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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PICRUSt2 Resource Report Resource Website 500+ mentions |
PICRUSt2 (RRID:SCR_022647) | simulation software, software resource, software application | Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases. | predicting functional abundances, marker gene sequences, metagenome functions prediction | is related to: PICRUSt | NSF IOS CAREER 1942647; NIDDK U54DK102557; NIDDK R24DK110499; NSERC ; GlaxoSmithKline |
PMID:32483366 | Free, Available for download, Freely available | https://github.com/picrust/picrust2 | SCR_022647 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | 2026-08-18 09:45:43 | 583 | ||||||
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Pediatric Cancer Data Commons Resource Report Resource Website 1+ mentions |
Pediatric Cancer Data Commons (RRID:SCR_022369) | PCDC | data or information resource, portal, topical portal, disease-related portal | PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors. | pediatric cancer, clinical data, genomic data, imaging data, uniform data standards, common core data dictionary, common governance structure, | is related to: University of Chicago; Illinois; USA | pediatric cancer, neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, Hodgkin lymphoma | Free, Freely available | SCR_022369 | 2026-08-18 09:45:47 | 2 | ||||||||
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Open Brain Consent Resource Report Resource Website |
Open Brain Consent (RRID:SCR_022972) | data or information resource, portal, topical portal | Platform for informing research participants and obtaining consent to share brain imaging data. Provides suggested wording/templates for MRI studies human participant consent forms (including GDPR version), reference of tools for data anonymization, etc to make prospective data sharing possible. | MRI, obtaining consent to share brain imaging data, consent, share brain imaging data, MRI studies human participant consent forms, data sharing | Free, Freely available | SCR_022972 | 2026-08-18 09:45:43 | 0 | |||||||||||
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Jekyll Tutorial Resource Report Resource Website |
Jekyll Tutorial (RRID:SCR_022859) | data or information resource, portal, topical portal | Website tutorial for creating Jekyll-based scientific website, including editing in GitHub, working locally with Jekyll and applying Jekyll and Markdown formatting basics, and using custom themes. | creating Jekyll based scientific website creation | has parent organization: Harvard Medical School; Massachusetts; USA | Free, Freely available | SCR_022859 | 2026-08-18 09:45:45 | 0 | ||||||||||
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DistillerSR Resource Report Resource Website 10+ mentions |
DistillerSR (RRID:SCR_023078) | data management software, software resource, software application | Literature review software by DistillerSR Inc. Automates management of literature collection, screening, and assessment using AI and intelligent workflows. From systematic literature review to rapid review to living review, makes any project simpler to manage and configure to produce transparent, audit-ready, and compliant results. | DistillerSR Inc., management of literature collection, screening, and assessment, project to manage, literature review software | Restricted | SCR_023078 | 2026-08-18 09:45:47 | 11 | |||||||||||
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Natural Scenes Dataset Resource Report Resource Website 10+ mentions |
Natural Scenes Dataset (RRID:SCR_023648) | NSD | data or information resource, portal, topical portal, data set | Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry. | Natural scenes, vision, fMRI measurements, fMRI dataset, whole brain, healthy adult subjects, images, visual representation and cognition, benchmark, training data | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | PMID:34916659 | Free,Freely available | https://github.com/cvnlab/nsdcode/ | SCR_023648 | 2026-08-18 09:45:58 | 44 | |||||||
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Global Alzheimers Association Interaction Network Resource Report Resource Website 10+ mentions |
Global Alzheimers Association Interaction Network (RRID:SCR_023699) | GAAIN | data or information resource, portal, topical portal, disease-related portal | Open access integrated research platform, which links scientists, shared data, and analysis tools to accelerate Alzheimer’s disease research, disease preventions, treatments and cure. Unites diverse and geographically distributed network of data partners to foster cohort discovery, collaboration and sharing. Researchers can discover clinical, genetic, imaging and other data collected across many independent studies. | USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Alzheimer’s disease research, disease preventions, treatments and cure, network of data partners, cohort discovery, collaboration and sharing, clinical data, genetic data, imaging data, Alzheimer data discovery, | has parent organization: University of Southern California; Los Angeles; USA | Alzheimer’s disease | Alzheimer Association | Free, Freely available | SCR_023699 | 2026-08-18 09:45:56 | 30 | |||||||
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KinasePhos 3.0 Resource Report Resource Website 1+ mentions |
KinasePhos 3.0 (RRID:SCR_023595) | simulation software, software resource, software application | Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool. | redesign and expansion of prediction, kinase specific phosphorylation sites, kinase specific phosphorylation site prediction, site prediction, kinase specific phosphorylation, | National Natural Science Foundation of China ; Science ; Technology and Innovation Commission of Shenzhen Municipality ; Guangdong Province Basic and Applied Basic Research Fund ; Ganghong Young Scholar Development Fund ; Warshel Institute for Computational Biology |
PMID:35781048 | Free, Available for download, Freely available | https://github.com/tom-209/KinasePhos-3.0-executable-file | SCR_023595 | 2026-08-18 09:45:55 | 3 | ||||||||
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TIGER Data Portal Resource Report Resource Website 10+ mentions |
TIGER Data Portal (RRID:SCR_023626) | data or information resource, portal, topical portal, disease-related portal | Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets. | Type 2 Diabetes, genetic and epigenetic, functional data, molecular data, clinical data, pancreatic beta cells. | is related to: T2DSystems | Type 2 Diabetes | European Union Horizon 2020 ; Spanish government ; Swiss State Secretariat for Education‚ Research and Innovation ; American Diabetes Association Innovative and Clinical Translational Award ; Research England ; Wellcome Trust ; NIDDK U01 DK105535; NIDDK U01 DK085545 |
PMID:34644572 | SCR_023626 | Translational Human Pancreatic Islet Genotype Tissue-Expression Resource | 2026-08-18 09:46:03 | 23 | |||||||
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RIsearch Resource Report Resource Website 1+ mentions |
RIsearch (RRID:SCR_023503) | simulation software, software resource, software application | Software tool for prediction of RNA–RNA, RNA–DNA, and DNA–DNA interactions. Both RIsearch1 and RIsearch2 enable quick localisation of potential near complementary interactions between given query and target sequences. RIsearch1 performs computation with whole sequences. RIsearch2 focuses on perfect complementary seed regions and extends them on both ends. User defined seed and extension constraints makes RIsearch2 applicable to all kinds of interaction predictions (e.g., siRNA and Cas9–gRNA off-target predictions). | interaction predictions, RNA–RNA interactions, RNA–DNA interactions, DNA–DNA interactions, | Danish Council for Independent Research ; Danish Council for Strategic Research ; Danish Center for Scientific Computing ; Innovation Fund Denmark |
PMID:22923300 PMID:28108657 |
Free, Available for download, Freely available | SCR_023503 | RIsearch2, RIsearch1 | 2026-08-18 09:45:55 | 5 | ||||||||
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Musculoskeletal Knowledge Portal Resource Report Resource Website 10+ mentions |
Musculoskeletal Knowledge Portal (RRID:SCR_023171) | MSK-KP | data or information resource, portal, topical portal, disease-related portal | Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data. | genomic data mining, human genetic data, genomic information, musculoskeletal traits and diseases data, DRKB | musculoskeletal disease | NIH AR085003 | PMID:34686856 | Free, Freely available | https://msk.hugeamp.org/ | SCR_023171 | 2026-08-18 09:45:48 | 26 | ||||||
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FunGAP Resource Report Resource Website 1+ mentions |
FunGAP (RRID:SCR_023213) | FunGAP | simulation software, software resource, software application | Software tool to predict protein coding genes in fungal genome assembly. Performs gene prediction on given genome assembly and RNA-seq reads. Runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences. | Genome annotation, predict protein-coding genes, fungal genome assembly, RNA-seq reads, gene prediction | Rural Development Administration ; Republic of Korea ; School of Life Sciences and Biotechnology for BK21 PLUS ; Korea University |
PMID:28582481 | Free, Available for download, Freely available | SCR_023213 | Fungal Genome Annotation Pipeline | 2026-08-18 09:45:49 | 2 | |||||||
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Enroll-HD Resource Report Resource Website 10+ mentions |
Enroll-HD (RRID:SCR_023300) | data or information resource, portal, topical portal, disease-related portal | Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments. | Clinical Research, clinical trails, Huntington’s Disease families, therapeutics, effective treatments, | Huntington’s disease | Cure HD Initiative Foundation | Free, Freely available | SCR_023300 | 2026-08-18 09:46:00 | 13 | |||||||||
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NicheNet Resource Report Resource Website 50+ mentions |
NicheNet (RRID:SCR_023158) | simulation software, software resource, software application | Software tool as R implementation of NicheNet method to predict active ligand-target links between interacting cells. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest. | predict ligand-receptor interactions, intercellular communication, predict active ligand target interactions, interacting cells prediction, | Research Foundation—Flanders ; Flemish Government |
PMID:31819264 | Free, Available for download, Freely available | SCR_023158 | 2026-08-18 09:45:59 | 73 | |||||||||
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PROFisis Resource Report Resource Website |
PROFisis (RRID:SCR_024179) | simulation software, software resource, software application | Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures. | identifies interacting residues from sequence alone, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_13706 | https://sources.debian.org/src/profisis/ | SCR_024179 | profisis | 2026-08-18 09:46:03 | 0 | |||||||
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Sparrow-data Resource Report Resource Website |
Sparrow-data (RRID:SCR_024432) | database, data or information resource, software resource, software application | Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking. | geology, managing geochemical data, individual geochronology laboratory, metadata tracking, | Free, Freely available | SCR_024432 | 2026-08-18 09:46:01 | 0 | |||||||||||
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DrugSim2DR Resource Report Resource Website 1+ mentions |
DrugSim2DR (RRID:SCR_024564) | simulation software, software resource, software application | Software R package to predict drug functional similarity to drug repurposing. | predict drug functional similarity, similarity to drug repurposing, | is listed by: CRAN | Free, Available for download, Freely available | SCR_024564 | 2026-08-18 09:46:02 | 1 | ||||||||||
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CONTRAfold Resource Report Resource Website 1+ mentions |
CONTRAfold (RRID:SCR_023994) | CONTRAfold | simulation software, software resource, software application | Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction. | sequence prediction, | is listed by: Debian | PMID:16873527 | Free, Available for download, Freely available | OMICS_03452 | https://sources.debian.org/src/CONTRAfold/ | SCR_023994 | CONditional TRAining for RNA Secondary Structure Prediction, contrafold | 2026-08-18 09:46:06 | 2 | |||||
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toppred Resource Report Resource Website 1+ mentions |
toppred (RRID:SCR_024385) | simulation software, software resource, software application | Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins. | Membrane protein structure prediction, transmembrane topology prediction, predicting topology, bacterial inner membrane proteins topology prediction, | is listed by: Debian | PMID:1593632 | Free, Available for download, Freely available, | OMICS_07268 | https://sources.debian.org/src/toppred/ | SCR_024385 | 2026-08-18 09:46:08 | 3 | |||||||
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pRRophetic Resource Report Resource Website 10+ mentions |
pRRophetic (RRID:SCR_024417) | simulation software, software resource, software application | Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data, | clinical chemotherapeutic response prediction, tumor gene expression levels, predict phenotypes, | is listed by: SoftCite | U01GM61393 ; GM089941 ; CA139278 ; University of Chicago ; UL1RR024999 |
PMID:25229481 | Free, Available for download, Freely available | SCR_024417 | 2026-08-18 09:46:08 | 33 |
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