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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OHSU Animal Model Support Core Facility Resource Report Resource Website 1+ mentions |
OHSU Animal Model Support Core Facility (RRID:SCR_009994) | OHSU TMM, TMM Core | access service resource, core facility, service resource | Core assists investigators with developing genetically engineered rodent models of human diseases for studying mutant genes and investigating molecular mechanisms underlying pathological processes. | ABRF, USEDit, developing genetically engineered rodent models, human diseases, mutant genes, pathological processes |
is listed by: Eagle I is related to: USEDit has parent organization: Oregon Health and Science University; Oregon; USA |
SciEx_9275, SCR_011002, nlx_156461 | http://ohsu.eagle-i.net/i/0000012a-2501-9822-d994-629180000000, http://www.scienceexchange.com/facilities/transgenic-mouse-models-ohsu | SCR_009994 | OHSU Transgenic Mouse Models Core Laboratory, Oregon Health & Science University Transgenic Mouse Models, Oregon Health and Science University Transgenic Mouse Models, OHSU Transgenic Mouse Model Shared Resource | 2026-08-12 10:50:09 | 2 | |||||||
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PANOGA Resource Report Resource Website 1+ mentions |
PANOGA (RRID:SCR_006242) | PANOGA | production service resource, data analysis service, analysis service resource, service resource | A web server to devise functionally important pathways through the identification of single nucleotide polymorphism (SNP)-targeted genes within these pathways. The strength of the methodology stems from its multidimensional perspective, where evidence from the following five resources is combined: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways. | single nucleotide polymorphism, genome-wide association study, pathway, function, gene, genetic association, protein-protein interaction network, linkage disequilibrium, protein-protein interaction |
is listed by: OMICtools has parent organization: Sabanci University; Istanbul; Turkey |
PMID:24413675 | Free, Public, Free for academic use, (source code upon request) | OMICS_02238 | SCR_006242 | Pathway and Network-Oriented GWAS Analysis, Pathway and Network Oriented GWAS (Genome-Wide Association Study) Analysis, Pathway and Network Oriented GWAS Analysis | 2026-08-12 10:49:24 | 7 | ||||||
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Haldanes Sieve Resource Report Resource Website 1+ mentions |
Haldanes Sieve (RRID:SCR_007178) | Haldane?s Sieve | data or information resource, narrative resource, blog | Blog discussing preprints in population and evolutionary genetics. | is listed by: OMICtools | OMICS_01714 | SCR_007178 | 2026-08-12 10:49:35 | 3 | ||||||||||
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GC/GCF Resource Report Resource Website 1+ mentions |
GC/GCF (RRID:SCR_009075) | software resource, software application | Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, linux | is listed by: Genetic Analysis Software | nlx_154072, SCR_000846, nlx_154584 | SCR_009075 | R/GCF, R/GC, Genomic Control | 2026-08-12 10:49:54 | 1 | |||||||||
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Homeobox Genes DataBase Resource Report Resource Website 1+ mentions |
Homeobox Genes DataBase (RRID:SCR_007723) | HoxPro | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 11th,2023. The database HOX Pro contains information about organization, functions and evolution of gene ensembles, key roles in which play homeobox-genes. It is aimed at: 1. analysis and classification of regulatory and coding regions in diverse homeobox and related genes; 2. describing mutations and knock-outs of hox-genes, as well as hereditary diseases related to these genes; 3. graphical representation, comparisons and classification of hox-genes expression patterns and profiles (sea urchin blastula, Drosophila blastoderm and imaginal discs, vertebrate limbs, mammalian brain, human EC cells); 4. comparative analysis of organization of hox-based genetic networks the nematode Caenorhabditis elegans the sea urchins Strongylocentrotus purpuratus and other echinids, the fruit flies Drosophila melanogaster and D.virilis, the vertebrates chicken and mouse; 5. analysis of phylogeny and evolution of homeobox genes and clusters. | homeobox, homeobox-genes, hox genes | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20854, SCR_008115, nif-0000-02982 | SCR_007723 | 2026-08-12 10:49:44 | 1 | |||||||||
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The Loom Resource Report Resource Website 1+ mentions |
The Loom (RRID:SCR_006877) | Loom | data or information resource, narrative resource, blog | The Loom is a blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer. Carl Zimmer writes about science regularly for the New York Times and magazines such as Discover, where he is a contributing editor and columnist. | has parent organization: Discover Magazine | nlx_83062 | SCR_006877 | 2026-08-12 10:49:33 | 1 | ||||||||||
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Sapienta Resource Report Resource Website 1+ mentions |
Sapienta (RRID:SCR_006993) | SAPIENTA | software application, software resource, source code | Software to help researchers process scientific papers faster and get the information they are interested in out of them. This is achieved by automating the recognition of core scientific concepts such as Motivation, Method, Result, Conclusion in papers and uses them to generate automatic summaries. This SAPIENTA tool adds additional functionality to the SAPIENT tool, an annotation tool implemented as a web application which enables experts to annotate scientific papers, sentence by sentence manually, according to the Core Scientific Concept (CSC) schema. | semantic mark up, semantic, annotation, annotation software | is listed by: FORCE11 | JISC | nlx_151311 | SCR_006993 | SAPIENTA - Automating the Semantic Annotation of Papers, Semantic Annotation of Papers: Interface & ENrichment Tool Automated | 2026-08-12 10:49:36 | 1 | |||||||
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GOstat Resource Report Resource Website 100+ mentions |
GOstat (RRID:SCR_008535) | GOstat | production service resource, data analysis service, analysis service resource, service resource | GOstat is a tool that allows you to find statistically overrepresented Gene Ontologies within a group of genes. The Gene-Ontology database (GO: http://www.geneontology.org) provides a useful tool to annotate and analyze the function of large numbers of genes. Modern experimental techniques, as e.g. DNA microarrays, often result in long lists of genes. To learn about the biology in this kind of data it is desirable to find functional annotation or Gene-Ontology groups which are highly represented in the data. This program (GOstat) should help in the analysis of such lists and will provide statistics about the GO terms contained in the data and sort the GO annotations giving the most representative GO terms first. Run GOstat: * Go to search form - Computes GO statistics of a list of genes selected from a microarray. * GOstat Display - You can store results from a previously run and view them here, either by uploading them as a file or putting them on a selected URL. * Upload Custom GO Annotations - This allows you to upload your own GO annotation database and use it with GOstat. Variants of GOstat: * Rank GOstat - Takes input from all genes on microarray instead of using a fixed cutoff and uses ranks using a Wilcoxon test or either ranks or pvalues to score GOs using Kolmogorov-Smirnov statistics. * Gene Abundance GOstats - Takes input from all genes on microarray and sums up the gene abundances for each GO to compute statistics. * Two list GOstat - Compares GO statistics in two independent lists of genes, not necessarily one of them being the complete list the other list is sampled from. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene ontology, annotation, statistical analysis, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia |
DFG | PMID:14962934 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30625 | SCR_008535 | 2026-08-12 10:49:47 | 159 | ||||||
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Pythonxy Resource Report Resource Website 10+ mentions |
Pythonxy (RRID:SCR_006903) | Python-xy, Python(x, y) | software development tool, software application, software resource, source code | Scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment. Used to interpreted languages (such as MATLAB or IDL) or compiled languages (C/C++ or Fortran) to switch to Python. | program, language, python, computation, data analysis, data visualization, plugin | is related to: Spyder | Free, Available for download, Freely available | nlx_149232 | http://www.pythonxy.com, https://code.google.com/p/pythonxy/wiki/Welcome | SCR_006903 | pythonxy - Scientific-oriented Python Distribution based on Qt and Spyder, Python(x, y) - Scientific oriented Python Distribution based on Qt and Spyder | 2026-08-12 10:49:34 | 10 | ||||||
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IRESite Resource Report Resource Website 50+ mentions |
IRESite (RRID:SCR_007753) | data or information resource, database | Database of experimentally verified IRES structures. Presents information about experimentally studied Internal Ribosome Entry Site segments. | bio.tools, experimentally verified IRES structures, Internal Ribosome Entry Site segments, IRES structures, IRES segments |
is listed by: bio.tools is listed by: Debian has parent organization: Charles University; Prague; Czech Republic |
nif-0000-03047, nif-0000-03046, SCR_007754, biotools:iresite | https://bio.tools/iresite | http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ | SCR_007753 | IRESdb, , IRESdb - the Internal Ribosome Entry Site database, Internal Ribosome Entry Site | 2026-08-12 10:49:44 | 52 | |||||||
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GeneTerm Linker Resource Report Resource Website 1+ mentions |
GeneTerm Linker (RRID:SCR_006385) | GTLinker | production service resource, data analysis service, analysis service resource, service resource | Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service. | gene, functional annotation, function, functional metagroup, p-value, annotation, web service |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: InterPro has parent organization: Spanish National Research Council; Madrid; Spain |
PMID:21949701 | Acknowledgement requested | OMICS_02227 | SCR_006385 | GeneTerm Linker - post enrichment functional association by non-redundant reciprocal linkage | 2026-08-12 10:49:25 | 2 | ||||||
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GENECOUNTING Resource Report Resource Website 10+ mentions |
GENECOUNTING (RRID:SCR_009189) | GENECOUNTING | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data. | gene, genetic, genomic, c, ms-windows, unix, solaris, linux | is listed by: Genetic Analysis Software | PMID:12490459 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154329 | http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/ | SCR_009189 | 2026-08-12 10:49:52 | 12 | ||||||
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GCHAP Resource Report Resource Website 1+ mentions |
GCHAP (RRID:SCR_009186) | GCHAP | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals. By excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes. | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | PMID:14555636 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154325 | SCR_009186 | Gene Counting method for HAPlotype analysis. GENEPI.JAR | 2026-08-12 10:49:52 | 7 | ||||||
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LAMARC Resource Report Resource Website 10+ mentions |
LAMARC (RRID:SCR_009252) | LAMARC | software resource, software application | Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, ms-windows, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1016/j.tree.2008.09.007 | OMICS_28408, nlx_154420 | https://sources.debian.org/src/lamarc/ | SCR_009252 | Likelihood Analysis with Metropolis Algorithm using Random Coalescence | 2026-08-12 10:49:53 | 46 | ||||||
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KING Resource Report Resource Website 1000+ mentions |
KING (RRID:SCR_009251) | KING | software resource, software application | Software toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) for applications such as family relationship inference and population structure identification (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, (64bit), ms-windows, ms-dos, macos, ubuntu, (32bit) | is listed by: Genetic Analysis Software | nlx_154419 | SCR_009251 | Kinship-based INference for Gwas | 2026-08-12 10:49:57 | 1175 | ||||||||
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JLIN Resource Report Resource Website 1+ mentions |
JLIN (RRID:SCR_009247) | JLIN | software resource, software application | Software application designed for customizable, intuitive visualisation of LD analysis across all common computing platforms. Customisation allows the researcher to choose particular visualisation, statistical measures and measurement ranges. JLIN also allows the researcher to export images of the LD visualisation in several common document formats. As there appears to be no single best measure of LD under all possible circumstances, JLIN allows the researcher to visually compare and contrast the results of a range of statistical measures on the input data set(s). These measures include the commonly used D'' and R2 statistics and empirical p-values. New additions include calculation of HWE, a completely revamped interface, and a numer of minor bug fixes. We have added a display measure to show marker distances visually, embedded fonts to improve image clarity and additional LD measures including d,OR,Pexcess and Q. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, any with java 1.5 support | is listed by: Genetic Analysis Software | nlx_154415 | SCR_009247 | Java based LINkage disequilibrium plotter | 2026-08-12 10:49:53 | 9 | ||||||||
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JOINMAP Resource Report Resource Website 1000+ mentions |
JOINMAP (RRID:SCR_009248) | JOINMAP | software resource, software application | Software application for construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family. Can combine (''join'') data derived from several sources into an integrated map. Further: linkage group determination, automatic phase determination for outbreeders full-sib family, several diagnostics, and map charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software) | gene, genetic, genomic, ansi c, delphi, ms-windows, (95/98/me/nt4.0/2000) | is listed by: Genetic Analysis Software | nlx_154416 | SCR_009248 | Software for the calculation of genetic linkage maps | 2026-08-12 10:49:57 | 1072 | ||||||||
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IMPUTE Resource Report Resource Website 500+ mentions |
IMPUTE (RRID:SCR_009245) | IMPUTE | software resource, software application | Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software) | gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154411 | SCR_009245 | 2026-08-12 10:49:57 | 639 | |||||||||
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MDR-PDT Resource Report Resource Website 1+ mentions |
MDR-PDT (RRID:SCR_009243) | MDR-PDT | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154406 | SCR_009243 | Multifactor Dimensionality Reduction and genotype Pedigree Disequilibrium Test | 2026-08-12 10:49:53 | 2 | ||||||||
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INTERSNP Resource Report Resource Website 10+ mentions |
INTERSNP (RRID:SCR_009244) | INTERSNP | software resource, software application | Software application for genome-wide interaction analysis (GWIA) of case-control SNP data. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, unix, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154409 | SCR_009244 | genome-wide association and INTERaction analysis of SNP | 2026-08-12 10:49:53 | 18 |
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