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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Onto-Design Resource Report Resource Website |
Onto-Design (RRID:SCR_000601) | Onto-Design | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online tool | microarray, gene, biological process, molecular function, cellular component, data-mining, browser, visualization, analysis, design, search engine, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, other analysis, design custom microarrays based on go terms of interest |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149109 | SCR_000601 | 2026-09-12 01:02:23 | 0 | |||||||
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MRH Resource Report Resource Website |
MRH (RRID:SCR_000841) | MRH | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, unix, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154493 | SCR_000841 | Minimum Recombinant Haplotype | 2026-09-12 01:02:24 | 0 | |||||||
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QTL CAFE Resource Report Resource Website |
QTL CAFE (RRID:SCR_000844) | QTL CAFE | software application, software resource | Software application providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression. (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | nlx_154563 | SCR_000844 | 2026-09-12 01:02:24 | 0 | |||||||||
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PELICAN Resource Report Resource Website 10+ mentions |
PELICAN (RRID:SCR_001695) | PELICAN | software application, software resource | Software utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file. | gene, genetic, genomic, java, pedigree, linkage analysis, editor |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Google Sites |
PMID:15059819 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00215, nlx_154035 | http://www.mrc-bsu.cam.ac.uk/personal/frank/software/pelican/, http://www.rfcgr.mrc.ac.uk/Software/PELICAN/ | SCR_001695 | Pedigree Editor for LInkage Computer ANalysis | 2026-09-12 01:02:26 | 15 | |||||
|
OSA Resource Report Resource Website 1+ mentions |
OSA (RRID:SCR_002016) | OSA | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on. | gene, genetic, genomic, c++, unix, solaris, linux |
is listed by: Genetic Analysis Software has parent organization: Duke University; North Carolina; USA |
NIMH R01 MH59528 | PMID:18473393 PMID:15185403 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154504 | http://wwwchg.duhs.duke.edu/software/osa.html | SCR_002016 | Ordered Subset Analysis, OSA Program, Ordered Subset Analysis Program | 2026-09-12 01:02:27 | 1 | ||||
|
METAL Resource Report Resource Website 1000+ mentions |
METAL (RRID:SCR_002013) | software application, software resource | Software application designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. (entry from Genetic Analysis Software) | gene, genetic, genomic, whole genome |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:20616382 | nlx_154476, OMICS_00239 | SCR_002013 | Metal - Meta Analysis Helper, METa AnaLysis Helper | 2026-09-12 01:02:27 | 2413 | ||||||||
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Partners HealthCare Biobank Resource Report Resource Website 1+ mentions |
Partners HealthCare Biobank (RRID:SCR_001316) | biomaterial supply resource, material resource | Blood biobank for the Partners research program, which investigates the affects of genes, lifestyle and environment on human health. | biology, biobank, specimen, research, gene, lifestyle, environment, blood | Free, Freely Available | nlx_31066 | https://biobank.partners.org | http://www.partners.org/researchcores/DFHCC/virtual_specimen_DFHCC.html | SCR_001316 | 2026-09-12 01:02:26 | 4 | ||||||||
|
SVA Resource Report Resource Website 10+ mentions |
SVA (RRID:SCR_002155) | SVA | commercial organization, software application, software resource | Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits. | gene, genetic, genomic, annotate, visualize, genetic variant, next-generation sequencing, whole-genome sequencing, exome, sequencing, genome, disease, trait, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Duke University School of Medicine; North Carolina; USA |
PMID:21624899 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154666, OMICS_00190, biotools:sequencevariantanalyzer | http://www.svaproject.org/, https://bio.tools/sequencevariantanalyzer | SCR_002155 | Sequence Variant Analyzer, SVA: Sequence Variant Analyzer | 2026-09-12 01:02:27 | 17 | |||||
|
EASE: the Expression Analysis Systematic Explorer Resource Report Resource Website 50+ mentions |
EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) | EASE | data processing software, software application, software resource | Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible | gene, microarray, genome, gene ontology, statistical analysis, enrichment analysis, FASEB list |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Database for Annotation Visualization and Integrated Discovery |
NIAID | PMID:12734009 PMID:19131956 PMID:19033363 |
Free for academic use | nlx_149218 | SCR_013361 | Expression Analysis Systematic Explorer | 2026-09-12 01:01:01 | 94 | |||||
|
SCENIC Resource Report Resource Website 100+ mentions |
SCENIC (RRID:SCR_017247) | data processing software, software application, software resource | Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data. | single, cell, regulatory, network, inference, clustering, simultaneous, gene, reconstruction, single, RNA-seq, data | ERC Consolidator Grant ; Foundation Against Cancer ; Special Research Fund (BOF) KU Leuven ; The Research Foundation - Flanders |
PMID:28991892 | Free, Available for download, Freely available | https://aertslab.org/#scenic | SCR_017247 | 2026-09-12 01:01:05 | 161 | ||||||||
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Primer Express Software Resource Report Resource Website 1+ mentions |
Primer Express Software (RRID:SCR_017376) | data analytics software, data processing software, software application, software resource | Software tool by Applied Biosystems to design primers and probes using TaqMan and SYBR Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed for use with StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, and QuantStudio real-time PCR systems. Provides customized application specific documents for absolute⁄relative quantitation and allelic discrimination. | Applied Biosystems, ThermoFisher Scientific, design, primer, probe, TaqMan, SYBR Green, gene, quantitation, allelic, discrimination, RT PCR | Restricted | SCR_017376 | Primer Express Software v3.0.1, Primer Express™ Software v3.0.1 License, Primer Express™ Software v3.0.1 | 2026-09-12 01:01:05 | 6 | ||||||||||
|
4D Nucleome Resource Report Resource Website 10+ mentions |
4D Nucleome (RRID:SCR_016925) | data or information resource, portal, project portal | Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes. | nuclear, organization, gene, expression, cellular, function, normal, development, disease, map, structure, human, mouse, genome |
is listed by: NIDDK Information Network (dkNET) is related to: International Human Epigenome Consortium |
NIH Common Fund | PMID:28905911 | Public | SCR_016925 | 4D Nucleome Network; 4DN Web Portal, The 4D nucleome project, 4DN Portal | 2026-09-12 01:01:04 | 30 | |||||||
|
Digital Expression Explorer 2 Docker Image Resource Report Resource Website 1+ mentions |
Digital Expression Explorer 2 Docker Image (RRID:SCR_016931) | data processing software, software application, software resource | Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript. | transcriptome, pipeline, bulk, reprocess, public, RNAseq, data, SRA, gene, read |
is related to: Digital Expression Explorer 2 Project is related to: Digital Expression Explorer 2 Source Code |
DOI:10.5281/zenodo.1561840 | Free, Registration required | SCR_016931 | 2026-09-12 01:01:05 | 1 | |||||||||
|
mirDIP Resource Report Resource Website 100+ mentions |
mirDIP (RRID:SCR_016770) | data or information resource, database, portal | microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies. | data, integral, portal, DIP, collect, predict, microRNA, gene, human | Canada Foundation for Innovation ; Canadian Cancer Society Research Institute ; Krembil Foundation ; Natural Sciences Research Council ; Ontario Research Fund |
PMID:29194489 | Free, Download available, Freely available, email address required to download, Acknowledgement requested | SCR_016770 | mirDIP 4.1, mirDIP, microRNA Data Integration Portal | 2026-09-12 01:01:04 | 229 | ||||||||
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rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | data processing software, software application, software resource | Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software. | evaluation, quality, RNA-Seq, assembly, data, transcriptome, assembler, reference, genome, gene, database, raw, read, , bio.tools |
uses: BUSCO is listed by: Debian is listed by: bio.tools is related to: rnaSPAdes is related to: Python Programming Language is related to: SPAdes |
EMC Research and Development Department ; St. Petersburg State University ; Russia |
PMID:27153654 | Free, Available for download, Freely available | biotools:rnaQUASt | https://bio.tools/rnaQUAST | SCR_016994 | 2026-09-12 01:01:05 | 4 | ||||||
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LiGeA Resource Report Resource Website 1+ mentions |
LiGeA (RRID:SCR_015940) | LiGeA | data or information resource, database, portal | Portal provides an easy access to a comprehensive database designed for storing, displaying and annotating gene fusion events detected from NGS data. It can query a database of somatic fusion genes events predicted and annotated starting from paired-end RNA-seq data. | database, portal, gene, fusion, cell, line, somatic, gene, detection, cancer, prediction, annotation, rna, rnaseq | Cancer | Free, Public, Available for download | SCR_015940 | LiGeA: a comprehensive database of human gene fusion events, cancer cell LInes GEne-fusions portAl, LiGeA Portal, LiGeA - a comprehensive database of human gene fusion events | 2026-09-12 01:01:04 | 1 | ||||||||
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AutoEVM Resource Report Resource Website |
AutoEVM (RRID:SCR_017556) | data processing software, software application, software resource | Software tool as Autorun Evidence Modeler. Requires EVidenceModeler (aka EVM) software which combines ab into gene predictions and protein and transcript alignments into weighted consensus gene structures. | Autorun, Evidence, Modeler, gene, prediction, protein, transcript, elignment, weighted, gene, structure | Free, Available for download, Freely available | SCR_017556 | Autorun EVidence Modeler | 2026-09-12 01:01:06 | 0 | ||||||||||
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PRESTO: Genetic Association Analysis Software Resource Report Resource Website 1+ mentions |
PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) | software application, software resource | Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data. | gene, genetic, genomic, java, ms-windows, unix, solaris, linux, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu138 | nlx_154549 | SCR_013285 | 2026-09-12 01:02:48 | 2 | |||||||||
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THESIAS Resource Report Resource Website 50+ mentions |
THESIAS (RRID:SCR_013449) | THESIAS | software application, software resource | Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btm058 | nlx_154102, OMICS_19747, biotools:tHESIAS | https://bio.tools/THESIAS, https://sources.debian.org/src/thesias/ | http://ecgene.net/genecanvas/downloads.php?cat_id=1 | SCR_013449 | Testing Haplotype EffectS In Association Studies | 2026-09-12 01:02:49 | 53 | |||||
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DMLE Resource Report Resource Website 10+ mentions |
DMLE (RRID:SCR_013454) | DMLE | software application, software resource | Software application for high-resolution mapping of the position of a disease mutation relative to a set of genetic markers using population linkage disequilibrium (LD). (entry from Genetic Analysis Software) | gene, genetic, genomic, linux, ms-windows | is listed by: Genetic Analysis Software | nlx_154218 | SCR_013454 | Disease Mapping using Linkage disEquilibrium | 2026-09-12 01:02:49 | 22 |
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