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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PSORT II Resource Report Resource Website 10+ mentions |
PSORT II (RRID:SCR_018772) | production service resource, web service, data access protocol, software resource, service resource, analysis service resource | Web tool for prediction of protein sorting signals and localization sites in amino acid sequencies. Recommended for animal/yeast sequences. Analyzes input sequence by applying stored rules for various sequence features of known protein sorting signals to report possiblity for input protein to be localized at each candidate site with additional information. | Protein sorting signal prediction, protein localization site, localization site prediction, amino acid sequence, sequence analysis, protein sorting signal | is related to: Psort | Free, Freely available | https://psort.hgc.jp/, https://www.psort.org/ | SCR_018772 | prediction of protein sorting signals and localization sites in amino acid sequencies, psort2, psort II | 2026-08-14 09:28:06 | 49 | ||||||||
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DoubletFinder Resource Report Resource Website 1000+ mentions |
DoubletFinder (RRID:SCR_018771) | data processing software, software application, data analysis software, software resource | Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data. | Doublet detection in single cell RNA, single cell RNA, doublet detection, RNA sequencing data, gene expression data, artificial nearest neighbors |
is related to: Seurat has parent organization: University of California at San Francisco; California; USA |
Department of Defense Breast Cancer Research Program ; NICHD DP2 HD080351; NSF MCB 1330864; UCSF Center for Cellular Construction ; NSF Science and Technology Center ; Damon Runyon Cancer Research Foundation |
PMID:30954475 | Free, Available for download, Freely available | SCR_018771 | 2026-08-14 09:28:23 | 1250 | ||||||||
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RAPIDO Resource Report Resource Website 1+ mentions |
RAPIDO (RRID:SCR_018935) | image analysis software, data processing software, web service, data access protocol, software application, software resource, alignment software | Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains. | Protein structure alignment, rapid alignment, protein domain, conformational changes presence, 3D alignment, crystal structure, protein molecule, conformational change presence, identify structural region, distant sequence, movable domains | European Molecular Biology Laboratory ; Associazione Italiana per la Ricerca sul Cancro |
PMID:18460546 PMID:18727838 |
Free, Freely available | SCR_018935 | Rapid Alignment of Proteins in terms of Domains, Rapid alignment of proteins in terms of domains | 2026-08-14 09:28:08 | 2 | ||||||||
|
QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | software toolkit, data processing software, software application, data analysis software, software resource | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | 2026-08-14 09:27:56 | 27 | ||||||||
|
Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | software toolkit, data processing software, software application, data analysis software, software resource | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq, https://bio.tools/preseq | SCR_018664 | 2026-08-14 09:28:05 | 21 | |||||||
|
AsPredicted Resource Report Resource Website 100+ mentions |
AsPredicted (RRID:SCR_018789) | data or information resource, portal, topical portal | Website for study pre-registration. Defines minimum required criteria for pre-registration and allows authors to pre-register their study. It is standardized pre-registration that requires only what is necessary to separate exploratory from confirmatory analyses. | Study pre-registration, publish paper, evaluation, minimum required criteria, author study pre-registration, standardized pre-registration | has parent organization: University of Pennsylvania; Philadelphia; USA | Restricted | SCR_018789 | 2026-08-14 09:28:23 | 165 | ||||||||||
|
Discrete Morse Resource Report Resource Website |
Discrete Morse (RRID:SCR_018662) | DM | data processing software, software application, image processing software, software resource | Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections. | Neuron tracing, tracer injection, single neuron data set, set of trees summarization generation, neuron image data, extract individual neuron tree skeleton, volumetric brain image data, summarize collection, tracer injection labelled neuron | DOI:10.1101/2020.03.21.000323v1 | Free, Freely available | SCR_018662 | DiscreteMorse | 2026-08-14 09:27:56 | 0 | ||||||||
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | software toolkit, data processing software, software application, data analysis software, network analysis software, software resource | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | Mutual Information NETworks | 2026-08-14 09:28:04 | 0 | |||||
|
FunGene Resource Report Resource Website 50+ mentions |
FunGene (RRID:SCR_018749) | software toolkit, database, data repository, production service resource, storage service resource, data or information resource, software resource, service resource, analysis service resource | Functional gene pipeline and repository. Functional gene repository provides collections of genes in interactive platform, while functional gene pipeline offers suite of tools for functional gene amplicon processing and analysis. Together they enable key steps in functional gene based microbial community analysis, from target selection and primer analysis to amplicon processing and ecological discovery. | Gene processing, microbial ecology, functional genes, amplification primers, phylogeny, biogeochemical cycles, amplicon analysis, ecological discovery, microbial community | has parent organization: Michigan State University; Michigan; USA | NIEHS P42 ES004911; USDA National Institute of Food and Agriculture ; NIDDK UH3 DK083993; Office of Science U.S. Department of Energy ; NIEHS |
PMID:24101916 | Free, Freely available | SCR_018749 | FunGene Pipeline | 2026-08-14 09:27:58 | 58 | |||||||
|
syngo DynaCT Resource Report Resource Website |
syngo DynaCT (RRID:SCR_018902) | data processing software, software application, software resource, data visualization software, 3d visualization software | Software tool to construct 3D models of soft tissue using CT-like cross sectional imaging. | 3D model, soft tissue, soft tissue 3D model, 3D model construction, cross sectional imaging | Restricted | SCR_018902 | Siemens Healthineers syngo DynaCT | 2026-08-14 09:28:24 | 0 | ||||||||||
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RatsPub Resource Report Resource Website |
RatsPub (RRID:SCR_018905) | web service, data access protocol, software application, software resource, text-mining software | Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords. | Literature mining, addiction gene, PubMed abstract, gene, addiction, addiction relationship, neurogenetics | NIDA P30 DA044223; NIDA U01 DA047638 |
Free, Freely available | https://github.com/chen42/ratspub | SCR_018905 | rats.pub, Rats.pub, Relationship with Addiction Through Searches of PubMed | 2026-08-14 09:28:24 | 0 | ||||||||
|
ABCD-ReproNim Course Resource Report Resource Website |
ABCD-ReproNim Course (RRID:SCR_018911) | data or information resource, training resource, knowledge environment resource, portal | Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes. | Adolescent Brain Cognitive Development Study data analysis, reproducible analysis, ABCD study data analysis, reprReproNim workflow instruction |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ReproNim: A Center for Reproducible Neuroimaging Computation |
Free, Freely available | SCR_018911 | Adolescent Brain Cognitive Development ReproNim Course | 2026-08-14 09:28:08 | 0 | |||||||||
|
NanoGalaxy Resource Report Resource Website 10+ mentions |
NanoGalaxy (RRID:SCR_018912) | software toolkit, data processing software, web service, software application, data analysis software, data access protocol, software resource, data visualization software | Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance. | European Galaxy Project, Oxford Nanopore Technologies, Oxford Nanopore Technologies data, data analysis, long reads technology, ONT oriented tools collection, custom Galaxy instance, , Galaxy, Nanopore, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy is related to: University of Freiburg; Baden-Wurttemberg; Germany |
Free, Freely available | biotools:nanogalaxy | https://galaxyproject.org/use/nanogalaxy/, https://bio.tools/nanogalaxy | SCR_018912 | 2026-08-14 09:28:00 | 10 | ||||||||
|
BadMedicine Resource Report Resource Website 1+ mentions |
BadMedicine (RRID:SCR_018879) | software toolkit, software development tool, code testing framework, software application, software resource, software library | Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes. | Electronic Health Record, electronic health record data generation, health data, testing health data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:badmedicine | https://bio.tools/badmedicine | SCR_018879 | 2026-08-14 09:28:07 | 1 | ||||||||
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robvis Resource Report Resource Website 100+ mentions |
robvis (RRID:SCR_018755) | robvis | software toolkit, web application, software resource | Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project. | Risk of bias assessment, publication figure, publication quality figure, figure production, systematic review, research synthesis project | is related to: Shiny | University of Bristol ; University Hospitals Bristol NHS Foundation Trust |
DOI:10.1002/jrsm.1411 | Free, Freely available | SCR_018755 | Risk Of Bias VISualization | 2026-08-14 09:27:58 | 100 | ||||||
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scTHI Resource Report Resource Website 1+ mentions |
scTHI (RRID:SCR_018918) | scTHI | data processing software, software application, data analysis software, software resource | Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment. | Ligand receptor, active pair, active pair ligand receptor, single cell, tumor interaction, tumor microenvironment, cells clasification | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018918 | 2026-08-14 09:28:00 | 1 | |||||||||
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T2DSystems Resource Report Resource Website 1+ mentions |
T2DSystems (RRID:SCR_018913) | topical portal, project portal, portal, data or information resource, consortium, disease-related portal, organization portal | Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D. | Human islet study, cellular data, medical data, diabetes, pancreatic beta cell failure, impaired glucose tolerance, type 2 diabetes, glucose tolerance | is related to: TIGER Data Portal | Type 2 Diabetes | EU Horizon 2020 | Restricted | SCR_018913 | Type 2 Diabetes Systems, T2DSystems | 2026-08-14 09:28:24 | 1 | |||||||
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Diabetic Foot Consortium Resource Report Resource Website |
Diabetic Foot Consortium (RRID:SCR_018914) | DFC | topical portal, portal, data or information resource, consortium, disease-related portal, organization portal | Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes. | Academic institution group, diabetic, diabetic foot, diabetic foot condition, foot ulcer, wound healing, biomarker |
is related to: Indiana University; Indiana; USA is related to: University of Pittsburgh; Pennsylvania; USA is related to: University of Miami; Florida; USA is related to: University of California at San Francisco; California; USA is related to: Stanford University; Stanford; California is related to: University of Michigan; Ann Arbor; USA |
diabetic | NIDDK | SCR_018914 | 2026-08-14 09:28:08 | 0 | ||||||||
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ScanITD Resource Report Resource Website 1+ mentions |
ScanITD (RRID:SCR_018886) | data processing software, software application, data analysis software, software resource, sequence analysis software | Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation. | Internal tandem duplication, FLT3, acute myeloid leukemia, TCGA, chimeric alignment, variant allele frequency, variant allele, frequency estimation, , bio.tools |
is listed by: Debian is listed by: bio.tools |
Acute Myeloid Leukemia | DOI:10.5524/100775 | Free, Available for download, Freely available | biotools:ScanItD | https://bio.tools/ScanITD, http://gigadb.org/dataset/100775 | SCR_018886 | Scan Internal Tandem Duplications | 2026-08-14 09:28:07 | 1 | |||||
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ROSIE Resource Report Resource Website 10+ mentions |
ROSIE (RRID:SCR_018764) | ROSIE | data access protocol, application programming interface, web application, software resource | Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community. | Web interface for Rosetta, Rosetta online server, Rosetta application serverification, Rosetta user interface | works with: Rosetta | NIGMS R01 GM073151; NIGMS R01 GM07822; NIGMS R21 GM102716; NCRR R00 RR024107; NCI U54 CA143907; NEI PN2 EY016586; NIGMS T32 GM 88118; Taiwan Governmental Scholarship for Study Abroad ; Howard Hughes Medical and Institute International Student Research Fellowship ; NSF |
PMID:23717507 | Restricted | https://rosie.rosettacommons.org/ | SCR_018764 | Rosetta Online Server that Includes Everyone | 2026-08-14 09:28:23 | 10 |
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