.com/aertslab/GRNBoost | SCR_025614 | GRNBoost, Gene Regulatory Network Boost | 2026-08-09 09:09:17 | 11 | ||||||||
|
Cloud-SPAN Resource Report Resource Website 1+ mentions |
Cloud-SPAN (RRID:SCR_025594) | software application, software resource | Cloud-based high performance computing for specialised analyses on environmental omics. | specialised analyses, environmental omics, | Free, Freely available, | SCR_025594 | Cloud SPecialised ANalyses | 2026-08-09 09:09:16 | 1 | ||||||||||
|
ISOLDE Resource Report Resource Website 10+ mentions |
ISOLDE (RRID:SCR_025577) | software application, software resource | Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate "static" maps from pre-calculated F/phi data. | software environment, model building, building macromolecular models, low resolution electron density maps, experimental maps, | is a plug in for: UCSF ChimeraX | Wellcome Trust | PMID:29872003 | Free, Freely available | SCR_025577 | 2026-08-09 09:08:47 | 13 | ||||||||
|
Automated Systematic Search Deduplicator Resource Report Resource Website 1+ mentions |
Automated Systematic Search Deduplicator (RRID:SCR_025607) | ASySD | software application, software resource | Open source, interoperable software tool to remove duplicate citations in biomedical systematic reviews. | automated deduplication, systematic searches, biomedical reviews, | has parent organization: University of Edinburgh; Scotland; United Kingdom | European Union’s Horizon 2020 ; Alzheimer Research UK Pilot Grant ; Stroke Association |
PMID:37674179 | Free, Freely available | SCR_025607 | Automated Systematic Search Deduplicator:ASySD | 2026-08-09 09:08:48 | 2 | ||||||
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Invicro Vivoquant Resource Report Resource Website 1+ mentions |
Invicro Vivoquant (RRID:SCR_025778) | software application, software resource | Software multi-modality post-processing suite for SPECT, CT, PET, MR, Optical and and Autoradiography imaging data. | preclincial imaging, imaging data processing, | Restricted | SCR_025778 | Vivoquant | 2026-08-09 09:09:19 | 6 | ||||||||||
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EuCanImage FHIR ETL Implementation Resource Report Resource Website 1+ mentions |
EuCanImage FHIR ETL Implementation (RRID:SCR_025824) | source code, software resource | Software application as ETL implementation for EuCanImage, encouraging semantic interoperability of clinical data obtained in studies by transforming it into machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create dictionaries following FHIR compliant structure. Code Language is written in Python 3.11. Outputs are JSON files compliant with FHIR 4.3 schemas.This script is specifically created for the Extract, Transform and Load implementation for EuCanImage, and will follow the structures obtained from the REDCap databases within the study. | FHIR, ETL, EGA, semantic interoperability of clinical data, FHIR standard, FHIR compliant structure, | European Union's Horizon 2020 research and innovation programme 952103 | DOI:10.1101/2024.03.15.24303032 | Free, Available for download, Freely available | https://workflowhub.eu/collections/25 | SCR_025824 | 2026-08-09 09:09:20 | 1 | ||||||||
|
SEER*Stat Resource Report Resource Website 100+ mentions |
SEER*Stat (RRID:SCR_025808) | software application, software resource | Statistical software for analysis of SEER and other cancer-related databases.Used to view individual cancer records and to produce statistics for studying impact of cancer on population. | Statistics, analysis of SEER data, cancer records, |
is listed by: SEER Datasets and Software is related to: Surveillance Epidemiology and End Results works with: ProjPrev |
Restricted | https://seer.cancer.gov/seerstat/download/ | SCR_025808 | 2026-08-09 09:09:19 | 146 | |||||||||
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Bruker OPUS Resource Report Resource Website 10+ mentions |
Bruker OPUS (RRID:SCR_025806) | software application, software resource | Software developed by Bruker for analysis and processing of spectroscopic data. Used for measurement, processing and evaluation of IR, NIR and Raman spectra. | Bruker, spectroscopic data, measurement, processing, evaluation, IR, NIR, Raman, spectra | Restricted | https://www.bruker.com/en/products-and-solutions/infrared-and-raman/opus-spectroscopy-software/downloads.html | SCR_025806 | OPUS 8.2, OPUS | 2026-08-09 09:09:20 | 30 | |||||||||
|
Ratan-lab (SUMO) Resource Report Resource Website 10+ mentions |
Ratan-lab (SUMO) (RRID:SCR_025687) | SUMO | source code, software resource | Software for multiomic nonnegative matrix factorization. | multiomic nonnegative matrix factorization, matrix factorization | DOI:10.1016/j.crmeth.2021.100152 | Free, Available for download, Freely available, | SCR_025687 | 2026-08-09 09:08:50 | 42 | |||||||||
|
DevATLAS Resource Report Resource Website |
DevATLAS (RRID:SCR_025718) | data or information resource, atlas, reference atlas | Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome. | Whole brain developmental map, neuronal circuit maturation, whole brain spatiotemporal mapping, circuit maturation, early postnatal development, mouse models of neurodevelopmental disorders, | Human Frontier Science Program ; Brain Research Foundation Seed Grant ; Simons Center for the Social Brain Equipment Grant ; Paul and Lilah Newton Brain Science Award ; NIMH RF1MH124605; NIDCD DC014701; NINDS NS123710; NINDS NS115543; NIMH MH116673 |
PMID:38260331 | Free, Freely available | DevATLAS | SCR_025718 | Developmental Activation Timing-based Longitudinal Acquisition System | 2026-08-09 09:09:19 | 0 | |||||||
|
ElemeFE element-angular Resource Report Resource Website 1+ mentions |
ElemeFE element-angular (RRID:SCR_025725) | source code, software resource | Open-source angularjs theme. Element for Angular. | Element for Angular, angularjs theme, | Free, Available for download, Freely available | SCR_025725 | 2026-08-09 09:08:51 | 1 | |||||||||||
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PAL:Proactive Automatized Lifestyle intervention Resource Report Resource Website |
PAL:Proactive Automatized Lifestyle intervention (RRID:SCR_025727) | software application, software resource | Behavior change intervention software. Participants enter their data as part of online survey, and software generates individualized feedback letters. | Behavior change intervention, behavior change, intervention | German Cancer Aid ; German Research Foundation ; German Ministry of Education and Research |
PMID:36123081 | Restricted | SCR_025727 | 2026-08-09 09:09:18 | 0 |
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