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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software resource, software toolkit | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950; NCI U24CA143835; American Cancer Society Research Scholar Grant |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SYstems Genetic Network AnaLysis | 2026-02-16 09:50:37 | 1 | ||||||||
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simplePHENOTYPES Resource Report Resource Website 1+ mentions |
simplePHENOTYPES (RRID:SCR_022523) | software resource, software toolkit | Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy. | Multiple traits simulation, pleiotropy, partial pleiotropy, spurious pleiotropy, causal mutations affecting multiple traits |
is related to: CRAN is related to: R Project for Statistical Computing |
NSF 1733606 | PMID:33129253 | Free, Available for download, Freely available | https://github.com/samuelbfernandes/simplePHENOTYPES | SCR_022523 | Simulation of Pleiotropic, Linked and Epistatic Phenotypes | 2026-02-16 09:50:17 | 2 | ||||||
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AmpliconArchitect Resource Report Resource Website 10+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software resource, software toolkit | Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. | call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon | NIGMS R01GM114362; NHGRI HG010149; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-02-16 09:50:35 | 42 | ||||||||||
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Automated Fiber Quantification in Python Resource Report Resource Website 10+ mentions |
Automated Fiber Quantification in Python (RRID:SCR_023366) | pyAFQ | software resource, software toolkit | Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry. | Automates tractometry, automated delineation of major fiber tracts, individual human brains, quantification of tissue properties, tissue properties within fiber tracts, diffusion MRI data, | NIMH 1RF1MH121868; The BRAIN Initiative ; Gordon and Betty Moore Foundation ; Alfred P. Sloan Foundation ; NIBIB R01EB027585; NSF 1551330 |
PMID:35079748 | Free, Available for download, Freely available | SCR_023366 | 2026-02-16 09:50:29 | 12 | ||||||||
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MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software resource, software toolkit | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NSF DEB-2028280; NIAID U19AI110820; NHGRI R01HG005220; NIDDK R24DK110499; NIDDK U54DK102557 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-02-16 09:50:36 | 170 | ||||||||
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rockd Resource Report Resource Website |
rockd (RRID:SCR_024431) | database, data or information resource | Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils. | Map database, record geological observations, | NSF ; UW Geoscience |
Free, Freely available | SCR_024431 | 2026-02-16 09:50:48 | 0 | ||||||||||
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VirusDetect Resource Report Resource Website 10+ mentions |
VirusDetect (RRID:SCR_023669) | software resource, software toolkit | Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs. | Virus discovery, analyze large scale sRNA datasets, virus identification, deep sequencing of small RNAs, sequencing, small RNAs | NSF | PMID:27825033 | Free, Available for download, Freely available | https://github.com/kentnf/VirusDetect | SCR_023669 | 2026-02-16 09:50:50 | 16 | ||||||||
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Lamont-Doherty Core Repository Resource Report Resource Website |
Lamont-Doherty Core Repository (RRID:SCR_002216) | LDEO-DSSR, LDCR | service resource, core facility, access service resource | Core repository and one of the world's most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. They also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions. Samples from cores and dredges, as well as descriptions of cores and dredges (including digital images and other cruise information), are provided to scientific investigators upon request. Materials for educational purposes and museum displays may also be made available in limited quantities when requests are adequately justified. Various services and data analyses, including core archiving, carbonate analyses, grain size analyses, and RGB line scan imaging, GRAPE, P-wave velocity and magnetic susceptibility runs, can also be provided at cost. The Repository operates a number of labs and instruments dedicated to making fundamental measurements on material entering the repository including several non-destructive methods. Instruments for conducting and/or assisting with analyses of deep-sea sediments include a GeoTek Multi-Sensor Core Logger, a UIC coulometer, a Micromeritics sedigraph, Vane Shear, X-radiograph, Sonic Sifter, freeze dryer, as well as a variety of microscopes, sieves, and sampling tools. They also make these instruments available to the scientific community for conducting analyses of deep-sea sediments. If you are interested in borrowing any field equipment, please contact the Repository Curator. | deep sea, sediment, ocean, sea, geoscience, metadata |
is listed by: CINERGI is listed by: DataCite is listed by: re3data.org has parent organization: Columbia University; New York; USA |
NSF ; Lamont -Doherty Earth Observatory |
Free, Freely available | DOI:10.26022, DOI:10.17616/R3PV10, nlx_154738 | https://doi.org/10.17616/R3PV10 https://doi.org/10.17616/r3pv10 https://doi.org/10.26022/ https://dx.doi.org/10.26022/ |
SCR_002216 | LDEO-Deep Sea Sample Repository, LDEO Core Repository, Lamont -Doherty Earth Observatory | 2026-02-16 09:45:46 | 0 | |||||
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National Lacustrine Core Facility Resource Report Resource Website |
National Lacustrine Core Facility (RRID:SCR_002215) | LacCore | service resource, core facility, access service resource | Archive of almost 20,000 meters of high quality sediment cores from large and small expeditions to lakes all around the world. LacCore advocates for, coordinates, and facilitates core-based research on Earth's continents through collaborative support for logistics, field and laboratory, and data and sample curation and dissemination. They provide a wide variety of fee-based analytical services, as well as offer training and instrument time to lab visitors. They also develop Standard Operating Procedures (SOPs) for local training and adoption by individuals at other labs. | lacustrine, lake, sediment, climate, environment, biota, microscopic, microscopy, marine, mineral, mineraloid, metadata |
is listed by: CINERGI has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NSF EAR-1226265 | Free, Freely available | nlx_154737 | SCR_002215 | Limnological Research Center LacCore Facility, LRC LacCore Facility | 2026-02-16 09:45:43 | 0 | ||||||
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Fungal Genome Initiative Resource Report Resource Website 10+ mentions |
Fungal Genome Initiative (RRID:SCR_003169) | FGI | data set, data or information resource | Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics. | sequence, fungi, gene annotation, genome |
is listed by: 3DVC has parent organization: Broad Institute |
NHGRI ; NSF ; NIAID ; USDA |
Free, Freely available | nif-0000-30591 | SCR_003169 | 2026-02-16 09:45:56 | 18 | |||||||
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CIS-BP Resource Report Resource Website 100+ mentions |
CIS-BP (RRID:SCR_017236) | web service, data access protocol, database, software resource, data or information resource | Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs. | catalog, inferred, sequence, binding, preference, transcription, factor, DNA, motif, FASEB list | Canadian Institutes of Health Research ; Canadian Institute for Advanced Research Junior Fellows Genetic Networks Program ; NICHD P01 HD39691; NIGMS GM082971; EU Marie Curie International Outgoing Fellowship ; NSF MCB-1024999; Howard Hughes Medical Institute ; Gordon and Betty Moore Foundation ; Millennium Nucleus for Fungal Integrative and Synthetic Biology ; Fondo Nacional de Desarrollo Científico y Tecnológico |
PMID:25215497 | Free, Freely available | r3d100013971 | https://doi.org/10.17616/R31NJN9V | SCR_017236 | Catalog of Inferred Sequence Binding Preferences | 2026-02-16 09:49:11 | 104 | ||||||
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Academic Seismic Portal at UTIG Resource Report Resource Website |
Academic Seismic Portal at UTIG (RRID:SCR_000403) | ASP at UTIG, ASP_UTIG | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links. | seismic, metadata, image, reflection, refraction, marine geology, geophysics |
is listed by: re3data.org is listed by: CINERGI is related to: Academic Seismic Portal at LDEO has parent organization: University of Texas at Austin; Texas; USA |
NSF | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154745, r3d100010631 | https://doi.org/10.17616/R3CP6C | SCR_000403 | Academic Seismic Portal (ASP) at UTIG | 2026-02-16 09:45:15 | 0 | |||||
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Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | project portal, database, software resource, portal, web application, data or information resource | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-02-16 09:48:51 | 20 | |||||||
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CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | software application, data processing software, software toolkit, data analytics software, data analysis software, software resource | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI134713; NIAID R21 AI142667; NIAID R01 AI134246; NIAID R01 AI076327; NIAID U19 AI135976; NIAID T32 AI10667; NIGMS T32 GM007270; NICHD T32 HD007233; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-02-16 09:49:58 | 22 | |||||||
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SuperSegger Resource Report Resource Website 1+ mentions |
SuperSegger (RRID:SCR_018532) | software application, data processing software, software toolkit, image analysis software, software resource | Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells. | Image cell segmentation, fluorescence quantification, data analysis, high throughput, time lapse, fluorescence microscopy, bacteria cell, image segmentation |
is related to: MATLAB has parent organization: University of Washington; Seattle; USA |
University of Washington Royalty Research Fund ; Sloan BR2011‐110; NSF PHY‐084845; NSF MCB‐1151043‐CAREER; Danish National Research Foundation |
PMID:27569113 | Free, Available for download, Freely available | https://github.com/wiggins-lab/SuperSegger | SCR_018532 | 2026-02-16 09:49:28 | 3 | |||||||
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VirtualPlant Resource Report Resource Website 1+ mentions |
VirtualPlant (RRID:SCR_022576) | data access protocol, software resource, web service | Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses. | genomic data integration, support systems biology, genomic data visualization and analysis | NSF DBI 0445666; NSF IOB 0519985; NSF MCB–0209754; FONDECYT ; Grape Genomics ; Millennium Nucleus for Plant Functional Genomics ; NIGMS R01 GM 032877; NIGMS 5F32GM75600 |
PMID:20007449 | Free, Available for download, Freely available | SCR_022576 | VirtualPlant 1.3 | 2026-02-16 09:50:17 | 2 | ||||||||
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T-REX Resource Report Resource Website 100+ mentions |
T-REX (RRID:SCR_010715) | T-REX | production service resource, service resource, data analysis service, analysis service resource | T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model. | has parent organization: Cornell University; New York; USA | Microsoft Corporation ; NSF DGE 0221658 |
PMID:19500385 | nlx_89468 | SCR_010715 | T-REX (T-RFLP analysis EXpedited), T-REX: Software for the processing and analysis of T-RFLP data, T-RFLP analysis EXpedited | 2026-02-16 09:47:52 | 119 | |||||||
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CRAVAT Resource Report Resource Website 10+ mentions |
CRAVAT (RRID:SCR_012776) | CRAVAT | production service resource, service resource, data analysis service, analysis service resource | A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis. |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
Cancer | NCI CA 152432; NSF DBI 0845275; NCI 1U01CA180956-01 |
OMICS_00147 | SCR_012776 | cancer-related analysis of variants toolkit | 2026-02-16 09:48:12 | 26 | |||||||
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GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool Resource Report Resource Website 1+ mentions |
GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool (RRID:SCR_003191) | GOLEM | data analysis service, analysis service resource, software resource, source code, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Welcome to the home of GOLEM: An interactive, graphical gene-ontology visualization, navigation,and analysis tool on the web. GOLEM is a useful tool which allows the viewer to navigate and explore a local portion of the Gene Ontology (GO) hierarchy. Users can also load annotations for various organisms into the ontology in order to search for particular genes, or to limit the display to show only GO terms relevant to a particular organism, or to quickly search for GO terms enriched in a set of query genes. GOLEM is implemented in Java, and is available both for use on the web as an applet, and for download as a JAR package. A brief tutorial on how to use GOLEM is available both online and in the instructions included in the program. We also have a list of links to libraries used to make GOLEM, as well as the various organizations that curate organism annotations to the ontology. GOLEM is available as a .jar package and a macintosh .app for use on- or off- line as a stand-alone package. You will need to have Java (v.1.5 or greater) installed on your system to run GOLEM. Source code (including Eclipse project files) are also available. GOLEM (Gene Ontology Local Exploration Map)is a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet. | gene ontology, ontology visualization, ontology analysis |
is related to: Gene Ontology has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NSF IIS-0513552; NIGMS P50 GM071508 |
PMID:17032457 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30620 | https://lsi.princeton.edu/golem-interactive-graph-based-gene-ontology-navigation-and-analysis-tool | SCR_003191 | GOLEM An interactive graphical gene-ontology visualization navigation and analysis tool, GOLEM An interactive graphical gene-ontology visualization navigation analysis tool | 2026-02-16 09:46:10 | 3 | ||||
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NLSdb: a database of nuclear localization signals Resource Report Resource Website 1+ mentions |
NLSdb: a database of nuclear localization signals (RRID:SCR_003273) | NLSdb | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree | nuclear localization signal, nuclear protein, nucleus, motif, predict, protein | has parent organization: Columbia University; New York; USA | NIGMS 1-P50-GM62413-01; NSF DBI-0131168 |
PMID:12520032 | Free for academic use, Acknowledgement requested, All others should inquire about a commercial license | nif-0000-03191 | http://cubic.bioc.columbia.edu/db/NLSdb/ | SCR_003273 | NLSdb - a database of nuclear localization signals | 2026-02-16 09:45:58 | 4 |
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