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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins Resource Report Resource Website 10+ mentions |
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins (RRID:SCR_003039) | DP-Bind | analysis service resource, data analysis service, production service resource, service resource | This web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA. Prediction can be performed using a profile of evolutionary conservation of the input sequence automatically generated by the web-server or the input sequence alone. Three prediction methods are run for each input sequence and consensus prediction is generated. | dna binding | has parent organization: University at Albany; New York; USA | NLM 1R03LM009034-01 | PMID:17237068 PMID:16568445 |
Free, Freely available | nif-0000-30426 | SCR_003039 | 2026-09-12 01:01:27 | 20 | ||||||
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Distant Regulatory Elements Resource Report Resource Website 10+ mentions |
Distant Regulatory Elements (RRID:SCR_003058) | DiRE | analysis service resource, data analysis service, production service resource, service resource | Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. | regulatory element, enhancer identification, genome, prediction, transcription factor binding site, gene, co-expression, co-function, function, transcription factor, comparative genomics, regulatory function, gene locus, chromosome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NLM ; Intramural Research Program |
PMID:18487623 | Free, Freely available | nif-0000-30448, biotools:dire | https://bio.tools/dire | SCR_003058 | Distant Regulatory Elements of co-regulated genes | 2026-09-12 01:01:27 | 25 | ||||
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NCBI BioSample Resource Report Resource Website 100+ mentions |
NCBI BioSample (RRID:SCR_004854) | BioSample | data or information resource, database | Database containing descriptions of biological source materials used in experimental assays. Sources include: GenBank, Sequence Read Archive (SRA), Coriell, ATCC. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their samples. As the capacity and complexity of biological data sets expands, databases face new challenges in ensuring that the information is adequately organized and described. The NCBI BioSample database is being developed to help address the challenges by providing the means by which data generators can organize and describe a broad range of sample types, and link to corresponding sets of experimental data in archival databases. | RIN, Resource Information Network, dna, rna, cell, cell line, stem cell, biomaterial, gold standard, RRID Community Authority |
is listed by: OMICtools is listed by: Resource Information Network is related to: GenBank is related to: BioSample Database at EBI is related to: ATCC is related to: NCBI Sequence Read Archive (SRA) is related to: Coriell Cell Repositories is related to: CannSeek Database of Cannabis sativa SNPs has parent organization: NCBI |
NLM | PMID:22139929 | The community can contribute to this resource | nlx_143929, r3d100012828, OMICS_01024 | https://doi.org/10.17616/R31NJME4 | SCR_004854 | BioSample Database, NCBI BioSample Database | 2026-09-12 01:01:34 | 432 | ||||
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SpikeHunter Resource Report Resource Website 1+ mentions |
SpikeHunter (RRID:SCR_024831) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins. | identifying phage tailspike proteins, phage tailspike protein, deplolymerase, right-handed beta-helix, | NLM ; NSF |
PMID:37503040 | Free, Available for download, Freely available | SCR_024831 | 2026-09-12 01:04:32 | 1 | |||||||||
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Scupa Resource Report Resource Website 1+ mentions |
Scupa (RRID:SCR_025755) | Scupa | data analysis software, data processing software, software application, software resource, source code | Software R package for immune cell polarization assessment of scRNA-seq data. Single-cell unified polarization assessment of immune cells using single-cell foundation model. Used for comprehensive immune cell polarization analysis. | immune cell polarization analysis, immune cell polarization assessment, scRNA-seq data, | Cancer Prevention and Research Institute of Texas ; NIA R01CA276513; NIA U01AG079847; NLM R01LM012806 |
PMID:39229048 | Free, Available for download, Freely available | SCR_025755 | Single-Cell Unified Polarization Assessment | 2026-09-12 01:04:51 | 2 | |||||||
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Penn machine learning benchmark repository Resource Report Resource Website |
Penn machine learning benchmark repository (RRID:SCR_017138) | PMLB | data or information resource, data set | Python wrapper for Penn Machine Learning Benchmark data repository. Large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Part of PyPI https://pypi.org/ | benchmark, suite, machine, learning, evaluation, comparison, repository, curated, dataset | NCATS TR001263; NEI EY022300; NHLBI HL134015; NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NLM LM009012; NLM LM010098; NLM LM011360; Warren Center for Network and Data Science |
PMID:29238404 | Free, Restricted | https://github.com/EpistasisLab/penn-ml-benchmarks | SCR_017138 | Penn Machine Learning Benchmark | 2026-09-12 01:03:59 | 0 | ||||||
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SNPs3D Resource Report Resource Website 100+ mentions |
SNPs3D (RRID:SCR_010787) | SNPs3D | data or information resource, database | A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. | single nucleotide polymorphism, single nucleotide variation, gene, FASEB list |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM | The community can contribute to this resource | OMICS_00163 | SCR_010787 | 2026-09-12 01:02:06 | 117 | |||||||
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ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-09-12 01:02:09 | 26 | ||||
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NCBI Resource List Resource Report Resource Website |
NCBI Resource List (RRID:SCR_005628) | NCBI Resources | data or information resource, organization portal, portal | The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation. | database, download, submission, tool, chemical, bioassay, data, software, dna, rna, domain, structure, gene, expression, genetics, medicine, genomes, map, homology, literature, protein, sequence analysis, taxonomy, training, tutorial, variation, gold standard | has parent organization: NCBI | NLM | nlx_146242 | SCR_005628 | NCBI Resource Guide, NCBI Resource List (A-Z) | 2026-09-12 01:00:56 | 0 | |||||||
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pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software resource, software toolkit | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-09-12 01:02:26 | 72 | ||||||
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Gene functional conservation across cell types and species Resource Report Resource Website |
Gene functional conservation across cell types and species (RRID:SCR_023292) | data or information resource, portal, project portal | We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain. | Brain Initiative Cell Census Network, single-nucleus atlases, middle temporal gyrus, human, chimp, gorilla, macaque, marmoset, 57 consensus cell types common to all species, 57 consensus cell types identification, | is related to: BICCN | NARSAD Young Investigator Award ; NHGRI R01HG009318; NLM F32MH114501; NLM R01LM012736; NLM R01MH113005; NLM U01MH114812; NLM U19MH114821 |
DOI:10.1101/2022.09.20.508736 | Free, Freely available | SCR_023292 | 2026-09-12 01:01:12 | 0 | ||||||||
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LINCS Data Portal 2.0 Resource Report Resource Website 1+ mentions |
LINCS Data Portal 2.0 (RRID:SCR_022566) | LDP v2 | data or information resource, portal | Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures. | LINCS Data Portal, Cell, molecules, drug | is related to: LINCS Data Portal | BD2K-LINCS Data Coordination and Integration Center ; NCATS U24TR002278; NHLBI U54HL127624; NLM U01LM012630 |
PMID:31701147 | Free, Freely available | SCR_022566 | Library of Integrated Network Based Cellular Signatures 2.0 | 2026-09-12 01:01:11 | 2 | ||||||
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ReBATE Resource Report Resource Website |
ReBATE (RRID:SCR_017139) | software resource, software toolkit | Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . | compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic | has parent organization: University of Pennsylvania; Philadelphia; USA | NCATS TR001263; NEI EY022300; NHLBI HL134015; NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NLM LM009012; NLM LM010098; NLM LM011360; Warren Center for Network and Data Science |
PMID:30030120 | Free, Available for download, Freely available | https://epistasislab.github.io/ReBATE/ | SCR_017139 | Relief Based Algorithm Training Environment | 2026-09-12 01:02:54 | 0 | ||||||
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MUMmerGPU Resource Report Resource Website 1+ mentions |
MUMmerGPU (RRID:SCR_001200) | MUMmerGPU | data processing software, software application, software resource | Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer. | parallel computation 4, high-throughput sequencing, sequence alignment, dna, graphics processing unit |
is listed by: OMICtools is related to: MUMmer has parent organization: SourceForge has parent organization: University of Maryland; Maryland; USA |
NIGMS R01 GM083873; NLM R01 LM006845 |
PMID:20161021 | Free, Available for download, Freely available | OMICS_02151 | SCR_001200 | High-throughput sequence alignment using Graphics Processing Units | 2026-09-12 01:00:52 | 5 | |||||
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SimpleITK Resource Report Resource Website 50+ mentions |
SimpleITK (RRID:SCR_024693) | software library, software resource, software toolkit | Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms. | multi dimensional image analysis, Insight Segmentation and Registration Toolkit, | is related to: Insight Segmentation and Registration Toolkit | NLM | PMID:24416015 | Free, Available for download, Freely available | https://github.com/SimpleITK/SimpleITK | SCR_024693 | Simple Insight Segmentation and Registration Toolkit | 2026-09-12 01:01:18 | 69 | ||||||
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MedGen Resource Report Resource Website 1+ mentions |
MedGen (RRID:SCR_000111) | MedGen | data or information resource, database | A database of organized information related to human medical genetics, such as attributes of conditions with a genetic contribution. | medical genetics, medical, genetics, disease, clinical |
is listed by: OMICtools is listed by: Genetic Testing Registry has parent organization: NCBI |
NLM 1ZIHLM200888-05 | PMID:32329672 | nlx_156941, OMICS_01549 | SCR_000111 | 2026-09-12 01:01:18 | 6 | |||||||
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Automated Microarray Pipeline Resource Report Resource Website |
Automated Microarray Pipeline (RRID:SCR_001219) | AMP | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis. | microarray, normalization |
is listed by: OMICtools is related to: Gene Ontology has parent organization: TM4 |
NLM R01-LM008795 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02125 | http://www.tm4.org/amp.html | SCR_001219 | TM4 AMP, AMP: Automated Microarray Pipeline, AMP (TM4 Microarray Software Suite), TM4 Microarray Software Suite: Automated Microarray Pipeline, TM4 Microarray Software Suite: AMP | 2026-09-12 01:01:21 | 0 | |||||
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Alignable Tight Genomic Cluster Resource Report Resource Website 1+ mentions |
Alignable Tight Genomic Cluster (RRID:SCR_001894) | ATGC | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis. | gene, genomic cluster, genomic sequence, ortholog, paralog, prokaryotic genomic, protein, protein classification | has parent organization: Lawrence Berkeley National Laboratory | Department of Energy Joint Genome Institute ; NLM ; DOE DE-AC02-05CH11231 |
PMID:28053163 PMID:18845571 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02581 | SCR_001894 | 2026-09-12 01:01:23 | 1 | ||||||
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Robot Reviewer Resource Report Resource Website 1+ mentions |
Robot Reviewer (RRID:SCR_018961) | software application, software resource, text extraction software | Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments. | Automated review, data mining, manuscript screening, artificial intelligence, automatic evidence synthesis, evidence synthesis, trial conduct information, data trial, bias, bias assessement | NCI UH2 CA203711; NLM R01 LM012086; UK Medical Research Council |
PMID:26104742 | Free, Freely available | SCR_018961 | 2026-09-12 01:02:19 | 7 | |||||||||
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iPOP Resource Report Resource Website 10+ mentions |
iPOP (RRID:SCR_008991) | iPOP | data or information resource, data set | Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. | genomics, proteomics, transcriptional profiling, saliva, blood, maternal data, metabolomics, personalized medicine, adult human, genetics, transcriptome, male | has parent organization: Stanford University; Stanford; California | Healthy | Breetwor Family Foundation ; Korber Foundation ; Fundacion Marcelino Botin ; Fundacion Lilly ; NLM T15-LM007033; NIGMS R24-GM61374; NHLBI T32 HL094274; NHLBI KO8 HL083914; NIH New Investigator DP2 award OD004613; Spanish Ministry of Science and Innovation Projects ; Spanish Ministry of Science and Innovation Projects ; European Union FP7 Genica ; European Union FP7 TELOMARKER ; European Research Council Advanced Grant |
PMID:22424236 | Free for personal, Non-exclusive, Non-transferable, Non-commercial access., Please cite. | nlx_152492 | SCR_008991 | Snyderome, Integrated Personal Omics Profiling | 2026-09-12 01:03:18 | 14 |
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