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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FGED Resource Report Resource Website 10+ mentions |
FGED (RRID:SCR_001897) | FGED | data or information resource, knowledge environment, portal | Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications. | gene expression, gene modification, biological, biologist, biomedical, computer scientist, data analyst, genomic, integration, life science, microarray, technology, functional genomics, annotate, data sharing, genome, data integration, software |
is listed by: OMICtools is parent organization of: MINSEQE is parent organization of: MAGE is parent organization of: MIAME |
OMICS_01778, nif-0000-10466 | http://www.mged.org/ | SCR_001897 | Functional Genomics Data Society, MGED Society, The Microarray Gene Expression Data Society, The Functional Genomics Data Society, MGED | 2026-08-29 11:28:29 | 24 | |||||||
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GoMiner Resource Report Resource Website 100+ mentions |
GoMiner (RRID:SCR_002360) | GoMiner | data processing software, software application, software resource | GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches. | experiment, expression, function, gene, genomics, biological, genomic, microarray, omic, process, gene expression, gene ontology, biological process, biological function, biological component, proteomic, database, FASEB list |
is related to: Gene Ontology is related to: High-Throughput GoMiner has parent organization: Georgia Institute of Technology; Georgia; USA has parent organization: Emory University; Georgia; USA has parent organization: National Cancer Institute |
NCI ; Georgia Institute of Technology; Georgia; USA ; Emory University; Georgia; USA |
PMID:12702209 | nif-0000-21181 | SCR_002360 | 2026-08-29 11:28:31 | 115 | |||||||
|
LAPSTRUCT Resource Report Resource Website 1+ mentions |
LAPSTRUCT (RRID:SCR_007550) | software application, software resource | 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 | 2026-08-29 11:28:44 | 3 | ||||||||
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Pedigree-Draw Resource Report Resource Website 1+ mentions |
Pedigree-Draw (RRID:SCR_008302) | commercial organization, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software) | gene, genetic, genomic, macos, bio.tools |
is listed by: Genetic Analysis Software is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154520, OMICS_00213, SCR_010795 | SCR_008302 | PEDIGREE/DRAW | 2026-08-29 11:28:44 | 1 | ||||||||
|
Caltech, The Beckman Institute: The Biological Network Modeling Center Resource Report Resource Website 50+ mentions |
Caltech, The Beckman Institute: The Biological Network Modeling Center (RRID:SCR_008060) | data or information resource, organization portal, portal | The Beckman Institute BNMC brings together researchers from many disciplines at Caltech to address problems in the mechanistic modeling of coupled genomic, intercellular and intracellular processes. It represents an attempt to encourage closer interaction and collaboration between groups in Biology, Control and Dynamical Systems, and the Center for Advanced Computing Research. The focus of BNMC is biochemical phenomena occurring within and between cells, in particular the mechanistic modeling of molecular networks of all kinds (e.g., transcriptional, regulatory, metabolic, signal transduction, mechanical, etc.) with and without spatial variation and intercellular communication. BNMC is formed as a coordinated effort aimed at (1) applying existing capabilities to collaboratively solve biological modeling problems that arise in answering scientific questions in Caltech laboratories, (2) exploring a diversity of novel approaches in order to achieve fundamental advances necessary to address the classes of modeling problems biologists want to solve, and (3) organizing projects to better share human experience as well as common infrastructure to avoid duplication and maximize solution interoperability. | dynamical system, advanced computing, biochemical, biological model, biologist, biology, cell, control system, genomic, interaction, intercellular, intercellular communication, intracellular, mechanical, mechanistic modeling, metabolic, regulatory, signal transduction, transcriptional | has parent organization: California Institute of Technology; Pasadena; USA | nif-0000-10444 | SCR_008060 | BNMC | 2026-08-29 11:28:38 | 95 | |||||||||
|
IBDREG Resource Report Resource Website |
IBDREG (RRID:SCR_013127) | software application, software resource | 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 | 2026-08-29 11:28:47 | 0 | ||||||||
|
NeLS Resource Report Resource Website 1+ mentions |
NeLS (RRID:SCR_016301) | NeLS | data or information resource, organization portal, portal | Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project. | genomic, data, analyze, store, share, archive, electronic, infrastructure, administration, Norway, bio.tools |
is listed by: bio.tools is listed by: Debian |
Research Council of Norway | Free, Freely available | biotools:nels | https://bio.tools/nels, https://github.com/elixir-no-nels/nels-core, https://bio.tools/nels | SCR_016301 | Norwegian e-Infrastructure for Life Sciences | 2026-08-29 11:28:45 | 3 | |||||
|
Mnemiopsis Genome Project Portal Resource Report Resource Website |
Mnemiopsis Genome Project Portal (RRID:SCR_018293) | MGP Portal | data or information resource, portal, project portal | Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis. | Genomic, data, metazoan development, Mnemiopsis leidyi, Ctenophore, moel organisms, genomic data analysis |
is related to: University of Michigan; Ann Arbor; USA is related to: Brown University; Rhode Island; USA is related to: University of Florida; Florida; USA |
Free, Freely available | SCR_018293 | 2026-08-29 11:28:49 | 0 | |||||||||
|
tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | analysis service resource, data analysis service, production service resource, service resource, software resource, software toolkit | Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis. | analysis, 10x, single, cell, RNA, sequencing, data, genomic, platform, mapping, quantitation | Free, Available for download, Freely available | SCR_016957 | 2026-08-29 11:27:43 | 13 | |||||||||||
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Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | data or information resource, data repository, database, disease-related portal, organization portal, portal, service resource, storage service resource, topical portal | Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects. | pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis | is recommended by: National Library of Medicine | pediatric cancer, birth defect | NIH ; the Common Fund’s Gabriella Miller Kids First Pediatric Research Program |
Restricted | SCR_016553 | https://commonfund.nih.gov/kidsfirst, https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1, https://commonfund.nih.gov/kidsfirst | SCR_016493 | Data Resource Portal | 2026-08-29 11:28:08 | 6 | ||||
|
OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, data processing software, software application, software resource | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder | SCR_017118 | OrthoFinder2, OrthoFinder | 2026-08-29 11:28:10 | 3413 | |||||
|
ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data analysis software, data processing software, data visualization software, software application, software resource | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
BMBF ; German Cancer Research Center-Heidelberg Center for Personalized Oncology |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap, https://bio.tools/complexheatmap | SCR_017270 | 2026-08-29 11:28:11 | 3949 | ||||||
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Seurat Resource Report Resource Website 10000+ mentions |
Seurat (RRID:SCR_016341) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is used by: scSidekick is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers works with: Connectome |
NHGRI 1DP2HG009623; NIMH 5R01MH071679; NSF |
PMID:29608179 | Free, Available for download, Freely available | https://satijalab.org/seurat/get_started.html | SCR_016341 | 2026-08-29 11:28:07 | 11480 | |||||||
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GENERA Resource Report Resource Website 1+ mentions |
GENERA (RRID:SCR_023113) | data or information resource, narrative resource, training material, workflow | Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. | Genomic, Genome assembly, Phylogeny, Phylogenomic, comparative genomic, metabolic analyses, prokaryotes, eukaryotes | Free, Available for download, Freely available | SCR_023113 | GEN-ERA toolbox | 2026-08-29 11:28:24 | 9 | ||||||||||
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GS-EM Resource Report Resource Website |
GS-EM (RRID:SCR_003992) | GS-EM | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154366 | SCR_003992 | GenoSpectrum Expectation-Maximuzation | 2026-08-29 11:30:55 | 0 | ||||||||
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Platypus Resource Report Resource Website 100+ mentions |
Platypus (RRID:SCR_005389) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data. | Haplotype based variant caller, next generation sequence data, gene, genomic, high throughput sequencing data, |
is listed by: OMICtools is related to: SAMTOOLS has parent organization: Wellcome Trust Centre for Human Genetics |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_009046, nlx_154021, OMICS_00068 | SCR_005389 | Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data, PLAYPUS | 2026-08-29 11:30:57 | 200 | ||||||||
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TDTPOWER Resource Report Resource Website |
TDTPOWER (RRID:SCR_005021) | TDTPOWER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software) | gene, genetic, genomic, sas macro | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154678 | SCR_005021 | 2026-08-29 11:31:00 | 0 | ||||||||
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POPDIST Resource Report Resource Website |
POPDIST (RRID:SCR_004904) | POPDIST | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, (aix/irix/decalpha), linux, macos, ms-dos, ms-windows, (95) | is listed by: Genetic Analysis Software | PMID:21564908 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154542 | SCR_004904 | 2026-08-29 11:30:59 | 0 | |||||||
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HAPLOCLUSTERS Resource Report Resource Website |
HAPLOCLUSTERS (RRID:SCR_007439) | HAPLOCLUSTERS | software application, software resource | Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
Aging | nlx_154014, biotools:haploclusters | https://bio.tools/haploclusters | SCR_007439 | 2026-08-29 11:30:49 | 0 | |||||||
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LDSUPPORT Resource Report Resource Website |
LDSUPPORT (RRID:SCR_007036) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, linux | is listed by: Genetic Analysis Software | nlx_154427 | SCR_007036 | 2026-08-29 11:30:59 | 0 |
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