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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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abSENSE Resource Report Resource Website 1+ mentions |
abSENSE (RRID:SCR_023223) | software resource, source code | Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally. | undetected homolog, gene homolog detection failure, homology search, lineage-specific genes, homology detection failure | Howard Hughes Medical Institute ; NHGRI R01-HG009116; NIGMS RO1-GM43987; NSF 1764269; Simons Center for the Mathematical and Statistical Analysis of Biology 594596; Harvard University |
PMID:33137085 | Free, Available for download, Freely available | http://www.eddylab.org/abSENSE/ | SCR_023223 | 2026-08-03 09:37:57 | 1 | ||||||||
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University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility (RRID:SCR_024793) | HSTRI Core | service resource, access service resource, core facility | Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies. | ABRF, Image acquisition and analysis, high spatial and temporal resolution imaging, |
is listed by: ABRF CoreMarketplace has parent organization: University of Nevada at Reno; Nevada; USA |
NIGMS P20GM130459 | Open | ABRF_2596 | https://coremarketplace.org/?FacilityID=2596&citation=1 | SCR_024793 | , University of Nevada High Spatial and Temporal Resolution Imaging Core | 2026-08-03 09:38:51 | 1 | |||||
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PEPhub Resource Report Resource Website 1+ mentions |
PEPhub (RRID:SCR_024892) | web service, database, data access protocol, data or information resource, software resource | Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end. | Portable Encapsulated Projects, biological metadata server, sharing, retrieving, validating, sample metadata, | NIGMS R35 GM128636; NHGRI R01 HG012558 |
PMID:37645717 | Free, Available for download, Freely available | https://github.com/pepkit/pephub | SCR_024892 | Portable Encapsulated Projects hub | 2026-08-03 09:38:22 | 2 | |||||||
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PLAAC Resource Report Resource Website 10+ mentions |
PLAAC (RRID:SCR_024973) | web service, data access protocol, software resource | Web and command-line application to identify proteins with prion-like amino acid composition. Searches protein sequences to identify probable prion subsequences using hidden-Markov model algorithm. | protein sequences search, identify proteins with prion-like amino acid composition, identify proteins, identify probable prion subsequences, | G. Harold and Leila Y. Mathers Foundation ; Howard Hughes Medical Institute ; NIGMS GM025874 |
PMID:24825614 | Free, Freely available | SCR_024973 | Prion Like Amino Acid Composition | 2026-08-03 09:38:55 | 25 | ||||||||
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PyContact Resource Report Resource Website 1+ mentions |
PyContact (RRID:SCR_025066) | software resource, data processing software, software application, data analysis software | Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package. | non-covalent interactions, molecular dynamics trajectories, | is related to: MDAnalysis | German Research Foundation ; NIGMS P41 GM104601; NSF |
PMID:29414703 | Free, Available for download, Freely available, | https://github.com/maxscheurer/pycontact | SCR_025066 | 2026-08-03 09:38:25 | 3 | |||||||
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Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | data or information resource, atlas, knowledge base | Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles. | FAIR principles, microbial natural products discovery, natural product structures, bacterial and fungal natural products, visualize chemical diversity, | has parent organization: Simon Fraser University; British Columbia; Canada | NSERC Discovery ; NCCIH U41 AT008718; NIGMS R01 GM125943; NCCIH F31 AT010098; NCI F31 CA236237; NCCIH T32 AT007533; NIH D43 TW010530; NSF ; BBSRC ; Carnegie Trust for the Universities of Scotland ; Netherlands eScience Center ; Sao Paulo Research Foundation ; NCCIH AT008718; NIGMS GM124461; Natural Sciences and Engineering Research Council of Canada ; Ministry of Science ; Technology and Telecommunications of Costa Rica |
PMID:31807684 DOI:10.1093/nar/gkab941 |
Free, Freely available, | SCR_025107 | , The Natural Products Atlas, The Natural Products Atlas 2.0 | 2026-08-03 09:38:33 | 19 | ||||||
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FusionGDB2 Resource Report Resource Website 1+ mentions |
FusionGDB2 (RRID:SCR_025299) | data or information resource, database | Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level. | Functional annotation database, human fusion genes, fusion gene breakage tendency score, | NIGMS R35GM138184; University of Texas |
PMID:34755868 | Free, Freely available | SCR_025299 | FusionGDB 2.0 | 2026-08-03 09:38:29 | 2 | ||||||||
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MAP Database Guide for Membrane Protein Solubilization Resource Report Resource Website 1+ mentions |
MAP Database Guide for Membrane Protein Solubilization (RRID:SCR_025656) | data or information resource, database | Open access web app that allows users to search for optimal condition for extraction of membrane proteins into membrane active polymers which allows for retention of native membrane environment around target protein. | optimal condition for extraction of membrane proteins, membrane active polymers, retention of native membrane environment, target protein, | has parent organization: Yale University; Connecticut; USA | NIGMS RM1GM149406; NIGMS R01GM141192; NIGMS R35GM147095; Michael J. Fox Foundation |
PMID:38405833 | Free, Freely available | SCR_025656 | Membrane Active Polymers Database Guide for Membrane Protein Solubilization | 2026-08-03 09:38:35 | 1 | |||||||
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SpaGCN Resource Report Resource Website |
SpaGCN (RRID:SCR_025978) | software resource, software application, source code | Software graph convolutional network to integrate gene expression and histology to identify spatial domains and spatially variable genes. SpaGCN integrates information from gene. | Integrating gene expression and histology, graph convolutional network, identify spatial domains, identify spatially variable genes, | NIGMS R01GM125301; NEI R01EY030192; NEI R01EY031209; NHLBI R01HL113147; NHLBI R01HL150359; NIA P01AG066597 |
PMID:34711970 | Free, Available for download, Freely available | SCR_025978 | 2026-08-03 09:39:13 | 0 | |||||||||
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LinDA Resource Report Resource Website 1+ mentions |
LinDA (RRID:SCR_025966) | software application, data processing software, source code, data analysis software, software resource | Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models. | differential abundance analysis, microbiome compositional data, differential abundance analysis, | NIGMS R01GM144351; NSF ; Mayo Clinic Center for Individualized Medicine |
PMID:35421994 | SCR_025966 | Linear models for differential abundance analysis of microbiome compositional data (LinDA), Linear models for differential abundance analysis of microbiome compositional data | 2026-08-03 09:38:39 | 1 | |||||||||
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Conditional AutoRegressive Deconvolution Resource Report Resource Website 1+ mentions |
Conditional AutoRegressive Deconvolution (RRID:SCR_026310) | CARD | software toolkit, software resource, source code | Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations. | Deconvolution method, spatial transcriptomics, cell-type-specific expression, single-cell RNA sequencing, cell-type composition across tissue locations, | NIGMS R01GM126553; NHGRI R01HG011883; NIGMS R01GM144960 |
PMID:35501392 | Free, Available for download, Freely available | SCR_026310 | , CARD: Conditional AutoRegressive Deconvolution, Conditional autoregressive-based deconvolution | 2026-08-03 09:38:55 | 3 | |||||||
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NucleAIzer Resource Report Resource Website 1+ mentions |
NucleAIzer (RRID:SCR_026500) | software resource, source code | Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool. | nucleus segmentation, image style transfer, | NIGMS R35 GM122547; European Regional Development Funds ; Academy of Finland ; Swedish Research Council |
DOI:10.1016/j.cels.2020.04.003 | Free, Available for download, Freely available | SCR_026500 | 2026-08-03 09:39:17 | 4 | |||||||||
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MeTPeak Resource Report Resource Website 10+ mentions |
MeTPeak (RRID:SCR_026533) | software toolkit, software resource, source code | Software package for finding the location of m6A sites in MeRIP-seq data. | finding location of m6A sites, MeRIP-seq data | NCI P30CA54174; NCI U54 CA113001; NIGMS R01 GM113245; Natural Science Foundation of China ; NSF |
PMID:27307641 | Free, Available for download, Freely available | SCR_026533 | 2026-08-03 09:38:57 | 10 | |||||||||
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Liftoff Resource Report Resource Website 10+ mentions |
Liftoff (RRID:SCR_026535) | software resource, source code | Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations. | Aligns genes, reference genome to target genome alignment, mapping of gene annotations, genome annotation lift-over, mapping genes between two assemblies of species, mapping genes, same or closely related species, | NHGRI R01 HG006677; NIGMS R35 GM130151 |
PMID:33320174 | Free, Available for download, Freely available | SCR_026535 | 2026-08-03 09:39:18 | 10 | |||||||||
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EndoMap Resource Report Resource Website 1+ mentions |
EndoMap (RRID:SCR_026690) | data or information resource, database | Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes. | Structural protein interactome, structural interactome viewer, endosomal protein-protein interactions, human early endosomes, | Aligning Science Across Parkinson ; NINDS R01NS110395; NIGMS RO1 GM132129; Michael J Fox Foundation |
DOI:10.1101/2025.02.07.636106 | Free, Freely available | SCR_026690 | EndoMAP.v1 | 2026-08-03 09:39:20 | 2 | ||||||||
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kraken2 Resource Report Resource Website 1000+ mentions |
kraken2 (RRID:SCR_026838) | software resource, software application, source code | Software tool as second version of Kraken taxonomic sequence classification system. | taxonomic sequence classification system, taxonomic, sequence, classification system, | NSF ; NIGMS R01 GM118568; NIGMS R35 GM130151 |
PMID:31779668 | Free, Available for download, Freely available | SCR_026838 | 2026-08-03 09:39:01 | 1107 | |||||||||
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PHATE Resource Report Resource Website 1+ mentions |
PHATE (RRID:SCR_027119) | software application, data processing software, 3d visualization software, source code, software resource, data visualization software | Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances. | visualizing high dimensional data, high dimensional data, | NICHD F31HD097958; NHGRI 1R01HG008383; NSF ; NIGMS R01GM107092; NIGMS R01GM130847 |
PMID:31796933 | Free, Available for download, Freely available, | SCR_027119 | Potential of Heat-diffusion for Affinity-based Transition Embedding | 2026-08-03 09:39:25 | 2 | ||||||||
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iDEP: Integrated Differential Expression and Pathway analysis Resource Report Resource Website 1+ mentions |
iDEP: Integrated Differential Expression and Pathway analysis (RRID:SCR_027373) | iDEP | software resource, web application | Integrated web application for differential expression and pathway analysis of RNA-Seq data. | differential expression, pathway analysis, RNA-Seq data, | NIGMS GM083226; NSF ; State of South Dakota |
PMID:30567491 | Free, Freely available | SCR_027373 | 2026-08-03 09:39:28 | 8 | ||||||||
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COACH Resource Report Resource Website 1+ mentions |
COACH (RRID:SCR_027684) | web service, data access protocol, software resource | Web application for protein-ligand binding site prediction. Starting from given structure of target proteins, COACH will generate complementray ligand binding site predictions using two comparative methods, TM-SITE and S-SITE, which recognize ligand-binding templates from the BioLiP protein function database by binding-specific substructure and sequence profile comparisons. | protein-ligand binding site prediction, protein, ligand, binding site prediction, | NSF Career Award ; NIGMS GM083107; NIGMS GM084222 |
PMID:23975762 | Free, Freely available | http://zhanglab.ccmb.med.umich.edu/COACH/ | SCR_027684 | , COACH server | 2026-08-03 09:39:15 | 5 | |||||||
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RCy3 Resource Report Resource Website 1+ mentions |
RCy3 (RRID:SCR_027668) | software toolkit, software resource, source code | Software R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort.Network biology using Cytoscape from within R. | Network biology using Cytoscape from within R, network biology, Cytoscape, R | works with: Cytoscape | NIGMS P41GM103504; Google Summer of Code |
PMID:31819800 | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/RCy3.html, https://zenodo.org/records/3473421 | SCR_027668 | RCy3: Network biology using Cytoscape from within R | 2026-08-03 09:39:32 | 8 |
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