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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SomaticSeq Resource Report Resource Website 1+ mentions |
SomaticSeq (RRID:SCR_024891) | software resource, software toolkit | Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification. | NGS variant calling and classification, somatic mutation detection, somatic mutation calls, single nucleotide variants, detect somatic mutations, | NHGRI R01 HG007834; NIGMS R01 GM109836 |
PMID:26381235 | SCR_024891 | 2026-09-05 06:34:44 | 6 | ||||||||||
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PEPhub Resource Report Resource Website 1+ mentions |
PEPhub (RRID:SCR_024892) | data access protocol, data or information resource, database, software resource, web service | 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, | NHGRI R01 HG012558; NIGMS R35 GM128636 |
PMID:37645717 | Free, Available for download, Freely available | https://github.com/pepkit/pephub | SCR_024892 | Portable Encapsulated Projects hub | 2026-09-05 06:34:44 | 2 | |||||||
|
PLAAC Resource Report Resource Website 10+ mentions |
PLAAC (RRID:SCR_024973) | data access protocol, software resource, web service | 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 | 2026-09-05 06:34:46 | 49 | ||||||||
|
Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software resource, software toolkit | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NHGRI R01 HG011883; NHGRI R01HG010773; NIGMS R01 GM126553; NIMH R01MH110531; NIMH R01MH116281; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-09-05 06:34:48 | 1 | ||||||||
|
PyContact Resource Report Resource Website 1+ mentions |
PyContact (RRID:SCR_025066) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:34:49 | 3 | |||||||
|
Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | atlas, data or information resource, 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 | BBSRC ; Carnegie Trust for the Universities of Scotland ; Ministry of Science ; Technology and Telecommunications of Costa Rica ; Natural Sciences and Engineering Research Council of Canada ; NCCIH AT008718; NCCIH F31 AT010098; NCCIH T32 AT007533; NCCIH U41 AT008718; NCI F31 CA236237; Netherlands eScience Center ; NIGMS GM124461; NIGMS R01 GM125943; NIH D43 TW010530; NSERC Discovery ; NSF ; Sao Paulo Research Foundation |
PMID:31807684 DOI:10.1093/nar/gkab941 |
Free, Freely available, | SCR_025107 | , The Natural Products Atlas, The Natural Products Atlas 2.0 | 2026-09-05 06:34:50 | 36 | ||||||
|
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 | 2026-09-05 06:34:55 | 4 | ||||||||
|
MeTPeak Resource Report Resource Website 10+ mentions |
MeTPeak (RRID:SCR_026533) | software resource, software toolkit, source code | Software package for finding the location of m6A sites in MeRIP-seq data. | finding location of m6A sites, MeRIP-seq data | Natural Science Foundation of China ; NCI P30CA54174; NCI U54 CA113001; NIGMS R01 GM113245; NSF |
PMID:27307641 | Free, Available for download, Freely available | SCR_026533 | 2026-09-05 06:35:25 | 11 | |||||||||
|
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 | 2026-09-05 06:35:25 | 10 | |||||||||
|
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 ; Michael J Fox Foundation ; NIGMS RO1 GM132129; NINDS R01NS110395 |
DOI:10.1101/2025.02.07.636106 | Free, Freely available | SCR_026690 | EndoMAP.v1 | 2026-09-05 06:35:29 | 2 | ||||||||
|
kraken2 Resource Report Resource Website 1000+ mentions |
kraken2 (RRID:SCR_026838) | software application, software resource, source code | Software tool as second version of Kraken taxonomic sequence classification system. | taxonomic sequence classification system, taxonomic, sequence, classification system, | NIGMS R01 GM118568; NIGMS R35 GM130151; NSF |
PMID:31779668 | Free, Available for download, Freely available | SCR_026838 | 2026-09-05 06:35:32 | 1421 | |||||||||
|
apeglm Resource Report Resource Website 1+ mentions |
apeglm (RRID:SCR_026951) | software resource, software toolkit | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NCI P01 CA142538; NHGRI R01 HG009125; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-09-05 06:35:35 | 2 | ||||||||
|
PHATE Resource Report Resource Website 1+ mentions |
PHATE (RRID:SCR_027119) | 3d visualization software, data processing software, data visualization software, software application, software resource, source code | 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, | NHGRI 1R01HG008383; NICHD F31HD097958; NIGMS R01GM107092; NIGMS R01GM130847; NSF |
PMID:31796933 | Free, Available for download, Freely available, | SCR_027119 | Potential of Heat-diffusion for Affinity-based Transition Embedding | 2026-09-05 06:35:39 | 5 | ||||||||
|
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 | Michael J. Fox Foundation ; NIGMS R01GM141192; NIGMS R35GM147095; NIGMS RM1GM149406 |
PMID:38405833 | Free, Freely available | SCR_025656 | Membrane Active Polymers Database Guide for Membrane Protein Solubilization | 2026-09-05 06:35:04 | 1 | |||||||
|
SpaGCN Resource Report Resource Website |
SpaGCN (RRID:SCR_025978) | software application, software resource, 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, | NEI R01EY030192; NEI R01EY031209; NHLBI R01HL113147; NHLBI R01HL150359; NIA P01AG066597; NIGMS R01GM125301 |
PMID:34711970 | Free, Available for download, Freely available | SCR_025978 | 2026-09-05 06:35:10 | 0 | |||||||||
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LinDA Resource Report Resource Website 1+ mentions |
LinDA (RRID:SCR_025966) | data analysis software, data processing software, software application, software resource, source code | 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, | Mayo Clinic Center for Individualized Medicine ; NIGMS R01GM144351; NSF |
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 | 2026-09-05 06:35:10 | 4 | |||||||||
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iDEP: Integrated Differential Expression and Pathway analysis Resource Report Resource Website 10+ 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 | 2026-09-05 06:35:46 | 19 | ||||||||
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COACH Resource Report Resource Website 1+ mentions |
COACH (RRID:SCR_027684) | data access protocol, software resource, web service | 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, | NIGMS GM083107; NIGMS GM084222; NSF Career Award |
PMID:23975762 | Free, Freely available | http://zhanglab.ccmb.med.umich.edu/COACH/ | SCR_027684 | , COACH server | 2026-09-05 06:35:55 | 7 | |||||||
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RCy3 Resource Report Resource Website 1+ mentions |
RCy3 (RRID:SCR_027668) | software resource, software toolkit, 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 | Google Summer of Code ; NIGMS P41GM103504 |
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 | 2026-09-05 06:35:55 | 9 | ||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, software resource, source code | Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer. | Cancer Genes, SNV, indel, gene-specific probabilistic estimates, strength of negative and positive selection, cancer | NCI U54 CA143874; NIGMS R01 GM078598; NIMH R01 MH101244 |
PMID:29106416 | Free, Available for download, Freely available | https://github.com/weghornlab/CBaSE, http://genetics.bwh.harvard.edu/cbase | SCR_027765 | Cancer Bayesian SElection estimation | 2026-09-05 06:35:57 | 0 |
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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 U24DK097771.
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