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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PIAGE Resource Report Resource Website |
PIAGE (RRID:SCR_013124) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program that performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects (Kraft P et al., 2007). Power and sample size estimations are based on Gauderman''s (2002) asymptotic approach for power and sample size estimations in direct studies of GxE. Hardy-Weinberg equilibrium and independence of genotypes and environmental exposures in the population are assumed. The estimates are based on genotypic codes (G=1 (G=0) for individuals who carry a (non-) risk genotype), which depend on the mode of inheritance (dominant, recessive, or multiplicative). A conditional logistic regression approach is used, which employs a likelihood-ratio test with respect to a biallelic candidate SNP, a binary environmental factor (E=1 (E=0) in (un)exposed individuals), and the interaction between these components. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154534, SCR_009372, nlx_154594 | SCR_013124 | R/PIAGE, Power of Indirect Association Studies of Gene-Environment Interactions | 2026-08-04 09:43:08 | 0 | ||||||||
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ENIGMA Resource Report Resource Website 100+ mentions |
ENIGMA (RRID:SCR_013400) | data processing software, software application, software resource, data analysis software | A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007 | genome, gene, genetic software, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium is parent organization of: ENIGMA-DTI Pipeline |
PMID:18402676 | biotools:enigma, nlx_144365 | https://bio.tools/enigma | SCR_013400 | 2026-08-04 09:43:12 | 130 | ||||||||
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BOOST Resource Report Resource Website 10+ mentions |
BOOST (RRID:SCR_013133) | BOOST | data processing software, software application, software resource, data analysis software | Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies. | gene, genetic, genomic, logistic regression model, gene-gene interactions | is listed by: Genetic Analysis Software | Free, Available for download | nlx_154249 | SCR_013133 | BOolean Operation based Screening and Testing | 2026-08-04 09:43:08 | 32 | |||||||
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R/FEST Resource Report Resource Website 1+ mentions |
R/FEST (RRID:SCR_013347) | software application, software resource | An R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154111, SCR_000830, nlx_154582 | SCR_013347 | FEST | 2026-08-04 09:43:11 | 2 | |||||||||
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Residual Variation Intolerance Score (RVIS) Resource Report Resource Website 1+ mentions |
Residual Variation Intolerance Score (RVIS) (RRID:SCR_013850) | RVIS | narrative resource, standard specification, data or information resource | A gene-based score intended to help in the interpretation of human sequence data. The score is designed to rank genes in terms of whether they have more or less common functional genetic variation relative to the genome wide expectation given the amount of apparently neutral variation the gene has. A gene with a positive score has more common functional variation, and a gene with a negative score has less and is referred to as intolerant. | gene, score, sequence, interpretation, rank, functional genetic variation | is listed by: Columbia University; New York; USA | NIH Epi4K Sequencing ; Bioinformatics and Biostatistics Core U01NS077303 |
DOI:10.1371/journal.pgen.1003709 | SCR_013850 | Residual Variation Intolerance Score | 2026-08-04 09:43:17 | 8 | |||||||
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DataAssist Resource Report Resource Website 100+ mentions |
DataAssist (RRID:SCR_014969) | data processing software, data analysis software, software resource, software application, data visualization software | Data analysis tool that utilizes the Comparative CT (ddCT) method to rapidly and accurately quantitate relative gene expression across a large number of genes and samples. Raw input from plates or arrays can be analyzed according to user-determined settings. | ddCT, QC analysis, comparative ct, gene expression, data analysis, gene, plot | has parent organization: Thermo Fisher Scientific | Free, Available for download, Account required | SCR_014969 | DataAssist Software | 2026-08-04 09:43:35 | 454 | |||||||||
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GenePattern Notebook Resource Report Resource Website 1+ mentions |
GenePattern Notebook (RRID:SCR_015699) | systems interoperability software, software resource, software application, web application, electronic laboratory notebook | Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. | gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools |
is listed by: bio.tools is listed by: Debian is affiliated with: GenePattern |
NIGMS R01-GM074024; NCI U24-CA194107 |
PMID:28822753 | Open Source, Free, Available for download, Account required | biotools:GenePattern_notebook | https://bio.tools/GenePattern_notebook | SCR_015699 | GenePattern Notebook environment | 2026-08-04 09:43:43 | 3 | |||||
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DISEASES Resource Report Resource Website 500+ mentions |
DISEASES (RRID:SCR_015664) | database, data or information resource | Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence. | disease, gene, disease-gene association, text-mining, , bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation Center for Protein Research NNF14CC0001; European Union Seventh Framework Programme n259348 |
PMID:25484339 | biotools:diseases | https://bio.tools/diseases | SCR_015664 | 2026-08-04 09:43:43 | 627 | |||||||
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Connectivity Map 02 Resource Report Resource Website 100+ mentions |
Connectivity Map 02 (RRID:SCR_015674) | cmap | web application, software resource, database, data or information resource | Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription, expression, gene, drug, disease pattern-matching algorithm, FASEB list |
has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
PMID:17008526 | THIS RESOURCE IS NO LONGER IN SERVICE | https://www.broadinstitute.org/cmap_build01 | SCR_015674 | Broad Institute Connectivity Map 02 Build, cmap | 2026-08-04 09:43:42 | 180 | ||||||
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funRiceGenes Resource Report Resource Website 10+ mentions |
funRiceGenes (RRID:SCR_015778) | data set, database, data or information resource | Dataset of functionally characterized rice genes and members of different gene families. The dataset was created by integrating data from available databases and reviewing publications of rice functional genomic studies. | rice, functional genomics, interaction network, genetic improvement, gene, data integration | National Key Research and Development Program of China 2016YFD0100903; National Natural Science Foundation of China 31771873 and National Natural Science Foundation of China; Outstanding Young Talents Program |
Freely available, Public, Available for download, Free | https://github.com/venyao/RICENCODE, http://funricegenes.ncpgr.cn/ | SCR_015778 | RICENCODE | 2026-08-04 09:43:44 | 44 | ||||||||
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CluePedia Cytoscape plugin Resource Report Resource Website 100+ mentions |
CluePedia Cytoscape plugin (RRID:SCR_015784) | data processing software, data analysis software, software resource, software application, data visualization software | Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments. | cytoscape, cluepedia, search tool, marker, pathway, experimental data, in silico data, linear dependence, gene, protein, miRNA | is a plug in for: Cytoscape | INCa ; Canceropole Ile de France ; INSERM ; MedImmune ; Qatar National Research Fund NPRP09-1174-3-291; European Commission 7FP Geninca 202230); LabEx Immuno-Oncology |
PMID:23325622 | Free for non-profits, Free for academic use, Available for download, Commercially available, Available for purchase | SCR_015784 | CluePedia: A ClueGO plugin, CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data | 2026-08-04 09:43:44 | 192 | |||||||
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Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | data processing software, software application, software resource, data analysis software | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | 2026-08-04 09:43:46 | 31 | ||||||||||
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National Gene Vector Laboratories Resource Report Resource Website 1+ mentions |
National Gene Vector Laboratories (RRID:SCR_015944) | NGVL | topical portal, portal, data or information resource | The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies. | gene, therapy, manufacturing, toxicology, human, research, vector, transfer, study | is used by: Adobe Illustrator | NIH | SCR_015944 | 2026-08-04 09:43:45 | 2 | |||||||||
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UK Brain Expression Consortium Resource Report Resource Website 1+ mentions |
UK Brain Expression Consortium (RRID:SCR_015889) | UKBEC | portal, organization portal, data or information resource, consortium | Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders. | neurodegenerative, brain, disorder, mrna, dna, eqtl, snp, gene, visualization, expression | is parent organization of: Braineac | SCR_015889 | 2026-08-04 09:43:46 | 3 | ||||||||||
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Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | data processing software, data analysis software, software resource, sequence analysis software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-08-04 09:43:47 | 568 | |||||||
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EnrichmentMap Resource Report Resource Website 500+ mentions |
EnrichmentMap (RRID:SCR_016052) | data processing software, source code, software resource, software application, data visualization software | Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together. | cytoscape, functional, visualization, enrichment, gene, mapping, genome, pathway, network, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: Cytoscape |
NHGRI P41 HG04118; Ontario Genomics Institute ; Heart and Stroke Foundation of Canada ; Canada Foundation for Innovation ; Ontario Research Fund (ORF) |
PMID:21085593 | biotools:enrichmentmap | https://github.com/BaderLab/EnrichmentMapApp, https://bio.tools/enrichmentmap | SCR_016052 | 2026-08-04 09:43:48 | 545 | |||||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | source code, analysis service resource, data set, storage service resource, software resource, data repository, production service resource, service resource, database, data or information resource | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-08-04 09:41:09 | 2 | ||||
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Handbook of Genetic Counseling Resource Report Resource Website |
Handbook of Genetic Counseling (RRID:SCR_004564) | Handbook of Genetic Counseling | narrative resource, data or information resource, wiki, book | The Handbook of Genetic Counseling is a wikibook designed as an introduction to the discipline and practice of genetic counseling. The text provides an introduction to genetic counseling as a clinical practice and includes sample counseling outlines and letters for students of genetic counseling. Additional outline and letter examples are highly encouraged. Wikibooks contains books on many medical topics; however, no warranty whatsoever is made that any of the books are accurate. | gene, counseling, genetic, syndrome, disease | has parent organization: Wikibooks | nlx_79147 | SCR_004564 | 2026-08-04 09:41:10 | 0 | |||||||||
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NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | data analysis service, analysis service resource, storage service resource, production service resource, service resource, data repository, database, data or information resource | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems, https://doi.org/10.17616/R31K80 | SCR_004690 | BioSystems Database, NCBI BioSystems | 2026-08-04 09:41:11 | 118 | |||||
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QuickGO Resource Report Resource Website 500+ mentions |
QuickGO (RRID:SCR_004608) | QuickGO | web service, software resource, controlled vocabulary, data access protocol, ontology, database, data or information resource | A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. | gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: STRAP has parent organization: European Bioinformatics Institute |
BBSRC BB/E023541/1 | PMID:19744993 PMID:20157483 |
Apache License, v2, Free for academic use | biotools:quickgo, nlx_60318, OMICS_02276 | https://bio.tools/quickgo | SCR_004608 | Quick GO | 2026-08-04 09:41:10 | 523 |
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