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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Bayesian Generalized Linear Regression Resource Report Resource Website 1+ mentions |
Bayesian Generalized Linear Regression (RRID:SCR_022522) | BGLR | software resource, software toolkit | Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures. | Bayesian regression models, parametric variable selection and shrinkage methods, semiparametric procedures |
is related to: CRAN is related to: R Project for Statistical Computing |
NIGMS R01GM099992; NIGMS R01GM101219 |
PMID:25009151 | Free, Available for download, Freely available | https://github.com/gdlc/BGLR-R | SCR_022522 | 2026-02-16 09:50:24 | 4 | ||||||
|
MR-PRESSO Resource Report Resource Website 50+ mentions |
MR-PRESSO (RRID:SCR_023697) | software resource, software toolkit | Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing. | Mendelian randomization, identify horizontal pleiotropic outliers, multi instrument summary level MR testing, | NIGMS R35 GM124836; NHLBI R01 HL139865; AstraZeneca ; Goldfinch Bio ; American Heart Association Cardiovascular Genome Phenome Discovery ; NIMH 1R01 MH094469; NIMH 1R01 MH107649; NHGRI 5U01 HG009088 |
PMID:29686387 | Free, Available for download, Freely available | SCR_023697 | Mendelian Randomization Pleiotropy RESidual Sum and Outlier | 2026-02-16 09:50:45 | 64 | ||||||||
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Resource for Biocomputing Visualization and Informatics Resource Report Resource Website 100+ mentions |
Resource for Biocomputing Visualization and Informatics (RRID:SCR_001374) | RBVI | biomedical technology resource center, training resource | Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas. | training resource, molecular modeling, software, molecular graphics, visualization, modeling, molecular structure, analysis, computation, computing and informatics technology center, FASEB list |
is listed by: 3DVC has parent organization: University of California at San Francisco; California; USA is parent organization of: Structure-function linkage database is parent organization of: UCSF Chimera |
NIGMS | nlx_152531 | SCR_001374 | 2026-02-16 09:45:28 | 154 | ||||||||
|
Intercellular Junction Organization Quantification Resource Report Resource Website 1+ mentions |
Intercellular Junction Organization Quantification (RRID:SCR_026026) | IJOQ | software application, data processing software, data analysis software, source code, software resource | Software Python tool for fully automated analysis of cell-cell junction integrity. Used for fluorescence microscopy analysis. | automated analysis, cell-cell junction integrity, fluorescence microscopy analysis, | NIGMS 1SC2GM141988; California State University Program for Education and Research in Biotechnology Graduate Student COVID-19 Research Restart Program |
PMID:35755841 | Free, Available for download, Freely available | SCR_026026 | 2026-02-16 09:51:04 | 1 | ||||||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | software application, data processing software, software toolkit, data analysis software, software resource, sequence analysis software | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Japan Society for the Promotion of Science ; NHGRI HG006039; NHGRI HG002096; Burroughs-Wellcome Fund ; NIGMS R01GM126567; NSF ABI 1661218; NIGMS R35GM139504 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-02-17 09:59:30 | 2763 | ||||
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LIPID Metabolites And Pathways Strategy Resource Report Resource Website 1000+ mentions |
LIPID Metabolites And Pathways Strategy (RRID:SCR_006579) | LIPID MAPS | data or information resource, narrative resource, standard specification, database | Multi-institutional supported website and database that provides access to large number of globally used lipidomics resources. Internationally led the field of lipid curation, classification, and nomenclature since 2003. Produces new open-access databases, informatics tools and lipidomics-focused training activities will be generated and made publicly available for researchers studying lipids in health and disease. | lipid, pathway, classification, metabolomics, metabolite, FASEB list |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of California at San Diego; California; USA is parent organization of: LIPID MAPS Proteome Database is parent organization of: LIPID MAPS Structure Database |
NIGMS ; Glue Grant |
Free, Freely available | nif-0000-00368, SCR_026208, r3d100012315 | https://doi.org/10.17616/R3WW7G | SCR_006579 | , LIPID Maps database, LIPID Metabolites And Pathways Strategy database, LIPID Maps | 2026-02-17 10:00:57 | 1266 | |||||
|
InterPro Resource Report Resource Website 5000+ mentions |
InterPro (RRID:SCR_006695) | InterPro | data access protocol, data or information resource, production service resource, analysis service resource, database, service resource, software resource, web service, data analysis service | Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries. | protein, classify, prediction, protein domain, genome, protein family, functional site, protein sequence, protein function, analysis, nucleic acid, amino acid, amino acid sequence, gold standard |
is listed by: re3data.org is listed by: OMICtools is related to: TIGRFAMS is related to: TIGRFAMS is related to: FlyMine is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Biomine is related to: InterProScan is related to: GeneTerm Linker is related to: Gene Ontology is related to: ProDom is related to: Algal Functional Annotation Tool has parent organization: European Bioinformatics Institute |
European Union FP7 Scientific Data Repositories 213037; BBSRC BB/F010508/1; NIGMS GM081084 |
PMID:22096229 PMID:21082426 PMID:18940856 PMID:18428686 PMID:18025686 PMID:17202162 PMID:16909843 PMID:15608177 PMID:12520011 PMID:12230031 PMID:11159333 PMID:11119311 PMID:11125043 |
Acknowledgement requested, Free, Public, The community can contribute to this resource | nif-0000-03035, OMICS_01694, r3d100010798 | https://doi.org/10.17616/R3FS61 | SCR_006695 | InterPro: protein sequence analysis & classification, InterPro protein sequence analysis and classification | 2026-02-17 10:01:06 | 7000 | ||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | data access protocol, web application, web service, software resource | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NIAAA U01 AA016662; NIAAA U01 AA013512; NIDA P01 DA015027; NIMH P50 MH078028; NIMH P50 MH096972; NCI U24 CA159988; NIGMS R01 GM088822 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-02-17 10:01:09 | 2760 | ||||
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Rankprop - Protein Ranking by Network Propagation Resource Report Resource Website |
Rankprop - Protein Ranking by Network Propagation (RRID:SCR_007159) | data access protocol, source code, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on May,18,2020. Ranking algorithm that exploits global network structure of similarity relationships among proteins in database by performing diffusion operation on protein similarity network with weighted edges. Source code and web server for searching non-redundant protein database. Web server ranks proteins found in NRDB40 (from PairsDB) against query sequence of amino acids using Rankprop algorithm. | Ranking algorithm, network structure, protein database, similarity relationship, protein similarity network, weighted adges, non redundat protein database, protein database search | has parent organization: University of Washington; Seattle; USA | NSF EIA-0312706; NSF DBI-0243257; NIGMS GM74257 |
PMID:16723003 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_50351 | http://rankprop.gs.washington.edu/info.php | SCR_007159 | Rankprop | 2026-02-17 10:01:11 | 0 | |||||
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HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism Resource Report Resource Website 50+ mentions |
HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) | HumanCyc | data or information resource, production service resource, analysis service resource, database, service resource, software resource, data analysis service | The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version. | enzyme, function, functional, gene, genome, genomic, human, human genome, metabolic, metabolism, mitochondrion, nucleotide, pathway, position, reaction, sequence, metabolomics, gene expression, bioreaction, metabolic pathway, nutrition, FASEB list |
is listed by: BioCyc is related to: Pathway Commons is related to: ConsensusPathDB is related to: BioCyc is related to: Pathway Tools has parent organization: Stanford Research Institute International |
Pharmaceutical company ; NIGMS GM092729 |
PMID:15642094 | Public | r3d100011286, nif-0000-21206 | https://doi.org/10.17616/R3ZS72 | SCR_007050 | 2026-02-17 10:01:11 | 60 | |||||
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Physiobank Resource Report Resource Website 10+ mentions |
Physiobank (RRID:SCR_006949) | PhysioBank | storage service resource, data or information resource, catalog, database, service resource, data repository | Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them. | physiologic, signal, data, biomedical, research, community, cardiopulmonary, neural, biomedical, health, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, bibliographic, normal, physiologic signal, time series, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is related to: PhysioToolkit is parent organization of: Gait in Aging and Disease Database is parent organization of: Gait in Parkinson's Disease is parent organization of: Gait Dynamics in Neuro-Degenerative Disease Data Base is parent organization of: Noise Enhancement of Sensorimotor Function |
Healthy, Sudden cardiac death, Congestive heart failure, Epilepsy, Gait disorder, Sleep apnea, Aging | NIGMS ; NIBIB U01-EB-008577 |
PMID:10851218 | Free, The community can contribute to this resource, Acknowledgement requested | nlx_48903, r3d100011236 | https://doi.org/10.17616/R3J048 | SCR_006949 | 2026-02-17 10:00:59 | 39 | ||||
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Protein Cross-Linking Database Resource Report Resource Website 1+ mentions |
Protein Cross-Linking Database (RRID:SCR_021027) | ProXL, proxl, Protein XL | data access protocol, data or information resource, database, software resource, web service | Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination. | Protein cross-linking, mass spectrometry data, analysis, visualization, sharing, structural analysis, quality control, private collaboration, public data dissemination |
uses: Kojak has parent organization: University of Washington; Seattle; USA |
NIGMS P41 GM103533; University of Washington Proteomics Resource |
PMID:27302480 | Free, Available for download, Freely available | https://github.com/yeastrc/proxl-web-app | SCR_021027 | Protein XL Database | 2026-02-17 10:03:42 | 5 | |||||
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Kojak Resource Report Resource Website 1+ mentions |
Kojak (RRID:SCR_021028) | data analysis software, software application, data processing software, software resource | Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets. | Mass spectra, cross-linked peptides identification, protein complexes analysis, novel data analysis, existing data analysis |
is used by: Protein Cross-Linking Database has parent organization: University of Washington; Seattle; USA |
National Science Foundation MRI grant 0923536; NIGMS P50 GM076547; NIGMS P50 GM08722150; NCRR S10 RR027584; NIGMS P41 GM103533 |
PMID:25812159 | Free, Available for download, Freely available | SCR_021028 | 2026-02-17 10:04:00 | 3 | ||||||||
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CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI RM1 HG009490; NIBIB R01 EB022376; NIGMS R35 GM118062; NIGMS R35 GM118158; NIDDK R03 DK109232; NHLBI P01 HL32262; NHGRI R00 HG008399; NIDDK P30 DK049216; NHLBI R01 HL119099; NHGRI R01 HG005085 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2 https://github.com/pinellolab/CRISPResso |
SCR_021538 | CRISPResso2 | 2026-02-17 10:04:06 | 21 | |||||||
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RepEnrich Resource Report Resource Website 10+ mentions |
RepEnrich (RRID:SCR_021733) | data analysis software, software application, data processing software, software resource | Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data. | profile enrichment, next generation sequencing reads, transposable elements, estimate repetitive element enrichment, genome wide transcriptional regulation, sequencing data | has parent organization: Brown University; Rhode Island; USA | NIA K25 AG028753; NIGMS T32 GM007601; NIA R37 AG016694 |
PMID:25012247 | Free, Available for download, Freely available | https://github.com/nerettilab/RepEnrich2 | SCR_021733 | RepEnrich2 | 2026-02-17 10:03:53 | 21 | ||||||
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DeepCell Resource Report Resource Website 10+ mentions |
DeepCell (RRID:SCR_022197) | software application, data processing software, software resource, segmentation software, image analysis software | Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software. | segmenting individual cells, microscopy image, cell segmentation | Paul Allen Family Foundation ; NIGMS F32 GM119319; NIGMS P50 GM107615; NLM DP1 LM01150 |
DOI:10.1371/journal.pcbi.1005177 | Free, Available for download, Freely available | SCR_022197 | Deepcell | 2026-02-17 10:04:00 | 10 | ||||||||
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SCIRun Resource Report Resource Website 10+ mentions |
SCIRun (RRID:SCR_002541) | SCIRun | software application, data processing software, software resource, simulation software, software toolkit, data visualization software | A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6. | modeling, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BioMesh3D is related to: BioMesh3D is related to: BioPSE is related to: BioPSE has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
Free, Available for download, Freely available | nlx_155949 | http://www.nitrc.org/projects/scirun | SCR_002541 | 2026-02-17 09:59:48 | 21 | ||||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | software application, image processing software, data processing software, software resource, software toolkit, image analysis software | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NINDS ; NIGMS RC2 GM092519; Wellcome Trust Strategic Award 095931; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; NIH ; NIMH |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, nif-0000-30467, SCR_018407 | https://imagej.net/ij/ http://rsbweb.nih.gov/ij https://imagej.nih.gov/ij/download.html https://imagej.nih.gov/ij/ https://sources.debian.org/src/imagej/ |
https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-02-17 09:59:55 | 27070 | ||||
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ToRNADo Resource Report Resource Website 50+ mentions |
ToRNADo (RRID:SCR_002706) | data visualization software, data processing software, software application, software resource | A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion. | duplex, protein, rna, visualization | has parent organization: Stanford University; Stanford; California | NIH ; NIGMS R01GM107340; NIGMS U54GM072970 |
Free, Available for download, Freely available | nif-0000-23335 | SCR_002706 | 2026-02-17 10:00:02 | 95 | ||||||||
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Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | alignment software, software application, data processing software, data analysis software, software resource, sequence analysis software, image analysis software | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml https://github.com/BenLangmead/bowtie2 https://bio.tools/bowtie2 |
SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-02-17 10:02:44 | 1745 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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