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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ARB project Resource Report Resource Website 10+ mentions |
ARB project (RRID:SCR_000515) | ARB | software resource | Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations. | rrna sequence, rrna, phylogeny, alignment, analysis, protein, gene |
is listed by: Debian is related to: SILVA is related to: SINA has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:14985472 | Free, Available for download, Freely available | OMICS_01515 | https://sources.debian.org/src/arb/ | SCR_000515 | The ARB project | 2026-08-01 12:01:23 | 28 | |||||
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PiNGO Resource Report Resource Website |
PiNGO (RRID:SCR_000692) | PiNGO | software resource | A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotation, network, candidate gene, biological network, ontology or annotation search engine, statistical analysis, term enrichment, functional similarity, functional prediction, search engine, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:21278188 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149330, OMICS_02281 | SCR_000692 | 2026-08-01 12:01:17 | 0 | |||||||
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ROSTLAB Resource Report Resource Website 1+ mentions |
ROSTLAB (RRID:SCR_000792) | group | A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research. | protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedical |
has parent organization: Columbia University; New York; USA is parent organization of: PredictNLS is parent organization of: SNPdbe |
NLM LM007329; NLM GM50291 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31417 | http://cubic.bioc.columbia.edu/services/disis | SCR_000792 | Rost Group | 2026-08-01 12:01:19 | 1 | ||||||
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iFad Resource Report Resource Website |
iFad (RRID:SCR_000271) | iFad | software resource | An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines. | r, gene expression, drug sensitivity, analysis, drug-pathway association, gene-pathway, pathway, gene, drug |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:22581178 | Free, Available for download, Freely available | OMICS_01959 | SCR_000271 | 2026-08-01 12:01:10 | 0 | |||||||
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MAGMA Resource Report Resource Website 100+ mentions |
MAGMA (RRID:SCR_005757) | MAGMA | software resource | Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem. | gene, genetic mapping, algorithm, genomics, single nucleotide polymorphism, population study, haplotype-block elucidation, java | has parent organization: SourceForge | Juvenile Diabetes Research Foundation | PMID:12875658 | Open unspecified license | nlx_149220 | SCR_005757 | Multiobjective Analyzer for Genetic Marker Acquisition, MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition | 2026-08-01 12:02:58 | 456 | |||||
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ClueGO Resource Report Resource Website 1000+ mentions |
ClueGO (RRID:SCR_005748) | ClueGO | software resource | A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | statistical analysis, function, gene ontology, pathway, annotation, network, plugin, gene |
is listed by: Gene Ontology Tools is listed by: SoftCite is related to: Gene Ontology is related to: Cytoscape is related to: KEGG is related to: BioCarta Pathways has parent organization: National Institute of Health and Medical Research; Rennes; France |
National Institute of Health and Medical Research; Rennes; France ; Ville de Paris ; INCa ; Austrian Ministry for Science and Research ; BINII ; European Union 7FP 202230 |
PMID:19237447 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149209 | SCR_005748 | 2026-08-01 12:02:58 | 2943 | ||||||
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ChIPXpress Resource Report Resource Website 1+ mentions |
ChIPXpress (RRID:SCR_006653) | ChIPXpress | software resource | A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target. | gene expression, chip-seq, chip-chip, transcription factor, target gene, gene, gene expression profile |
is listed by: OMICtools is related to: Gene Expression Omnibus has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00516 | SCR_006653 | ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles | 2026-08-01 12:03:17 | 2 | |||||||
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GREC Corpus Resource Report Resource Website 1+ mentions |
GREC Corpus (RRID:SCR_006719) | GREC | training set | A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format | annotation, information extraction, text mining, semantic role, semantic search, gene, computational linguistics, gene regulation |
is listed by: FORCE11 is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:19852798 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, For Copyright of abstracts refer to PubMed. | nif-0000-06688 | SCR_006719 | Gene Event Regulation Corpus | 2026-08-01 12:03:18 | 3 | |||||
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LAPSTRUCT Resource Report Resource Website 1+ mentions |
LAPSTRUCT (RRID:SCR_007550) | software resource, software application | Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | Free | nlx_154589, SCR_009367, nlx_154209 | SCR_007550 | R/LAPSTRUCT, LAPlacian eigenfunctions learn population STRUCTure | 2026-08-01 12:08:36 | 3 | ||||||||
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IBDREG Resource Report Resource Website |
IBDREG (RRID:SCR_013127) | software resource, software application | Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/s-plus | is listed by: Genetic Analysis Software | nlx_154588, SCR_009366, nlx_154407 | http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm | SCR_013127 | R/IBDREG | 2026-08-01 12:08:30 | 0 | ||||||||
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LDGROUP Resource Report Resource Website |
LDGROUP (RRID:SCR_006282) | software resource, software application | Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154422, SCR_009368, nlx_154590 | http://www.fumihiko.takeuchi.name/publications.html | SCR_006282 | R/LDGROUP | 2026-08-01 12:09:50 | 0 | ||||||||
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Zebrafish Gene Collection Resource Report Resource Website 1+ mentions |
Zebrafish Gene Collection (RRID:SCR_007054) | ZGC | biomaterial supply resource, material resource | Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cdna library, clone, sequence, full-length open reading frame, cdna clone, frozen, fish, gene, genetic, genome, genomic |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: Mammalian Gene Collection is related to: GenBank is related to: ATCC has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | nif-0000-00567 | https://genecollections.nci.nih.gov/ZGC/ | SCR_007054 | Zebrafish Gene Collection | 2026-08-01 12:10:50 | 1 | |||||
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TRANSMIT Resource Report Resource Website 50+ mentions |
TRANSMIT (RRID:SCR_007571) | TRANSMIT | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Software application that tests for association between genetic marker and disease by examining the transmission of markers from parents to affected offspring. The main features which differ from other similar programs are: (1) It can deal with transmission of multi-locus haplotypes, even if phase is unknown, and (2) Parental genotypes may be unknown. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154100 | SCR_007571 | 2026-08-01 12:10:51 | 50 | ||||||||
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Sanger Mouse Resources Portal Resource Report Resource Website 50+ mentions |
Sanger Mouse Resources Portal (RRID:SCR_006239) | Sanger Mouse Portal, WTSI Mouse Resources Portal, WTSI Mouse Resource Portal | biomaterial supply resource, material resource | Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. | bacterial artificial chromosome, vector, embryonic stem cell, mutant mouse line, phenotype, gene, knockout, gene expression, genetics, chromosome, mutant, mouse line, mammal, marker symbol |
is listed by: One Mind Biospecimen Bank Listing is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 079643; Wellcome Trust 098051; NHGRI UO1-HG004080; NCRR 1-U42RR033192; European Union LSHG-CT-2006-037188; European Union 227490; European Union 312325; European Union 261492 |
For the scientific community | nlx_151819 | SCR_006239 | Mouse Resources Portal, Wellcome Trust Sanger Institute Mouse Resources Portal | 2026-08-01 12:10:52 | 51 | ||||||
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LINKAGE - CEPH Resource Report Resource Website |
LINKAGE - CEPH (RRID:SCR_007048) | LINKAGE - CEPH | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, ms-dos, os2, unix, vms | is listed by: Genetic Analysis Software | nlx_154429 | SCR_007048 | three-generation pedigrees, FASTLINK | 2026-08-01 12:10:52 | 0 | ||||||||
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MULTIMAP Resource Report Resource Website 10+ mentions |
MULTIMAP (RRID:SCR_007168) | MULTIMAP | software resource, software application | Software program for automated construction of genetic maps (entry from Genetic Analysis Software) | gene, genetic, genomic, lisp, unix, (sun/compaq-alpha/hp..), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154013, biotools:multimap | https://bio.tools/multimap | http://compgen.rutgers.edu/Multimap/ | SCR_007168 | 2026-08-01 12:10:50 | 27 | |||||||
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MAPMAKER/SIBS Resource Report Resource Website 1+ mentions |
MAPMAKER/SIBS (RRID:SCR_008012) | MAPMAKER/SIBS | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Data analysis software for complete multipoint analysis. | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154465 | https://dsgweb.wustl.edu/aldi/software/manuals/mapmaker_sibs/mapmaker_sibs.pdf | ftp://ftp-genome.wi.mit.edu/distribution/software/sibs | SCR_008012 | GENEHUNTER | 2026-08-01 12:10:53 | 6 | |||||
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MORGAN Resource Report Resource Website 100+ mentions |
MORGAN (RRID:SCR_006906) | MORGAN | software resource, software application | Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits. | gene, genetic, genomic, c, unix, compaq-alpha, solaris, linux, linkage disequilibrium, gl_lods, ibd_haplo, identity by descent, segregation, linkage analysis, markov chain monte carlo |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Washington; Seattle; USA |
NIGMS GM-46255 | PMID:22298700 | nlx_154201, OMICS_00205 | SCR_006906 | MOnte caRlo Genetic ANalysis PANGAEA | 2026-08-01 12:10:50 | 305 | ||||||
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FAMOZ Resource Report Resource Website 1+ mentions |
FAMOZ (RRID:SCR_007477) | FAMOZ | software resource, software application | Software application that uses likelihood calculation and simulation to perform parentage studies with codominant, dominant, cytoplasmic markers or combinations of the different types (entry from Genetic Analysis Software) | gene, genetic, genomic, c, tcl/tk, unix, solaris, linux, ms-windows | is listed by: Genetic Analysis Software | nlx_154086 | SCR_007477 | FAther/MOther | 2026-08-01 12:10:40 | 5 | ||||||||
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CLUMP Resource Report Resource Website 100+ mentions |
CLUMP (RRID:SCR_007476) | CLUMP | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that uses Monte Carlo method for assessing significance of a case-control association study with multi-allelic marker. (entry from Genetic Analysis Software). | gene, genetic, genomic, c, ms-dos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154028 | SCR_007476 | 2026-08-01 12:10:50 | 104 |
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